Version 1604

Einsteinweg 17
6662 PW Elst
The Netherlands

T: +31 481 350 980

F: +31 842 105 702
askforinfo@artinis.com
www.artinis.com

2
Thank you for purchasing the Oxymon Mk III Near Infrared
Spectrophotometer from Artinis Medical Systems B.V. The Oxymon Mk III
Near Infrared Spectrophotometer (Oxymon) is a continuous wave near
infrared spectroscopy (NIRS) system with transmitters with each 2 or more
wavelengths of emitting light. The device is developed to measure
concentrations of substances using near infrared light. More information
about the Oxymon can be found in chapter 10. The software concerning to
this device is Oxysoft, which performs both data acquisition and analysis.
For more information about Oxysoft, see chapter 0.

Please read the entire manual thoroughly, including the safety information
(chapter 3) in order to get acquainted with the principles and usage of the
Oxymon.

The theory of NIRS is explained in chapter 4. More literature about NIRS

can be found in the folder “C:\Artinis Oxymon\NIRS documents” literature is
available. The thesis of dr. M. van Beekvelt contains useful information. The
most up to date list is available at our website:
http://www.artinis.com/product/oxymetry_publications..

For quick help use the index (page 173) and the table of contents (page 4). In
Oxysoft, Menu  Help a help file is available. This file is still under
construction. In the Oxysoft directory, folder “Data examples” an example
project (“Measurement examples.oxyproj”) is available. Use this example to
see how Oxysoft works; how to do calculations, how to work with cyclic
operators, how to add events, how to make new graphs, etc.

If installed, Oxysoft help files can be found at the C:\Artinis Oxymon”. Here
are this manual and “teamviewer support. If these files are not available on
the computer, look at the software CD/USB delivered with the system. With
“teamviewer support” we can assist remotely how to use Oxysoft.

If you still have question after reading the manual and watching the
instruction videos, you can always contact Artinis. Use the e-mail address of
your contact person or use the contact information at the front page of the
manual.

3
Manual Oxymon MkIII .................................................................................................1
For Oxysoft 3.0.103 and higher ................................................................................1
1 Introduction .........................................................................................................3
2 Content .................................................................................................................4
3 Safety information ..............................................................................................8
3.1 General Safety ........................................................................................ 8
3.2 Electrical safety ...................................................................................... 9
3.3 Optical safety ....................................................................................... 10
3.4 Servicing ............................................................................................... 11
3.5 Cleaning ............................................................................................... 11
3.6 Symbols ................................................................................................ 11
4 Introduction to Near Infrared Spectroscopy ............................................ 12
4.1 Optical Oximetry................................................................................... 12
4.2 Near Infrared Spectroscopy ................................................................... 13
4.3 Principles of NIRS .................................................................................. 14
4.4 Spectral extinction coefficients of the chromophores ............................. 15
4.5 The pathlength correction factor ........................................................... 17
4.6 Occlusion methods in NIRS .................................................................... 18
4.7 Venous occlusion technique .................................................................. 18
4.8 Arterial occlusion technique .................................................................. 19
4.9 Quantitation of absolute tissue blood volume........................................ 19
4.10 Quantitation of absolute blood flow ...................................................... 20
4.11 References ............................................................................................ 21
5 Hardware and software installation ............................................................ 25
5.1 Hardware installation ........................................................................... 25
5.2 Software installation ............................................................................ 27
5.3 Filesetup installation............................................................................. 30
5.4 Oxymon connection .............................................................................. 33
5.4.1 Installing on Windows 7 or 8 ................................................... 33
5.5 Polhemus Patriot Connection (Optional) ................................................ 37
6 Oxymon ............................................................................................................. 38
6.1 Oxymon ................................................................................................ 38
6.2 Interconnecting multiple Oxymons ........................................................ 41
6.2.1 Cables ...................................................................................... 42

4
 6.2.2 Interconnections ...................................................................... 42
6.2.3 Software ................................................................................... 42
6.3 AD input board ..................................................................................... 44
6.4 AD boxes .............................................................................................. 44
6.4.1 AD input box ............................................................................ 44
6.4.2 AD output box .......................................................................... 45
6.5 The PortaSync ....................................................................................... 49
6.6 Polhemus Patriot .................................................................................. 51
7 Oxysoft ............................................................................................................... 53
7.1 The program ......................................................................................... 53
7.2 Start Oxysoft ........................................................................................ 55
7.3 Close Oxysoft ........................................................................................ 55
7.4 About Oxysoft....................................................................................... 55
7.5 License ................................................................................................. 56
7.6 Program options ................................................................................... 56
7.6.1 Data collection ......................................................................... 57
7.6.2 Graph options .......................................................................... 58
7.6.3 Template file ............................................................................ 59
7.6.4 Default coefficient tables ......................................................... 60
8 Measuring ......................................................................................................... 61
8.1 How to do a measurement .................................................................... 61
8.1.1 Preparation .............................................................................. 61
8.1.2 Start experiment ...................................................................... 62
8.2 Connect the optical fibers ...................................................................... 63
8.3 The optode holder................................................................................. 65
8.4 Data Collection ..................................................................................... 67
8.5 DAQ status view ................................................................................... 68
8.6 Template DAQ STATE ............................................................................ 69
8.7 DAQ value view .................................................................................... 69
8.8 DAQ settings......................................................................................... 71
8.8.1 Laser output level .................................................................... 71
8.8.2 Gain settings ............................................................................ 71
8.8.3 Out of range ............................................................................. 73
8.9 Calibration............................................................................................ 74
9 Data management .......................................................................................... 76
9.1 Projects ................................................................................................ 76
9.1.1 A new project ........................................................................... 76
9.1.2 Open a project ......................................................................... 76
9.1.3 Save a project........................................................................... 77
9.1.4 Project properties .................................................................... 77
9.1.5 Close a project ......................................................................... 78

5
 9.2 Measurements...................................................................................... 78
9.2.1 A new measurement ............................................................... 78
9.2.2 DAQ measurement wizard ...................................................... 78
9.2.3 Create offline measurement ................................................... 85
9.2.4 Measurement properties ........................................................ 87
9.2.5 Rename a measurement ......................................................... 87
9.2.6 Duplicate a measurement ....................................................... 87
9.2.7 Remove a measurement ......................................................... 87
9.2.8 Digitize optode positions (3D plugin only) .............................. 87
9.3 Graphs ................................................................................................. 91
9.3.1 Create (a regular) Graph .......................................................... 92
9.3.2 Create all graphs ...................................................................... 96
9.3.3 Create graphs from a template ............................................... 96
9.3.4 Topo Graph .............................................................................. 97
9.3.5 Spectrum Graph..................................................................... 102
9.3.6 Indicator view ........................................................................ 103
9.3.7 Graph properties ................................................................... 104
9.3.8 Open a graph ......................................................................... 104
9.3.9 Rename a graph..................................................................... 105
9.3.10 Duplicate a graph................................................................... 105
9.3.11 Clear a graph.......................................................................... 105
9.3.12 Freeze a graph ....................................................................... 106
9.3.13 Arrange graphs ...................................................................... 106
9.3.14 Close a graph ......................................................................... 106
9.3.15 Remove a graph ..................................................................... 106
9.3.16 Printing .................................................................................. 107
9.3.17 Zoom ...................................................................................... 107
9.3.18 Time span .............................................................................. 107
9.4 Traces................................................................................................. 107
9.4.1 Create a trace ........................................................................ 108
9.4.2 Create all traces ..................................................................... 113
9.4.3 Trace properties .................................................................... 114
9.4.4 Duplicate a trace.................................................................... 114
9.4.5 Remove a trace ...................................................................... 114
9.4.6 Bias a trace ............................................................................ 114
9.5 Data import and export ...................................................................... 115
9.5.1 Open *.oxy3 files ................................................................... 115
9.5.2 Import an Oxysoft measurement .......................................... 115
9.5.3 Import other data files (ASCII) ............................................... 115
9.5.4 Export data ............................................................................ 119
9.5.5 Export data Real time (ASCII writer) ...................................... 123
9.5.6 Export data Real time (FieldTrip buffer) ................................ 123
10 Data analysis................................................................................................... 125
10.1 Events ................................................................................................ 125
10.1.1 Define event keys .................................................................. 125
10.1.2 Insert an event during measuring ......................................... 126
10.1.3 Insert an event after measuring ............................................ 126
10.1.4 Generate events automatically ............................................. 127

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 10.1.5 Event properties .................................................................... 129
10.1.6 Event list................................................................................. 129
10.1.7 Change or remove an event................................................... 130
10.2 Periods ............................................................................................... 130
10.3 Cyclic operators .................................................................................. 131
10.4 Calculation ......................................................................................... 135
10.5 Filters ................................................................................................. 139
10.5.1 Selection of an appropriate filter........................................... 139
10.5.2 Add a filter to a trace ............................................................. 139
10.5.3 Remove a filter from a trace .................................................. 139
10.5.4 Add a filter to all traces of a measurement ........................... 139
10.5.5 Remove a filter from all traces of a measurement ................ 140
10.5.6 Moving average filters ........................................................... 140
10.5.7 FIR filters ................................................................................ 142
11 Optode templates ......................................................................................... 148
11.1 Introduction........................................................................................ 148
11.2 Setup examples .................................................................................. 149
11.2.1 1 Channel setup ..................................................................... 149
11.2.2 2 Channel Setup ..................................................................... 150
11.2.3 4 Channel Setup ..................................................................... 150
11.2.4 8 Channel Setup ..................................................................... 151
11.2.5 24 channel Setup ................................................................... 152
12 Tissue saturation index ................................................................................ 155
12.1 Spatial resolved spectroscopy.............................................................. 155
12.2 Theory ................................................................................................ 155
12.2.1 Parameters............................................................................. 156
12.3 TSI Fit Factor ....................................................................................... 157
12.4 TSI Accesories ..................................................................................... 158
12.5 TSI Calibration .................................................................................... 158
12.6 TSI measurement ................................................................................ 160
12.7 Overview of MLB and SRS theories ...................................................... 161
13 Frequently Asked Questions ....................................................................... 162
13.1.1 General................................................................................... 162
13.1.2 Installation and license key .................................................... 163
13.1.3 Using the software ................................................................. 165
14 List of shortcuts ............................................................................................. 169
15 Abbreviations ................................................................................................. 170
16 Warranty policy .............................................................................................. 171
17 Index ................................................................................................................. 173

7
BEFORE OPERATING THE OXYMON:

READ AND UNDERSTAND THIS MANUAL CAREFULLY AND BECOME FAMILIAR

WITH THE INSTRUMENT. FOLLOW THE INSTALLATION INSTRUCTIONS OF
CHAPTER 5. IF YOU HAVE ANY QUESTION REMAINING AFTER READING THE
MANUAL, PLEASE CONTACT ARTINIS. ALL SAFETY INFORMATION APPLIES
FOR THE OXYMON AND THE AD-BOX.

1.1 THE USER MUST ALWAYS CHECK THE EQUIPMENT PRIOR TO USE
AND ENSURE IT IS SAFE AND PROPER USE.

1.2 THE OXYMON MAY ONLY BE USED BY PEOPLE WHO READ THE
MANUAL THOROUGHLY.

1.3 THE OXYMON MAY ONLY BE USED FOR RESEARCH PURPOSES: IT

CANNOT BE USED FOR SUBJECT ASSESSMENT.

1.4 NEVER OPEN THE OXYMON. DO NOT UNSCREW PARTS OF THE

OXYMON. NO USER-SERVICEABLE PARTS ARE INSIDE THE
OXYMON.

1.5 EXPLOSION HAZARD: DO NOT USE THE OXYMON IN THE

PRESENCE OF FLAMMABLE ANESTHETICS OR GASES.

1.6 TO ENSURE THE SUBJECT’S SAFETY, DO NOT PLACE THE OXYMON

IN SUCH A POSITION THAT IT MIGHT FALL ON THE SUBJECT.

1.7 AS WITH ANY MEDICAL EQUIPMENT, CAREFULLY ROUTE THE

OPTICAL FIBERS TO REDUCE THE POSSIBILITY OF SUBJECT
ENTANGLEMENT OR STRANGULATION.

1.8 DISCONNECT THE OXYMON AND THE FIBERS DURING MAGNETIC

RESONANCE IMAGING (MRI) SCANNING. THE USE DURING MRI
COULD CAUSE BURNS OR ADVERSELY AFFECT THE MRI IMAGE
OR THE MONITOR’S ACCURACY. IN ORDER TO AVOID BURNS,
REMOVE THE FIBERS FROM THE SUBJECT BEFORE CONDUCTING
MRI. IF YOU WANT TO USE THE OXYMON IN A MRI
ENVIRONMENT, PLEASE CONTACT ARTINIS MEDICAL SYSTEMS
FOR MRI COMPATIBLE FIBERS.

O O
1.9 USE THE OXYMON BETWEEN 10 C AND 40 C. FOR SPECIAL
CONDITIONS (LOW TEMPERATURE ETC.) PLEASE CONTACT
ARTINIS FOR FURTHER INSTRUCTIONS.

8
1.10 BE AWARE WHEN APPLYING THE DEVICE FOR MULTIPLE HOURS.
TOO MUCH SWEAT, STRESS AND/OR WARMTH CAN CAUSE SKIN
IRRITATION. DO NOT APPLY TOO MUCH PRESSURE ON THE SKIN
WITH THE PROBE ATTACHMENT AND STOP AND REMOVE PROBE
IF SUBJECT FEELS IRRITATION OF THE PROBE ATTACHMENT.

2.1 FIRE OR SHOCK HAZARD: DO NOT EXPOSE THE OXYMON TO

RAIN OR MOISTURE.

2.2 DO NOT CONNECT THE OXYMON TO AN ELECTRICAL OUTLET

CONTROLLED BY A WALL SWITCH BECAUSE THIS COULD RESULT
IN THE DEVICE ACCIDENTALLY TURNED OFF.

2.3 WHEN CONNECTING THE OXYMON TO ANY OTHER

INSTRUMENT, FIRST VERIFY ITS PROPER OPERATION BEFORE
USE. BOTH THE OXYMON AND THE INSTRUMENT CONNECTED
TO IT MUST BE CONNECTED TO A GROUNDED OUTLET.
ACCESSORY EQUIPMENT CONNECTED TO THE ANALOG
INTERFACE BOARD MUST BE CERTIFIED ACCORDING TO IEC
STANDARD 60950 FOR DATA-PROCESSING EQUIPMENT OR IEC
STANDARD 60601 FOR ELECTRO-MEDICAL EQUIPMENT. ALL
COMBINATIONS OF EQUIPMENT MUST COMPLY WITH IEC
STANDARD 601-1 SYSTEM REQUIREMENTS. ANYONE WHO
CONNECTS ADDITIONAL EQUIPMENT TO THE PORTS OF THE
ANALOG INTERFACE BOARD CONFIGURES A MEDICAL SYSTEM
AND IS THEREFORE RESPONSIBLE THAT THE SYSTEM COMPLIES
WITH THE REQUIREMENTS OF STANDARD IEC STANDARD 60601-
1. IF YOU ARE IN DOUBT, CONTACT THE TECHNICAL
DEPARTMENT OF ARTINIS MEDICAL SYSTEMS.

2.4 HANDLE THE POWER SUPPLY CORD CAREFULLY. ANY DAMAGED

CORD SHOULD BE REPLACED DIRECTLY. DO NOT LIFT THE
OXYMON BY ANY OF THE CABLES OR FIBERS ATTACHED TO IT.
HANDLE THE ADAPTER CAREFULLY. ANY DAMAGED ADAPTER
SHOULD BE REPLACED DIRECTLY.

2.5 THE OXYMON IS EQUIPPED WITH A SELF-SWITCHING POWER

SUPPLY, OPERATING BETWEEN 110 AND 230 VAC, EITHER 50 OR
60 HZ.

2.6 ONLY USE THE SUPPLIED ADAPTER AS POWER SUPPLY FOR THE
ADBOX.

2.7 ABSOLUTE MAXIMUM RATING OF THE AD INPUT CHANNELS IS

±4 V.

9
2.8 THE OXYMON IS A “CLASS I” LASER PRODUCT. THE LASER
PRODUCTS HAVE BE CLASSIFIED ACCORDING TO “IEC 60825-1
1993 AMENDMENT 2 2001”.

2.9 THE LASERS ARE HAVE WAVELENGTHS OF 850±10 NM AND

775±15 NM. IF PURCHASED OTHER THAN THOSE TWO
WAVELENGTHS, ADDITIONAL INFORMATION CAN BE REQUESTED
FROM ARTINIS MEDICAL SYSTEMS.

2.10 THE MAXIMUM LASER PEAK POWER IS 25 AND 17 WATT FOR

RESPECTIVELY THE 850 AND 775 NM LASER.

2.11 THE MAXIMUM PEAK POWER AT THE FIBER TIP (2.8 MM

DIAMETER) IS 5.5 AND 5.4 WATT FOR RESPECTIVELY THE 850 AND
775 NM LASER.

2.12 THE LASERS FIRE AT 1000, 2000 OR 4000 HZ (16 AND MORE
CHANNELS, 8 CHANNELS, 1-4 CHANNELS).

2.13 THE PULSE TIMES ARE ABOUT 70 NS (HALF WIDTH FULL MAX).

2.14 NEVER LOOK INTO A FIBER CONNECTED TO THE OXYMON.

NEVER USE DAMAGED FIBERS.

2.15 NEVER STICK ANYTHING INTO A HOLE OF THE OXYMON WITH

EXCEPTION OF FIBERS OR CABLES MADE FOR THOSE HOLES.

2.16 DO NOT SPILL ANY LIQUID ON OR INTO THE OXYMON.

2.17 USE ONLY FIBERS FROM ARTINIS MEDICAL SYSTEMS. CONNECT

THE FIBERS AS DESCRIBED IN PARAGRAPH 8.2.

2.18 THE LASERS ONLY WORK WHEN A FIBER FROM ARTINIS MEDICAL
SYSTEMS IS CONNECTED TO BOTH LASERS OF ONE
TRANSMITTER BECAUSE OF A SAFETY INTERLOCK MECHANISM.
THE RED “MEASURE” LAMP AT THE FRONT OF THE OXYMON
TURNS ON IF THE LASERS ARE FIRING.

2.19 HANDLE THE OPTICAL FIBERS WITH CARE. DO NOT OVERBEND

OR EXPOSE TO HIGH FORCES.

10
In case of problems, unplug the power cords and contact the
manufacturer. No user-serviceable parts are inside the Oxymon. Service
contracts are available from the manufacturer.

Turn off the Oxymon, and disconnect from the power supply. Clean the
Oxymon by using a soft cloth moistened with a non-aggressive general
purpose cleaner. Do not spill any liquid into the instrument.

Y Attention: refer to manual

Potential equalization

Type B equipment

M Manufacturing date

Send back to manufacturer

11
This chapter introduces the history of NIRS as well as a basic background on
how to use the technique. For a brief introduction into NIRS principles the first
chapter of the ‘Near Infrared Spectroscopy: Toy or Tool?’ thesis by dr. W.N.J.M.
Colier is included below. This part is not specific for the Oxymon.

During the second half of the 19th century it was discovered that blood
cells contain a coloring substance whose spectrum is influenced by various
blood gases [Hoppe, 1862]. Stokes discovered that this colored substance
was the oxygen carrier of the blood. Felix Hoppe-Seyler, a German chemist,
named the substance hemoglobin. He found that when shaking a solution
of hemoglobin with air this resulted in a spectral change. He called the
component responsible for this change "oxyhemoglobin". In 1876 Karl von
Vierordt published the first study in which spectroscopy was used to study
hemoglobin in tissue. He found a transition from oxyhemoglobin to
deoxyhemoglobin in the tissue of the finger after the arm was fully
occluded, a technique still practiced today to study oxygenation in muscles.

At the beginning of the 20th century oximetry developed rapidly in

Germany with scientists like Nicolai [1932], Kramer [1934] Matthes [1942]
and Gross. Last two scientists mentioned were the first to use a wavelength
region in the near infrared where absorption was independent of the
oxygenation status of blood and which could therefore compensate for
changes in blood volume, light scattering and tissue thickness [Matthes et
al. 1939]. Their instrumentation however was still bulky and not easy to use.

The first portable instrument measuring hemoglobin saturation in tissue

accurately and automatically was built and described by Millikan [1942]. He
named the instrument an "oximeter". The sensor weighed 30 grams, used
two wavelengths and could be slipped over the subject’s ear. To obtain
arterial saturation the ear was moderately heated, a method also used in
later versions of oximeters. Millikan's instrument had an accuracy of 3 to
5% at the higher end of the scale (~98% saturation) and an accuracy of 8%
at the lower end of the scale (~50% saturation).

The oximeter of Millikan was improved by Wood and Geraci [1949]. Further
developments on reflection oximetry were done by Brinkman and Zijlstra.
They developed the "Cyclops", a device measuring oxygen saturation on the
forehead of a subject [Brinkman et al. 1950]. In the following years,
oximetry was used more and more in clinical situations. The title of Zijlstra's
thesis [1951]: "Fundamentals and applications of clinical oximetry"

12
indicated that they were far ahead of their time.

In the seventies two important findings contributed to the development

and clinical applicability of oximetry. The first was by Aoyagi, who found that
the variations in arterial blood volume could be used to obtain a signal
dependent only on arterial blood changes. With this knowledge the arterial
oxygen saturation of the blood could be measured [Aoyagi et al. 1974,
Nakajima et al. 1975]. This technique was called pulse oximetry and has
been developed into a reliable and widely used method [Kelleher 1989].
The second finding was by Jöbsis [1977] and was the beginning of near
infrared spectroscopy (NIRS).

In his article in Science [1977] Jöbsis reported that biological tissues have a
relatively good transparency for light in the near infrared region (700-1300
nm). Therefore it is possible to transmit sufficient photons through organs
for in situ monitoring. In this region hemoglobin, which can be divided into
its main components oxyhemoglobin (O2Hb) and deoxyhemoglobin (HHb),
shows oxygen dependent absorption. The main attention by Jöbsis and his
co-workers however was given to the redox state of cytochrome a,a3
(Cyt.Ox.), the terminal enzyme of the mitochondrial respiratory electron
transport chain. Approximately 90% of the intracellular oxygen
consumption is catalyzed by this enzyme. It has been shown that the
absence of oxygen results in a complete reduction of Cyt.Ox. This reduction
can be monitored by measuring the change in absorption band of Cyt.Ox.
in the near infrared region (770-880 nm) [Chance 1966]. Information
gained from the near infrared spectrum can therefore give insight into the
oxygen availability at the intracellular level. Combined with the information
from the hemoglobin signal it is now possible to monitor both circulatory
oxygen supply and intracellular oxygen consumption of the tissue.

In the years following the first publication of Jöbsis many studies were
carried out focusing on the assessment of Cyt.Ox. within the brains of
animals or humans, especially neonates [Jöbsis 1979, Giannini et al. 1982,
Keizer et al. 1985, Proctor et al. 1985, Brazy et al. 1985, Brazy and Lewis
1986, Jöbsis-VanderVliet et al. 1987, Brazy 1988, Jöbsis-VanderVliet et al.
1988]. Due to technical improvements NIRS became a more widespread
method at the end of the eighties and into the nineties. Most clinical
studies still are in the neonatal field [Brazy 1991, Edwards et al. 1991, Livera
et al. 1991, Skov et al. 1991, Wickramasinghe et al. 1992, Skov et al. 1992,
McCormick et al. 1993, Bucher et al. 1993], some of them performed by the
Nijmegen group [Liem et al. 1992, 1994, 1995]. A short history of NIRS in
Milestones is given in Table 4.1.

13
Table 4.1. The history of NIRS in milestones

Year Authors Subject

1977 Jöbsis First publication on NIRS
1982 Giannini et al. Cyt.Ox monitoring after perfluorcarcon exchange
1985 Brazy et al. Neonatal brain monitoring
1986 Ferrari et al. Adult brain monitoring
1986 Wyatt et al. Quantitation of cerebral oxygenation in newborn
1988 Delpy et al. Quantitation of optical pathlength
1988 Edwards et al. Quantitation of cerebral blood flow
1990 Wyatt et al. Quantitation of cerebral blood volume
1991 de Blasi et al. Quantitation of oxygen consumption in muscle

The technique of NIRS relies on the Lambert-Beer law [Beer 1851], given
by:

𝐼0
𝑂𝐷𝜆 = 𝑙𝑜𝑔 ( ) = 𝜀𝜆 𝑐𝐿
𝐼

where ODλ is a dimensionless factor known as the optical density of the

medium, I0 is the incident radiation, I the transmitted radiation, ελ the
-1 -1
extinction coefficient of the chromophore (mM •cm ), c is the
concentration (mM) of the chromophore, L the distance (cm) between light
entry and light exit point and λ the wavelength (nm) used. In this case the
Lambert-Beer law is given for a system with a single component.

The Lambert-Beer law was intended for use in a clear, non-scattering

medium. When the law is applied to a scattering medium e.g. biological
tissue (Figure 4-1), a dimensionless pathlength correction factor B must be
incorporated. This factor, sometimes called "Differential Pathlength Factor
(DPF)", accounts for the increase in optical pathlength due to scattering in
the tissue. The modified Lambert-Beer law [Delpy et al. 1988] is given by:

𝑂𝐷𝜆 = 𝜀𝜆 𝑐𝐿𝐵 + 𝑂𝐷𝑅,𝜆

where ODR,λ represents the oxygen independent light losses due to

scattering in the tissue. Assuming ODR,λ is constant during a measurement
we can convert an optical density change into a concentration change:

∆𝑂𝐷𝜆
∆𝑐 =
𝜀𝜆 𝐿𝐵

This equation is valid for a medium with one chromophore. In the case of
more chromophores we need to measure at least as many wavelengths as
there are chromophores present. This results in a set of linear equations.
The solution of this set leads to the algorithm used in most NIRS systems.

14
Figure 4-1. A scattering medium with an incident and transmitted light ray. The chromophore is
symbolized by black dots. Light ray A is scattered, and therefore travels a distance which equals
the pathlength correction factor times the physical pathlength L. Light ray B is absorbed
completely after being scattered.

In biological tissue there are at least three oxygenation dependent

chromophores present: O2Hb, HHb and Cyt.Ox. The sum of O2Hb and HHb
is a measure for the total blood volume (tHb) in the tissue. If muscle tissue
is investigated there are two more chromophores present: oxy- and
deoxymyoglobin (O2Mb and HMb).

To define the algorithm the spectral extinction coefficients of the various

chromophores are needed. Those first to explore extensively the spectra of
hemoglobin were Hüfner [1900] and Horecker [1943]. More recent is an
investigation of van Assendelft [1970] who studied hemoglobin and its
derivatives. Due to the introduction of NIRS and pulse oximetry several
recent studies have focused on the spectra of hemoglobin and cytochrome
oxidase with special attention to the near infrared spectral region [Rea et
al. 1985, Harris et al. 1988, Wray et al. 1988, Zijlstra et al. 1991, Crowe
1994]. Harris and Zijlstra determined absorption spectra of both fetal and
adult hemoglobin. This is of importance as pulse oximetry and NIRS are
methods used in fetal and neonatal applications (Figure 4-2).

15
Figure 4-2. Extinction coefficients of adult oxy- and deoxyhemoglobin (O2Hb and HHb
respectively), determined by Wray [1988] (solid lines) and Zijlstra [1991] (• and ▲ symbols), and
cytochrome oxidase (Cyt.Ox, ● symbol), also from Wray [1988].

Small differences in absorption spectra might influence the quantitation of

the data. Studies of Wickramasinghe et al. [1993] and Colier et al. [1992]
showed that the transition from fetal to adult hemoglobin had no
significant influence on the quantitation of the hemoglobin data. Care
however has to be taken with the quantitation of cytochrome oxidase, e.g.,
during blood transfusion or extra corporeal membrane oxygenation
(ECMO), interventions where a transition from fetal to adult hemoglobin
takes place. A small change in the algorithm can then lead to unacceptable
high errors in the Cyt.Ox. signal. The change in Cyt.Ox. is highly associated
with changes in hemoglobin [Skov et al. 1994]. Therefore in general no
attention is paid to Cyt.Ox. in the literature anymore.

To distinguish between hemoglobin and myoglobin in muscle tissue the

spectra need to be sufficiently different. Unfortunately this is not the case
in the visible part of the spectrum [Theorell et al. 1955, Yamazaki et al.
1964, Samejima et al. 1964, Hardman et al. 1965]. About the near infrared
part of the spectrum only one publication is known [Thorniley et al. 1990],
showing a different spectrum of O2Mb compared to O2Hb. This finding
however has not yet been confirmed.

Up until now there exists no consensus about which of the data sets for
hemoglobin and cytochrome oxidase come closest to reality. It can
therefore be concluded that the existence of several spectral data sets
results in a non-uniform algorithm for NIRS.

16
Table 4.2. Values of the Differential Pathlength Factor (DPF) for various types of tissue determined
by either "time-of-flight" (TRS) or "frequency-resolved" (FRS) measurements. All DPF values are

Author Method Organ/Limb Male/Female Wavelength (nm) DPF

Wyatt, 1990a TRS Baby Head () ? 783 4.39 ± 0.28
van der Zee, 1991 TRS Baby Head () M/F 783 3.85 ± 0.57
Benaron, 1990 FRS Infant Head M/F 754 3.78 ± 0.31
Benaron, 1990 FRS Infant Head M/F 816 3.71 ± 0.30
Duncan, 1995 FRS Infant Head M/F 807 4.99 ± 0.45
van der Zee, 1991 TRS Adult Head M/F 761 5.93 ± 0.42
Essenpreis, 1993 TRS Adult Head M/F 800 6.32 ± 0.46
Duncan, 1995 FRS Adult Head M/F 807 6.26 ± 0.88
Essenpreis, 1993 TRS Adult Calf M 800 5.84 ± 0.65
Essenpreis, 1993 TRS Adult Calf F 800 5.63 ± 0.62
van der Zee, 1991 TRS Adult Calf M 761 3.98 ± 0.46
van der Zee, 1991 TRS Adult Calf F 761 5.14 ± 0.43
Duncan, 1995 FRS Adult Calf M 807 4.94 ± 0.67
Duncan, 1995 FRS Adult Calf F 807 6.09 ± 0.93
Duncan, 1995 FRS Adult Forearm M 807 3.74 ± 0.57
Duncan, 1995 FRS Adult Forearm F 807 4.57 ± 0.74
van der Zee, 1991 TRS Adult Forearm M/F 761 3.59 ± 0.32
Ferrari, 1992 TRS Adult Forearm M/F 800 4.3 ± 0.2
Essenpreis, 1993 TRS Adult Forearm M/F 800 4.48 ± 0.41

For the quantitation of the absorption changes not only the physical
pathlength L, is needed, but also the DPF. The DPF can be accessed via
different ways. The most common way is by "time-of-flight" measurements
[Delpy et al. 1988, Wyatt et al. 1990a, Ferrari et al. 1992, van der Zee et al.
1992]. An ultra-short laser pulse is fired into the tissue. The pulse is
detected by an ultrafast camera. The time of flight t can then be converted
into a travelled distance d using the formula:

𝑐𝑡
𝑑=
𝑛

where c is the velocity of light and n the refractive index of the tissue.
Division of d by L gives the DPF.

Although the technique of "time-of-flight" measurements gives good

results, the equipment needed for it is expensive and bulky and therefore
only available to a few dedicated research centers.

Another way of assessing the DPF is by making use of "frequency resolved"

systems [Benaron et al. 1990, Sevick et al. 1991, Duncan et al. 1995]. In this
technique the incident light is intensity modulated at a frequency of 200-
300 MHz. A phase sensitive detector measures the envelope phase shift

17
between the incident and transmitted light. From the phase shift the mean
pathlength can be obtained. A good set of pathlength data obtained with
this technique for brain and muscle tissue has recently been published by
Duncan [1995]. This technique still is cumbersome, relatively expensive and
insensitive compared to continuous wave techniques. An overview of
studies to DPF values is shown in Table 4.2.

By applying an arterial or a venous occlusion to a limb it becomes possible

to assess various hemodynamic variables, like limb blood flow or oxygen
consumption of muscle tissue during rest or during exercise.

When a venous occlusion is applied to the upper arm or leg by inflating a

blood pressure cuff to a pressure of approximately 50 mmHg this results in
(arterial) inflow of blood but no outflow. The observed rise in blood volume
equals the blood flow into the limb and can be measured with NIRS by
monitoring the rise of the tHb signal after the occlusion. This method has
been validated with strain gauge plethysmography by de Blasi et al. [1994].
Figure 4-3 gives an example of a NIRS tracing during venous occlusion of
the arm.

Figure 4-3. An example of a NIRS tracing. In this case two consecutive venous occlusions (V.O.)
were applied to the upper arm. The NIRS optodes were attached to the brachio-radialis muscle of
the forearm. During V.O. there is arterial inflow, but no venous outflow. This results in an increase
of both oxy- and deoxyhaemoglobin. From the rise in the tHb signal the blood flow into the limb
can be calculated.

18
The blood flow into a limb can be completely stopped by inflating a blood
pressure cuff to a pressure of more than 250 mmHg. It is then possible to
calculate the local oxygen consumption in rest [Cheatle et al. 1991, de Blasi
et al. 1993] or during (isometric) exercise [Colier et al. 1995] from the
gradient of the subsequent decrease of the O2Hb signal.

After the pressure of the cuff is released, the tissue will show a hyperemic
reaction. The recovery time of the re-saturation observed with NIRS can be
used as measure for, e.g., the vascularisation of the leg in patients with
peripheral vascular disease [McCully et al. 1994, Komiyama et al. 1994].

By combining the NIRS data with arterial saturation (SaO2), measured for
example by pulse oximetry, it is possible to quantitate the absolute value of
blood volume of the examined tissue. This method was first described by
Wyatt et al. [1990b] for the quantitation of cerebral blood volume.

The effect of a small, gradual and transient change in SaO2 on the O2Hb
concentration is monitored. A decrease in SaO2 of approximately 10%,
induced by lowering the inspired oxygen concentration, is sufficient to
calculate the blood volume. Provided blood flow, volume and oxygen
consumption remain constant during the procedure, the tissue blood
volume (TBV) in ml/100 g is given by:

∆(𝑂2 − 𝐻𝐻𝑏)
𝑇𝐵𝑉 = 𝑐𝐻𝑏 𝜌𝜏 𝑘
2𝑅∆𝑆𝑎𝑂2

3
where cHb (mM) is the hemoglobin concentration of whole blood, ρT (g/cm )
the specific density of the tissue, k a constant reflecting metric conversions
and R is, in case of cerebral tissue, the large-to-small vessel hematocrit ratio
with a value of 0.69 [Lammertsma et al. 1984]. The difference between the
O2Hb and HHb concentration is taken to obtain a better signal-to-noise
ratio. This difference is also called the hemoglobin difference signal (HbDiff).

Using this method an absolute change in arterial saturation is compared to

a relative change in concentration of O2Hb, which can then be quantified.

19
The principle of measuring organ blood flow with NIRS is based on the Fick
principle which states that the accumulation of a tracer in an organ equals
the difference between the inflow (arterial concentration x flow) and
outflow (venous concentration x flow). If we measure within the transit time
of the tracer through the organ the venous concentration will be zero. In
NIRS the tracer used is a bolus of O2Hb, which can be induced by suddenly
increasing the inspired oxygen concentration. The concentration of the
bolus can be measured by attaching a pulse oximetry probe onto the
organ. The increase of O2Hb as measured by NIRS represents the
-
accumulation of the bolus into the organ. The blood flow (BF, in ml●100g
1 -1
●min ) through the organ is then given by the change of O2Hb divided by
-1
the product of the arterial hemoglobin concentration (cHb, in g●ml ) times
the integral of change in arterial saturation (SaO2, in %) :

𝐾∆(𝑂2 𝐻𝑏)
𝐵𝐹 = 𝑡
𝑐𝐻𝑏 ∙ 10−2 ∙ ∫0 ∆(𝑆𝑎𝑂2 )𝑑𝑡

K is constant representing the molecular weight of hemoglobin, the tissue

density and a metric conversion factor. This methodology has first been
described by Edwards et al. [1988] for the determination of cerebral blood
flow in newborn and afterwards by others who made a comparison with
the 133Xe clearance method [Skov et al. 1991, Bucher et al. 1993], finding
an acceptable correlation between the two methods in newborn. Elwell et
al. [1992, 1993] have used it to determine the cerebral blood flow in adults.

Some of the disadvantages of the methodology are firstly that a certain

degree of hypoxia with subsequent hyperoxia is needed to induce the
O2Hb bolus. If this intervention is inert is not known. Furthermore an
adequate lung function is necessary. Secondly a reliable beat-to-beat pulse
oximeter is needed for the measurements, which is generally a problem.
Later studies have shown that this technique is not very reliable.

20
For more literature about NIRS, see the literature list.
Assendelft van, OW. Spectrophotometry of Haemoglobin Derivatives. Springfield, IL. CC
Thomas 1970; 355–359,
Aoyagi T, Kishi M, Yamaguchi K, Watanabe S. Improvement of the earpiece oximeter. In:
Abstracts of the Japanese Society of Medical Electronics and Biological
Engineering 1974; 90-91.
Beer A. Versuch der Absorptions-Verhältnisse des Cordierites für rothes Licht zu
bestimmen. Ann Physik Chem 1851; 84: 37-52.
Benaron DA, Gwiazdowski, Kurth CD, Steven J, Delvoria-Papadopoulos, Chance B. Optical
pathlength of 754nm and 816nm light emitted into the head of infants. IEEE Eng
Med Biol Soc 1990; 12: 1117-1119.
Brazy JE, Lewis DV, Mitnick MH, Jöbsis-VanderVliet FF. Noninvasive monitoring of cerebral
oxygenation in preterm infants: preliminary observations. Pediatrics 1985; 75:
217-225.
Brazy JE, Lewis DV. Changes in cerebral blood volume and cytochrome aa 3 during
hypertensive peaks in preterm infants. J Pediatr 1986; 108 983-987.
Brazy JE. Cerebral oxygen monitoring with near infrared spectroscopy: clinical application
to neonates. J Clin Monit 1991; 7: 325-334.
Brazy JE. Effect of crying on cerebral blood volume and cytochrome aa3. J Pediatr 1988; 112:
457-461.
Brinkman R, Zijlstra WG, Koopmans RK. A method for continuous observation of
percentage oxygen saturation in patients. Acta Chir Neerl 1950; 1: 333-344.
Bucher HU, Edwards AD, Lipp AE, Duc G. Comparison between near infrared spectroscopy
and 133Xenon clearance for estimation of cerebral blood flow in critically ill
preterm infants. Ped Res 1993; 33: 56-60.
Chance B. In: The Biochemistry of Copper (Peisach G, Aisen P, Blumberg WE, eds.) pp: 293-
301. Academic Press, New York. 1966.
Cheatle TR, Potter LA, Cope M, Delpy D, Coleridge Smith PD, Scurr JH. Near-infrared
spectroscopy in peripheral vascular disease. Br J Surg 1991; 78: 405-408.
Colier WNJM, Liem D, Oeseburg B. The effect of fetal hemoglobin on the algorithm used in
near infrared spectroscopy. In: Proc Int Soc Oxygen Transport to Tissue, P76,
1992.
Cope M. The application of Near Infrared Spectroscopy to non-invasive monitoring of
cerebral oxygenation in the newborn infant. PhD-Thesis of the University of
London, Department of Medical Physics and Bioengineering, UK, 1991.
Crowe J. Absorption spectra of cytochrome oxidase. In: Newsletter Concerted Action NIRS
& I, 1994; 3: 3-4.
De Blasi RA, Cope M, Elwell C, Safoue F, Ferrari M. Noninvasive measurement of human
forearm oxygen consumption by near infrared spectroscopy. Eur J Appl Physiol
1993; 67: 20-25.
De Blasi RA, Ferrari M, Natali A, Conti G, Mega A, Gasparetto A. Noninvasive measurement
of forearm blood flow and oxygen consumption by near infrared spectroscopy. J
Appl Physiol 1994; 76: 1388-1393.
Delpy DT, Cope M, Zee P van der, Arridge S, Wray S, Wyatt J. Estimation of optical
pathlength through tissue from direct time of flight measurements. Phys Med Biol
1988; 33: 1433-1442.
Duncan A, Meek JH, Clemence M, Elwell CE, Tyszczuk L, Cope M, Delpy DT. Optical
pathlength measurements on adult head, calf and forearm and the head of the
newborn infant using phase resolved optical spectroscopy. Phys Med Biol 1995;
40: 295-304.
Edwards AD, Brown C, Cope M, Wyatt JS, McCormick DC, Roth SC, Delpy DT, Reynolds EOR.
Quantification of concentration changes in neonatal human cerebral oxidized
cytochrome oxidase. J Appl Physiol 1991; 71: 1907-1913.
Edwards AD, Wyatt JS, Richardson CE, Delpy DT, Cope M, Reynolds EOR. Cotside
measurement of cerebral blood flow in ill newborn infants by near-infrared
spectroscopy (NIRS). Lancet 1988; 2: 770-771.

21
Elwell CE, Cope M, Edwards AD, Wyatt JS, Reynolds EOR. Measurement of cerebral blood
flow in adult humans using near infrared spectroscopy - methodology and
possible errors. Adv Exp Med Biol 1992; 317: 325-245.
Elwell CE, Owen-Reece H, Cope M, Wyatt JS, Edwards AD, Delpy DT, Reynolds EOR.
Measurement of adult cerebral haemodynamics using near infrared
spectroscopy. Acta Neurochir 1993; 59(Suppl): 74-80.
Essenpreis M, Elwell CE, Cope M, van der Zee P, Arridge SR, Delpy DT. Spectral dependence
of temporal point spread functions in human tissues. Appl Optics 1993; 32: 418-
425.
Ferrari M, Wei Q, Carraresi L, De Blasi RA, Zaccanti G. Time-resolved spectroscopy of
human forearm. J Photochem Photobiol 1992; 16: 141-153.
Giannini I, Ferrari M, Carpi A, Fasella P. Rat brain monitoring by near infrared spectroscopy:
an assessment of possible clinical significance. Physiol Chem Phys 1982; 14: 295-
305.
Hardman KD, Eylar EH, Ray DK, Banaszak LJ, Gurd FRN. Isolation of sperm whale myoglobin
by low temperature fractionation with ethanol and metallic ions. J Biol Chem
1966; 241: 432-442.
Harris AP, Sendak MJ, Donham RT, Thomas M, Duncan D. Absorption characteristics of
human fetal haemoglobin at wavelengths used in pulse oximetry. J Clin Monit
1988; 4: 175-177.
Horecker BL. The absorption spectra of haemoglobin and its derivatives in the visible and
near-infrared regions. J Biol Chem 1943; 148: 173-183.
Hüfner G. Ueber die gleichzeitige quantitative Bestimmung zweier Farbstoffe im Blute mit
Hilfe des Spectrophotometers. Arch Anat Physiol 1900; Physiol Abt 39.
Jöbsis FF. Noninvasive , infrared monitoring of cerebral and myocardial oxygen suffiency
and circulatory parameters. Science 1977; 198: 1264-1267.
Jöbsis FF. Oxidative metabolic effects of cerebral hypoxia. Adv Neurol 1979; 26: 299-318.
Jöbsis-VanderVliet FF, Fox E, Sugioka K. Monitoring of cerebral oxygenation and
cytochrome aa3 redox state. In: Advances in Oxygen Monitoring (Tremper KK,
Barker J, eds.) pp: 209-230. Little, Brown and Company, Boston 1987.
Jöbsis-VanderVliet FF, Piantadosi CA, Sylvia AL, Lucas SK, Keizer HH. Near-infrared
monitoring of cerebral oxygen sufficiency. I: Spectra of cytochrome c oxidase.
Neurol Res 1988; 10: 7-17.
Keizer HH, Jöbsis-VanderVliet FF, Lucas SS, Piantadosi CA, Sylvia AL. The near infrared (NIR)
absorption band of cytochrome aa3 in purified enzyme, isolated mitochondria
and in intact brain in situ. Adv Exp Med Biol 1985; 191: 823-832.
Kelleher JF. Pulse oximetry. J Clin Monit 1989; 5: 37-62.
Komiyama T, Shigematsu H, Yasuhara H, Muto T. An objective assessment of intermittent
cladication by near infrared spectroscopy. Eur J Vasc Surg 1994; 8: 294-296.
Kramer K. Fortlaufende Registrierung der Sauerstoffsättigung im Blute an uneröffneten
Blutgefässen. Klin Wochenschr 1934; 13: 379-380.
Lammertsma AA, Brooks DJ, Beaney RP, Turton DR, Kensett MJ, Heather JD, Marshall J,
Jones T. In vivo measurement of regional cerebral haematocrit using positron
emission tomography. J Cereb Blood Flow Metab 1984; 4: 317-322.
Liem KD, Hopman JCW, Kollée LAA , Oeseburg B. Effects of repeated indomethacin ad-
ministration on cerebral oxygenation and haemodynamics in preterm infants:
combined near infrared spectrophotometry and Doppler ultrasound study. Eur J
Pediatr 1994; 153: 504-509.
Liem KD, Hopman JCW, Oeseburg B, de Haan AFJ, Festen C, Kollee LAA. Cerebral
oxygenation and hemodynamics during induction of extracorpereal membrane
oxygenation as investigated by near infrares spectroscopy. Pediatrics 1995. (in
press).
Liem KD, Oeseburg B and Hopman JCW. Method for the fixation of optrodes in near
infrared spectrophotometry. Med Biol Eng Comput 1992; 30:120-121.
Livera LN, Spencer SA Thorniley MS, Wickramasinghe YABD, Rolfe P. Effect of hypoxaemia
and bradycardia on neonatal cerebral haemodynamics. Arch Dis Child 1991; 66:
376-380.
Matthes K, Gross F. Fortlaufende Registrierung der Lichtabsorption der Farbe des Blutes in
zwei verschiedenen Spektralbezirken. Arch Exp Pathol Pharmacol 1939; 191: 369-
380.
Matthes K. Untersuchungen über den Verlauf der Oxyhämoglobinreduktion in der
menschlichen Haut. Pflügers Arch 1942; 246: 70-91.

22
McCormick DC, Edwards AD, Brown GC, Wyatt JS, Potter A, Cope M, Delpy DT, Reynolds
EOR. Effect of indomethacine on cerebral oxidized cytochrome oxidase in
preterm infants. Ped Res 1993; 33: 603-608.
McCully KK, Halber C, Posner JD. Exercise-induced changes in oxygen saturation in the calf
muscles of elderly subjects with peripheral vascular disease. J Gerontol 1994; 49:
B128-B134.
Millikan GA. The oximeter, an instrument for measuring continuously the oxygen
saturation of arterial blood in man. Rev Sci Instrum 1942; 13: 434-444.
Nakajima S, Hirai Y, Takase H, Kuse, Aoyagi T, Kishi M, Yamaguchi K. Performances of new
pulse wave earpiece oximeter. Resp Circ 1975; 23: 41-45.
Nicolai L. Fortgesetzte Untersuchungen über den Verlauf der Oxyhämoglobinreduktion in
der menslichen Hut. Arch Ges Physiol 1931; 230: 328-245.
Patterson MS, Chance B, Wilson BC. Time resolved reflectance and transmittance for the
non-invasive measurement of tissue optical properties. Applied optic 1989; 28:
2331-2336
Proctor HJ, Cairns C, Fillipo D, Jöbsis-VanderVliet FF. Near infrared spectrophotometry:
potential role during increased intracranial pressure. Adv Exp Med Biol 1985; 191:
863-871.
Rea PA, Crowe J, Wickramasinghe Y, Rolfe P. Non-invasive optical methods for the study of
cerebral metabolism in the human newborn; a technique for the future? J Med
Eng Technol 1985; 9: 160-166.
Samejima T, Yang JT. Optical Rotary dispersion of sperm-whale myoglobin and its
derivatives. J Mol Biol 1964; 8: 863-871.
Sevick EM, Chance B, Leigh J, Nioka S, Maris M. Quantitation of time- and frequency-
resolved optical spectra for the determination of tissue oxygenation. Anal
Biochem 1991; 195: 330-351.
Skov L, Greissen G. Apparent cerebral cytochrome aa3 reduction during cardiopulmonary
bypass in hypoxaemic children with congenital heart disease. A critical analysis of
in vivo near-infrared spectrophotometric data. Physiol Meas 1994. 15: 447-457.
Skov L, Pryds O, Greissen G. Estimating cerebral blood flow in newborn infants:
comparison of near infrared spectroscopy and 133Xe clearance. Ped Res 1991; 30:
570-573.
Skov L, Rydling J, Pryds O, Greissen G. Changes in cerebral oxygenation and cerebral blood
volume during endotracheal suctioning in ventilated neonates. Acta Pediatr 1992;
81: 389-393.
Theorell H, Åkeson Å. Reversible splitting of a homogeneous horse myoglobin. Ann Acad
Scient Fennicæ 1955; 60: 303-312.
Thorniley MS, Houston R, Wickramasinghe YA, Rolfe P. Application of near-infrared
spectroscopy for the assessment of the oxygenation level of myoglobin and
haemoglobin in cardiac muscle in vivo. Biochem Soc Trans. 1990; 18: 1195-1196.
Vierordt K. Die quantitative Spektralanalyse in ihrer anwendung auf Physiologie, Chemie
und Technologie. Tubingen: H. Laup p'sche Buchhandlung. 1876.
Wickramasinghe YABD, Livera LN, Spencer SA, Rolfe P, Thorniley MS. Plethysmographic
validation of near infrared spectroscopic monitoring of cerebral blood volume.
Arch Dis Childhood 1992; 67: 407-411.
Wickramasinghe YABD, Palmer KS, Houston R, Spencer SA, Rolfe P, Thorniley MS, Oeseburg
B, Colier WNJM. Effects of fetal haemoglobin on the determination of neonatal
cerebral oxygenation by near-infrared spectroscopy. Pediatr Res 1993; 34: 15-17.
Wood E, Geraci JE. Photoelectric determination of arterial oxygen saturation in man. J Lab
Clin Med 1949; 34: 387-401.
Wray S, Cope M, Delpy DT, Wyatt JS, Reynolds EOR. Characterisation of the near infrared
absorption spectra of cytochrome aa3 and haemoglobin for the non-invasive
monitoring of cerebral oxygenation. Biochim Biophys Acta 1988; 933: 184-192.
Wyatt JS, Cope M, Delpy DT, Zee van der P, Arridge S, Edwards AD, Reynolds EOR.
Measurement of optical pathlength for cerebral near infrared spectroscopy in
newborn infants. Dev Neurosci 1990a; 12: 140-144.
Wyatt JS, Cope M, Delpy DT, Richardson CE, Edwards AD, Wray S, Reynolds EOR.
Quantitation of cerebral blood volume in newborn human infants by near
infrared spectroscopy. J Appl Physiol 1990b; 68: 1086-1091.
Yamazaki I, Yokota K, Shikama K. Preparation of crystalline oxymyoglobin from horse
heart. J Biol Chem 1964; 239: 4151-4153.

23
Zee van der P, Cope M, Arridge SR, Essenpreis M, Potter LA, Edwards AD, Wyatt JS,
McCormick DC, Roth SC, Reynolds EOR, Delpy DT. Experimentally measured
optical pathlengths for the adult head, calf and forearm and the head of the
newborn infant as a function of inter optode spacing. Adv Exp Med Biol 1992.
316: 143-153.
Zijlstra WG, Buursma A, Meeuwsen-van der Roest WP. Absorption spectra of human fetal
and adult oxyhemoglobin de-oxyhemoglobin, carboxyhemoglobin and
methemoglobin. Clin Chem 1991; 37: 1633-1638.
Zijlstra WG. Fundamentals and applications of clinical oxymetry. PhD-Thesis University of
Groningen, The Netherlands, 1951.

24
In this chapter the installation of both the hardware and the software is
described. It is important to read this chapter carefully. It is also important not
to switch on the Oxymon before the software is installed. Windows 7 and 8 are
supported.

Follow instructions as described below to install the hardware and the

software to the PC. If it does not work to install the drivers by searching for
them automatically, please select to search drivers from a specific location.
Add the following search path directory; “C:\Windows\ftdi” or
“C:\ProgramFiles\Artinis Medical Systems BV\ftdi_208\” or for Windows 7 on
your CD/USB: “E:\FTDI 2.08.08 for artinis Oxymon” and continue. For
installation of Oxysoft 3.0.53 or higher.

PLEASE CONTACT ARTINIS IF YOU DO NOT MANAGE TO INSTALL AN OLDER

OXYMON ON WINDOWS 8.

Before using the Oxymon, the system should be properly installed and
connected. Connections should only be changed when the instruments are
off.

Make sure that the mains voltage suits the needed operating voltage! This
value is at the power supply information. The Oxymon is equipped with a
self-switching power supply, operating between 110 and 230 VAC, either 50
or 60 Hz. Also, check the mains voltage supply of the additional instruments
or computers. A safety transformer can be used, but is not necessary
(Figure 5-1). Plug the power supply cable into an electric power supply and
connect it to the power supply inlet of the Oxymon.

Figure 5-1. Safety transformer

25
Figure 5-2. How to change the “Power Save” options of the computer

The Oxymon should be installed such way, that a free airflow is guaranteed.
No obstructions should be placed before an air in- and outlet.

For installation turn on the power of the computer and computer monitor
but DO NOT yet turn on the Oxymon or connect the USB cable. Wait until
all the software has been installed.

Note that for proper functioning, the 'Power Save' mode of the PC should
be de-activated. This can be found by right-clicking the mouse while
situated over the desktop. The “Display Properties” screen will appear. Set
“Select screensaver” to none. Click on the button “Power” and set all
settings for use with the Oxymon to “Never” (Figure 5-2).

26
Insert the CD/USB with the software delivered with the Oxymon system into
the PC. If the computer does not automatically open the CD/USB, go to “My
Computer” and open the CD/USB by double clicking. Open “ReadMe.txt”
and follow the instructions in the file. This paragraph will describe the steps
one by one. Note that the version number of the software can change
according to the version delivered.
Open “Oxysoft_x.msi”, where “x” is the version number of Oxysoft. The
“Setup wizard” will open (Figure 5-3). Click on “Next” to start the “Setup
Wizard”.

Figure 5-3. Setup wizard Oxysoft

This software has an “End-User License agreement”, which is shown in Figure

5-4. This license agreement has to be accepted before software installation.
Read it carefully before acceptance. Then, select “I accept the terms in the
license agreement” and click on “Next”.

To install the software, choose the destination folder (Oxysoft directory) in

the next field (Figure 5-5). We recommend keeping this name! Click on
“Next”.

27
Figure 5-4. End-User License Agreement

Figure 5-5. Destination folder

28
Figure 5-6. Start installation

Figure 5-7. Finish the setup wizard

The installation can be started now by clicking on “Install” (Figure 5-6). It is

possible that installation does not start until you say ‘yes’.
The installation will finish by clicking on “Finish” (Figure 5-7).

29
To install device specific files and some help files, open “FileSetup.exe” of
the installation CD/USB. When you run this file, it might be that Windows
asks for permission. Please click yes.

Select the language during installation in the next window (Figure 5-8). The
“Setup wizard” will open Figure 5-9. Click on “Next” to start the “Setup
Wizard”. Read the installation instructions on Figure 5-10 and click “Next”.

Figure 5-8. Language during installation

Figure 5-9. Welcome to OctaMonFilesSetup Wizard

30
Figure 5-10 Installation instructions

Figure 5-11 Select Destination location

To install the software, choose the destination folder. We recommend

keeping this folder (Figure 5-11).

Click on “Next”. In the following window, you can place the shortcuts in the
windows menu (Figure 5-12)

31
Figure 5-12. Select start menu folder

Click on “Next”. In the following window, the installation will start by clicking
on “Install” (Figure 5-13). After the installation, it will finish by clicking on
“Finish” (Figure 5-14).

Figure 5-13. Start installation

32
Figure 5-14. Finish installation

At page 38 all elements of the Oxymon are described. Now connect the
Oxymon to the PC or laptop using the USB cable. Put one end into the USB
connection of the Oxymon (Figure 5-15). Connect the other end to a free
USB port on the PC. This can be either a type 1.1 or 2.0 USB connection.

Figure 5-15. USB connection Oxymon and PC

Turn the Oxymon on by the main switch at the back of the Oxymon. The
power indicator on the front of the instrument will turn green. A balloon will
come up in the right corner of the monitor. Do NOT remove the CD/USB.
The PC will detect new hardware.

Once you connect the USB to your computer, Windows 7 and 8 will install
the device automatically. Please notice the information you see in the
bottom right of your screen (Figure 5-16).
The following steps might be necessary for Oxymon devices before 2015
on windows 7. Please contact Artinis if you wish to install such a device on
Windows 8.

33
Figure 5-16. Automatic driver installation notification

Figure 5-17. Failed driver installation notification

Figure 5-18. Device Manager with yellow marked Oxymon Mk3

If Windows gives an error which says “Device driver software was not
successfully installed” (Figure 5-17), the driver needs to be updated.

To update the driver follow the following steps:

1. go to control panel (on the right in the start menu)

2. go to System and Security or if possible, go directly to step 3
3. go to Device manager (Figure 5-18)
4. "Oxymon Mk3" is visible under “Other devices" with a yellow mark
(Figure 5-18)
5. Right click on this and select "Update Driver Software"
6. Select "Browse my computer for driver software" (Figure 5-19)
7. Click browse and go to the CD/USB folder (mostly E:\) and select the
folder:
“FTDI 2.08.08 for artinis Oxymon" and click "next" (Figure 5-20)

34
Figure 5-19. Choose to browse a file on my computer

Figure 5-20. Select the folder to search for the FTDI driver

8. If Windows gives a safety warning (Figure 5-21), choose to "install this

device software anyway".
9. A screen will appear that the driver is successfully installed (Figure
5-22). Windows might ask to restart your computer.

35
Figure 5-21. Safety warning. Please select to install anyway

Figure 5-22. Successfully updated the driver software

36
For installation on Winodws 7 or higher, insert the included Polhemus DVD
and the autostart screen will start. Click on the “Install Host Software”
button and follow the on-screen instructions. This will install both the driver
and some proprietary Polhemus software tools. You can uncheck the
“Polhemus SDK Files” option. Make sure that the Patriot device is not
connected before of while installing the software. After having successfully
installed the software, connect the Patriot device to a USB-port of your
computer. For more information, please see the Patriot manual also
included on the Polhemus DVD

37
This chapter introduces the Oxymon and explains how to connect it to the PC,
the subject and other devices. Please, follow the installation procedure as
described in chapter 5 before connecting the Oxymon(s) for the first time to the
computer.

The Oxymon is a continuous wave NIRS system with two or more

wavelengths of emitting light. The device is developed to measure
concentrations of substances with near infrared light. Which substances
can be measured with the Oxymon is dependent to the ordered
wavelengths. The wavelengths of the lasers are visible in the software
(paragraph 8.7).

Each component of the Oxymon is explained in Figure 6-1. The following

components are important for the use of the Oxymon:
1. Power indicator: lamp turns green if the power of the machine is on.
2. Measure lamp: lamp turns red if the lasers are on
3. Status lamp: lamp turns green if the machine is ready for data
acquisition, blinks red and green during the start-up of the machine.
4. Receiver optical fiber: transmits light from the skin to the receiver
5. Receiver module: contains the receivers
6. Transmitter optical fiber: transmits light from the laser to the skin
7. Transmitter/laser module: contains the lasers
8. Power supply: supplies electricity to the machine
9. Main switch: enables the machine
10. USB connection: connects the machine to a PC by an USB cable
11. Interconnection board: connects the machine to other Oxymons by
master-slave connector cables
12. Air in- and outlet
13. AD Channel board: connects machine to other devices
14. Power supply information: contains information about the required
power
15. Medical ground: to ground the device

38
Figure 6-1. Oxymon, front side (above) and back side (below)

The lasers of the Oxymon transmit light in the near infrared spectrum.
Usually, an Oxymon has two wavelengths about 850 nm and 760 nm. The
lasers of 850 nm are the upper lasers; the lasers of 760 nm are the lower
lasers. Two lasers with each a different wavelength forms a transmitter. If
the Oxymon has three or four wavelengths, the lasers are arranged in a
different way. In this case, the three or four lasers with each a different
wavelength forms a transmitter. Two lasers above each other form a
transmitter block, which is equal to a transmitter if just two wavelengths are
available in the Oxymon. Both lasers concerning to one transmitter block
have to be connected to an optical fiber before the lasers can be enabled.
The machine receives the light with an avalanche photodiode (APD), the
receiver. The lasers fire one by one, in that way the system can distinguish
between lasers. This principle is called the time-sequenced principle and also
works when multiple Oxymons are coupled.

The light is transmitted from the laser to the skin and from the skin to the
receiver by optical fibers containing glass fibers. A fiber ending connecting
to the Oxymon is called connector; a fiber ending at the skin is called
optode, transmitting to or receiving light from the skin. The optodes are
fixated in an optode holder (Figure 6-2). The distance between the optodes
is called the source-detector distance or the inter-optode distance. A
transmitter and receiver optode together form an optode combination or
channel.

39
Figure 6-2. Example of an optode holder. Optode holder with optodes to create a single
measurement point. The optodes stick out to get a good optical fiber-skin contact.

The optode configuration, which is used during the measurement, has to

be specified in Oxysoft in the measurement properties as optode template.
Optode templates define the optode combinations made by transmitter
and receiver optodes. The optode templates are essential to create the
correct graphs and to calculate the concentrations and TSI. More
information and examples of optode configurations are given in chapter
11.

Some configurations work with split optical fibers, to reduce the number of
needed transmitters and/or receivers and the complexity of the optode
holder. A split optical fiber has two or more optodes. However, the optodes
of a split transmitter fiber have to be combined with optodes of two
different receivers (or vice versa); otherwise, the system cannot distinguish
the optode combinations by the time sequence principle. A split fiber will
reduce the amount of light transmitted through the fiber with about 50%.
Using a combination of a split receiver fiber and a split transmitter fiber will
reduce the amount thus to 25%. Cover the optodes of the split fibers,
which are not used during a measurement or calibration with the black
shields or cloths.

The power level of the lasers can be set to “standard" or “dimmed" which is
using about half of the power of the laser. Various types of optical fibers
are available with respect to length and width of the fibers. Specially
designed optical fibers that are suitable for simultaneous measurement
with NMR/MRI are also optional.

The system can measure at, 1, 2, 5, 10, 25 and 50, which is called the
sample rate or frequency. If the system is designed for 250 Hz, it is possible
to measure at 125 and 250 Hz as well.

40
 The Oxymon can be switched on and off by the main switch. The power
indicator will turn green. The status lamp should blink green and orange
during starting up. After a while, it turns green and the device is ready for
data acquisition. If the status lamp continues blinking green/orange, please
contact Artinis. The measure lamp turns on if the lasers are firing!

6.1.1.1 Connection problems

If Oxysoft has troubles to make a connection to the Oxymon, check the
following:
- Is there a USB connection between the Oxymon and the computer
(paragraph 6.1)
- Is the Oxymon turned on?
- The system might have been connected or powered on wrongly. Please
restart all, follow the previous instructions and remember to power on
Oxymon before the AD box!
- Are the master-slave cables connected in the right way (paragraph
6.2.2)?
- Are the drivers of the Oxymon installed in the right way? For Windows 7
or 8 is used, it is necessary to run first a driver installation manually for
Oxysoft. Start “C:\Program Files\Artinis Medical Systems BV\Oxysoft
DAQ XXX\InstDrv.exe” and follow the instructions. Then continue by
plugging in the license key and follow the instructions. Choose the
option to install software automatically, and please wait because this
can take several minutes. If this is not working, go back and choose the
option to install from a specific location instead. Add the search path
directory “C:\windows\inf” and continue. This may take several minutes
to finish.

If more than one Oxymon is available, those can be interconnected. One

stack of Oxymons can consist of one up to four single Oxymons together.
One Oxymon will work as a master and the other ones as slaves. They are
connected by using master-slave (connector) cables. Each stack will be a
system on its own, and needs to be connected with a separate USB cable.
Orientate the different connectors by looking at the back of each Oxymon
cabinet (Figure 6-1).

Only the hardware installation of the master Oxymon has to be

accomplished if always the same stack configuration is used. However, to
make stand-alone use of all Oxymons possible, install all Oxymons one by
one on the computer. If the stack is changed (move Oxymons to other
master/slave positions), recalibrate the system.

The master Oxymon controls the slave Oxymons by the master-slave and
asynchronous cables. Therefore, the time sequence principle still works
using multiple Oxymons.

41
 Make sure that the correct cables are available for connecting the cabinets.
The connector cables look like normal Ethernet (network) cables, but are
not the same. An asynchronous connector cable has two identical ends,
marked with an “A”. A master-slave connector cable has different ends and
it is important that the one marked “M” is connected to a master device and
the other end to a slave device. The USB cable is a standard USB cable
(Figure 6-3).

Asynchronous connector cable: A A

Master-slave connector cable: M S

Oxymon USB cable: Oxymon Computer

Figure 6-3. Cables

Connect the cables as described in the connection scheme figure (Figure

6-4). Plug in the USB cable between each master Oxymon and computer,
before switching on power supply to the Oxymons. With two Oxymons,
connect Oxymon master A and Oxymon slave A1. With three or four,
connect also slave A2 and A3. With five or more Oxymons, it is necessary to
build a new stack as shown in Figure 6-4. A stack needs to be filled up in
the correct order (For example, it is not possible to have the first slave
unplugged and still use the second, or connect the first slave as a second
slave). Two stacks of Oxymons can be run without interference if they are
connected with the asynchronous connector cable. If less than four
Oxymons are in Stack A, it is suggested to place the asynchronous
connector cable in position 2 or 3 in master A instead of position 3 in slave
1.

To change the setup by plugging in or out an Oxymon: please switch off the
power supplies, then turn them on again and restart Oxysoft.

Software versions before Oxysoft 3 need to use a separate Oxysoft

program and computer for each stack of Oxymons. The programs have to
be run from a program folder together with the correct calibration files for
the devices in use. Therefore always use the correct separate program
folders for different Oxymon setups and never mix up these files. A
maximum of 8 receivers and 16 lasers (8 transmitter blocks) can be used in
one stack. This means that if four full cabinets are used with each 2
receivers and 4 transmitter blocks (8 lasers), only 8 transmitter blocks in total
can be used. Oxysoft 3 or higher can have multiple stacks, also combined with

42
other systems as the PortaMon and the PortaLite, in one Oxysoft package.
However, the Oxysoft version 3 or higher is limited to a combination of 8
receivers.

3 2 1 0
Oxymon master A
M M M

Oxymon slave 1A 1
*
S

Oxymon slave 2A
S
*

Computer A
Oxymon slave 3A
*
S

Oxysoft 3+

3 2 1 0
Oxymon master B
M M M A
Oxysoft 2.1.6
If full

Oxymon slave 1B Oxymon System Stack B

*
S

Oxymon slave 2B
S
*

Computer B
*
S

Figure 6-4. Masters, slaves and computers connection scheme

43
Analog-Digital channels (AD Channels) can be applied to connect an Oxymon
to other devices and measure synchronized with these devices. Using the
input AD Channels give the possibility to analyze all data in Oxysoft. The
input of the AD Channels can be shown in Oxysoft with traces; when an AD
Channel is selected as “type” at the channel A tab. The channels are only
available if ordered!

Warning: AD channel signals measured or displayed at a too low frequency

will be affected by aliasing. Aliasing refers to an effect that causes different
continuous signals to become indistinguishable (or aliases of one another)
when sampled. It also refers to the distortion or artifact which results when
a signal is sampled and reconstructed as an alias of the original signal. For
a high frequency signal, it is better to use the AD boxes or to filter the signal
strongly at half the sample rate.

With multiple Oxymons connected as master and slave(s), up to 16 AD

Channels can be available in Oxysoft. If two Oxymons are used (master and
slave) with 8 AD inputs each, the inputs from the first Oxymon can be
displayed by adding trace from channels 1-8. Inputs from the second
st th
Oxymon can be displayed by adding trace from channel 9-16 (1 – 8 input
in slave Oxymon).

Analog-Digital (AD) boxes give extra possibilities for the input and output of
data from the Oxymon. AD boxes are configured as input or as output box.

Important: If it is not possible to connect with the device in Oxysoft (or if the
inputs or outputs are not working), check your cables and connections and
see page 72. Make sure that you turn on the power of the Oxymon and the
AD box at the same time.

Using an AD input box instead of the AD channels of the Oxymon has the
following advantages:
- The signal of the AD Box is filtered at half the sample rate set in Oxysoft
for the Oxymon, which reduces the aliasing effects. The AD box has a
cutoff frequency with a maximum of 70 Hz.
- An input AD Box has 16 inputs, while an AD board has only eight
inputs.

The AD Channels of an Oxymon connected to an AD box are still working.

44
6.4.1.1 Installation
The AD input box can be installed as a second Oxymon, using only the USB
connection on the AD box to the computer. The AD box needs to be
selected when making a connection to the Oxymon as shown in Figure 6-5.

Figure 6-5. Connect to an AD input box by selecting it before connecting to both systems.

6.4.1.2 Input signals

AD input signals can be shown as traces in Oxysoft (paragraph 9.4.1). Add a
trace and select “AD Channel X” as source. Which channel has to be
selected depends on your system setup. The trace properties can be
scaled and modified in the “Transformation A” tab. The black button (bias
button) at the front side of the Oxymon does nothing; it is only working
when the AD box is configured as output box.

For example, a single Oxymon with AD input channels can be displayed in

Oxysoft by adding a trace, and selecting “AD Channel 1” (up to 8) as “type”
of source at the “Transformation A” tab. If this Oxymon is connected
together with an AD box, the AD Input channels of the Oxymon can be
displayed in Oxysoft by adding a trace and selecting “AD Channel 1” (up to
8) and the input of the AD Box can be displayed by selecting “AD Channel 9”
(up to 24).

- The output of the AD box are the concentrations measured by the

Oxymon, It is also possible to have TSI output instead of relative
concentrations.
- All concentrations measured by a full Oxymon cabinet (2 receivers, 4
transmitter blocks) are as output available at the AD box.
The AD Channels of an Oxymon connected to an AD box are still working.

45
6.4.2.1 Installation
The AD box has to be installed in combination with the Oxymon in this way:
- Connect the end marked “M” (master) of the cable to the AD box (in the
third position from the left, Figure 6-7).
- Connect the end marked “S” (slave) of a master slave cable to the
Oxymon (in the third position from the left).
- Connect the USB cable between the AD box and the computer (not to
the Oxymon!).
- Insert the power supply to the AD box.
- Turn on the power to the Oxymon and the AD box at the same time
(the status lamp and power indicator will turn green).

Figure 6-6. AD box – front side. Green lamp is turned on when the AD box is powered on. Blue
lamp is turned on during data acquisition, and blinks when AD output traces are being biased.
Bias button (press 1-2 s) will bias all the output signals

Figure 6-7. AD box – backside. The analog inputs or outputs (1-16) can be found on the backside,
and connectors for USB, Oxymon and power supply.

- Connect and start data acquisition in Oxysoft (the ‘measurement’ light

on the AD box turns blue when started with data acquisition).
- Check the AD input/output signal settings in Oxysoft, use AD box bias
button if needed.
- Use and perform regular measurements with the Oxymon and Oxysoft.
- The channels are numbered as:

46
 1 3 5 7 9 11 13 15
2 4 6 8 10 12 14 16

The BNC Connectors are only for 50 Ohm BNC types.

6.4.2.2 Output signal

When the Oxymon data acquisition is started, the signals are mapped and
biased to the AD outputs. The AD output signals can be set to 40 µM, 10
µM or 4 µM concentration changes per Volt under Data Collection>>AD/DA
settings, as shown in Figure 6-8. AD output signal gain settings. The output
signals are mapped according to the optode template used in Oxysoft.
Table 6.1 shows examples of some standard templates.

Figure 6-8. AD output signal gain settings.

With the black button (bias button) at the front side of the AD box is
pressed for a couple of seconds, the output of the AD box is biased to 0
Volt. The Oxymon only measures relative concentrations (see paragraph
9.4.6), therefore the absolute value of the concentrations are not relevant,
only the relative changes.

Remark: A receiver gain or laser output change will result in a jump in the
voltage. The calibration of the Oxymon is not valid for the AD Box. Please,
set the gain and output before the start of the experiment and do not
change it during the experiment.

47
 Table 6.1. Example of trace mapping of AD outputs
template 2 x 1 channel template 8 channel (split)
AD
output: Receiver: Transmitter: Transform: AD output: Receiver: Transmitter: Transform:
1 R1a - T1 O2Hb 1 R1 - T1 O2Hb
2 R1a - T1 HHb 2 R1 - T1 HHb
3 R1b - T2 O2Hb 3 R1 - T2 O2Hb
4 R1b - T2 HHb 4 R1 - T2 HHb
5 R1 - T3b O2Hb
template 4 channel square 6 R1 - T3b HHb
AD
output: Receiver: Transmitter: Transform: 7 R1 - T4b O2Hb
1 R1 - T1 O2Hb 8 R1 - T4b HHb
2 R1 - T1 HHb 9 R2 - T2 O2Hb
3 R1 - T2 O2Hb 10 R2 - T2 HHb
4 R1 - T2 HHb 11 R2 - T3a O2Hb
5 R2 - T1 O2Hb 12 R2 - T3a HHb
6 R2 - T1 HHb 13 R2 - T4a O2Hb
7 R2 - T2 O2Hb 14 R2 - T4a HHb
8 R2 - T2 HHb 15 R2 - T1 O2Hb
16 R2 - T1 HHb
template 4 channel cross
AD
output: Receiver: Transmitter: Transform: template 1 channel TSI Fit Factor + 2 x 1 channel (split)
1 R1 - T1 O2Hb AD output: Receiver: Transmitter: Transform:
2 R1 - T1 HHb 1 R1a - T1 O2Hb
3 R1 - T2 O2Hb 2 R1a - T1 HHb
4 R1 - T2 HHb 3 R1a - T2 O2Hb
5 R2 - T3 O2Hb 4 R1a - T2 HHb
6 R2 - T3 HHb 5 R1a - T3 O2Hb
7 R2 - T4 O2Hb 6 R1a - T3 HHb
8 R2 - T4 HHb 7 R2 - T4a O2Hb
8 R2 - T4a HHb
9 R1b - T4b O2Hb
10 R1b - T4b HHb

6.4.2.3 TSI as output

It is possible to have the TSI as output. For this you need to set the gain and
choose the AD output channel. This can be found under the TSI trace
properties (right mouse click on the trace) under the tab “transformation A”
(Figure 6-9. AD output signal gain settings.). Please be aware that the TSI
only updated 1/s and has 0.5 second delay.

48
Figure 6-9. AD output signal gain settings.

The PortaSync (Table 6.2) is a separate Bluetooth device which can be used
for generating an event signal. The system has two buttons, each creates a
distinct signal (2.5V and 5V).
The PortaSync also has a BNC input connection for analogue event signals
of other measuring modalities and a BNC output, to send the signal from
the buttons to any other measuring modality.
The PortaSync has the same Bluetooth range as the PortaMon and
PortaLite. However, the PortaSync must first be enabled for Bluetooth
before connecting. You can do so by pressing both buttons for 3 seconds.
The Event generator uses 2 AAA batteries, which last about 8 hours with
Bluetooth connection (blue LED). The orange power LED will blink when the
battery is almost empty.
Bluetooth has a delay of 100-200 milliseconds.

49
Table 6.2. Overview of PortaSync function
1 Power on/off button
2 Power indicator light
3 Bluetooth indicator light
4 Signal Button high
5 Signal Button low
6 Low frequency (10Hz sample
rate) analog input (0-5V max)
7 Analog output (low: 2.5V,
high: 5V)
Turns on power
Normally on, slow blink on low
power (2Hz).
Off after power on, slow blink when
Bluetooth enabled but
disconnected. On when connected.
Send a high signal level. 5V on
analog output, high level on
Bluetooth.
Send a low signal level. 2.5V on
analog output, low level on
Bluetooth.
Analog input can be used to
connect external signals. This allows
for importing signals (triggers) from
different measurement systems to
be imported into Oxysoft.
Analog output can be used to send
trigger signals to TTL signal
compatible systems.
50
The Patriot device is a 3D digitizer made by Polhemus Inc.
(http://www.polhemus.com) and is supported to be used in conjunction
with the Oxymon through Oxysoft. The Patriot device is used to measure
the shape of the participant’s head, to align (coregister) it with a template
brain in order to determine the locations of the optodes relative to the
template brain. For more information on this coregistration procedure see
paragraph 9.2.8. The Patriot device consists of several parts that need to be
connected to the main station. See Figure 6-10 for an overview.

Figure 6-10 Parts of the Polhemus Patriot device. To the left is the power supply. On the top left is
the main station, to which the power supply, source and the sensors are connected. On the top
right is the source (grey cuboid) and the stylus (pen-shaped tool) constituting sensor 1. To the
lower right is sensor 2. On the lower left is the headband, to which sensor 2 can be mounted and
two adhesive, foam inlays to increase wearing comfort.

The Patriot device uses an electromagnetic source to create a weak

electromagnetic field. Up to two sensors can be used to. The sensors are
inducing a small change in the electromagnetic field. This information is
used to determine the exact location of the sensor relative to the source.
For more information on the device, please see the Polhemus Patriot
manual.
As the Patriot device is sensitive to electromagnetic fields, it should only be
used in an environment without a lot of electromagnetic distortions. Also, it
should be relatively far away from other metallic objects. The source can be
screwed using the included the plastic screws to a fixed location, once a
setup is found that gives satisfactory results. Similarly, the headband
sensor should only be mounted using (e.g. the included) plastic screws.
In Oxysoft, by design the first sensor has to be the stylus, and the second
sensor is the mounted sensor on the headband. The stylus is used to
precisely digitize the optode location. Once the stylus is at the sensor

51
position, its button has to be pressed. Oxysoft then registers the current
position and automatically continues to the next step (see paragraph 9.2.8).
The headband including the second sensor is intended to be worn by the
participant. Data from the second sensor is then used to account for small
head movements during the digitization process. Consequently, the source
has to be connected to the Source port of the Patriot main device, the
stylus has to be connected to the Sensor 1 port of the Patriot main device
and the headband sensor has to be connected to the Sensor 2 port of the
Patriot main device.

52
Oxysoft is the program which can be used to record, manage and analyze data
measured by the NIRS device(s). This chapter illustrates how to work with
Oxysoft in order to handle data. The data acquisition is described in chapter 8.

An overview of the program is given in Figure 7-1. Each part is numbered.

The used abbreviation DAQ means “Data Acquisition”.

Part How to display:

1. Menu always
2. Toolbar Menu  View  toolbars and docking windows  Main
Tools
3. Project view Menu  View  toolbars and docking windows  Project
4. Template DAQ state Menu  View toolbars and docking windows 
Template DAQ state
5. DAQ status view Menu  View toolbars and docking windows  DAQ status
view
6. DAQ value view Menu  View toolbars and docking windows  DAQ value
view
7. Indicator view Menu  Graph  Create indicator view
8. Spectrum view Menu  Graph  Create spectrum view
9. Averaged data Menu  Trace  properties  Transformation A  Cyclic
operator
10. Topo Graph Menu  Graph  Create Topo Graph
11. Graphs Menu  Graph Create Graph
12. Legend Menu  Graph  (common) properties, Show legend
13. Status bar Menu  View toolbars and docking windows  DAQ
status
14. Mouse pointer by moving the mouse over a trace it will give the value

The menu contains several submenus, like “File”, “Measurement” and “Data
Collection”. If one of these is clicked, the submenu will open. Each submenu
contains functions to control the program. In the toolbar all frequently
used functions are available as buttons for a quick access. The toolbar can
be customized by right clicking on the bar and selecting “Customize…”.

In the project view a tree of all measurements, graphs and traces is

displayed. If there is a “plus” (instead of a “minus”) sign before a project ,
measurement , or graph , expand it by clicking on the “plus” sign;
the next layer (measurements, graphs or traces ) will become visible.

The DAQ value view and DAQ status view are important during the data
acquisition. In the DAQ status view the status of the NIRS device(s) is
displayed. In the DAQ value view it is displayed how much light is measured
by the NIRS device(s). The status bar shows the current state of the NIRS

53
device(s). The status bar displays the value in the graph at the mouse
pointer and displays if the data is acquired (DAQ) or data is recorded (REC).
The mouse pointer displays information about the trace that is under the
mouse point.

Figure 7-1. Oxysoft screenshot

The layout of the program can be changed by “drag-and-drop” and the

graphs can be resized with the mouse. Drag one of the windows to another
position and drop it there. If a window has disappeared, reopen it in Menu
 ViewToolbars and Docking Windows. Graphs can be opened by Menu 
Graph  Open Graph.

When you drag a window small boxes appear on each side of the screen as
well as a cross in the middle. If you drag a window on one of these figures,
the window will be fit to the chosen side.

54
The acquisition program “Oxysoft” can be started by clicking on the
shortcut on the desktop or by the Windows start button, “All
programs”, “Artinis Oxymon”, “Oxysoft X” or by going to the program
directory and click on “Oxysoft.exe”.

Figure 7-2. About Oxysoft

Oxysoft can be closed by Menu  File  Exit. First, save the project to save
all measurements and graphs if needed.

Information about the used Oxysoft version and options is in Menu  Help
 About Oxysoft (Figure 7-2): the copyright, license, version and contact
information. The license document “040303 AMS Software License
Agreement.rtf” is available in the Oxysoft installation folder.

“No Oxysoft 3 dongle detected” means there is no (correct) license key in

the computer for the software. The license key is a red USB stick, but it
cannot be opened or used to store any data files. Standard license key has
a maximum sampling rate of 50 Hz for the Oxymon. An upgrade up to 250
Hz is possible for the Oxymon.

55
If the software is not available with the (correct) license key plugged in the
USB of the PC, close Oxysoft and restart it. The license key has to be
plugged in before Oxysoft is started. If the software is still not working,
please try the following:
If Windows 7 or 8 is used, it can be necessary to first run (or use are repair)
a driver installation manually for the dongle. The drivers can be found on
the CD/USB with software. It could be possible the driver does not work
immediately. If not; go to the Windows start menu and go to devices and
printers. Here you will see the ROCKEY. Right click and go to properties. Go
to tab hardware and click properties and update the driver.

The data can look different in newer Oxysoft versions. The data may look
different in different versions of Oxysoft due to different offsets, but most
probably, the settings have changed. Check the settings, which have an
immediate impact on the graphical displaying. For example, “source-
detector distance” and “DPF” in the measurement properties and “bias” in
trace properties.

The license document “040303 AMS Software License Agreement.rtf” is

available in the Oxysoft installation folder.

By selecting Menu  View  Options the program options can be changed,

the window shown in Figure 7-3 will open. These settings are applied to all
measurements, but some can be adjusted specific for one measurement in
the properties of that measurement, graph or trace.

56
Figure 7-3. Program options – Data collection

Startup options
Start recording manually: Check if the recording has to start manually. If not
checked, the recording will start with the start of data acquisition. Bias
traces at start: Traces are biased at the start of the measurement. For more
information about biasing traces, see paragraph 9.4.6.

Out of range alert

If the measured intensities (see paragraph 8.7) are out of range, the
program can give a beeping sound.
- Low: Lower range, default is 0.4 % (~300 counts).
- High: Higher range, default is depending on system ID
- Beep when out of range: Check to get an beep when out of range
- Signal on optode template combinations only: Check to get only alerts on
the used optode combinations of the template (recommended).

Time spans per display mode

Rollover mode: the rollover mode displays the measured data in a short
time span (15 seconds, 30 seconds, 1 minute or 2 minutes)
Trend mode: the trend mode displays the measured data in a longer time
span (5, 15, 30 or 60 minutes)

57
Calibration
Select all gains high for TSI calibration to set the receiver gains to high
before the TSI calibration starts, also if you have set the receiver gains too
low for the measurements. We strongly recommend to use high gains
during calibration.

This tab (Figure 7-4) defines the general graph properties.

Graph font
The font used in the graph for labels, legends, etc. in graphs.

Editor font
The font used for the DAQ Value view.

Background color
Click on this button to change the background color of the graph.

Text color
Click on this button to change the text color of the graph.

Figure 7-4. Program options – Graph Options

Show user events

To show events in the graph, set this to 'show events'. For more
information about events, see paragraph 10.1. In case of cyclic data, the list
of options is expanded with traces based on cyclic data.

58
 Show legend
When checked, a legend of the traces is shown in the right of the graph.

Suppress Scale Factorization

The value numbers shown along the y-axis, will be scaled in order to limit
the number of digits used. For example: if the minimum value is 0, and the
maximum value .01, then (with steps) values from 0.0 to 10.0 are shown
and next to the graph, the unit 1e-3 is displayed as scale factor. When this
option is checked, the factorization is suppressed and the values are shown
in an unscaled way, at the expense of a wider space reserved for the y-axis
numbers.

Common auto scale/Auto scale/ Manual scale

These properties are equal to these in the regular graph properties
(paragraph 9.3.7).

This tab (Figure 7-5) defines the Measurement template file path selecting
the file which defines standard templates used to create measurements,
graphs and traces from a template. The template files are called *.oxypt.

7.6.3.1 Working with measurement templates

Measurements and graphs can be created from a standard template using
the function “Create measurement from a template”. The graphs, traces,
scaling, graph arrangement, and all measurement parameters (optode
template, source-detector distance, DPF, sample rate, etc.) are preset.
When required, the parameters can be adjusted at the specific tabs of the
measurement properties. In addition, the graphs and traces can be
adjusted afterwards. Always check the settings after choosing a certain
template, because the template parameters can be different from the
required parameters for your measurement!

Creating graphs from a template by the function “Create graphs from

template” creates only the graphs and traces according to the chosen
measurement template and does not set the measurement parameters!

It is possible to make your own measurement template. The standard

template file is “oxydaq.oxypt” and is saved in the folder “template” in the
Oxysoft installation directory.

7.6.3.2 Create a measurement template

Files can be added to an existing template file or a new one can be created:
- To add a new measurement template to an existing template file
browse to the template file (*.oxypt), copy and paste it, rename the file
to “*.oxyproj”; start Oxysoft, go to Menu  File  Open, browse to the
appropriate directory and select “*.oxyproj”. Click on “OK”.
- To create a new template file, first create a new project in Oxysoft.

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After creating/opening the project, create a measurement and name it like
the desired template. Make all graphs and traces and arrange the graphs
as desired. Save the project with the name of the desired template file and
close Oxysoft. Browse to the folder were the project is saved, copy and
paste it. Rename the project from “*.oxyproj” to “*.oxypt”. Start Oxysoft and
change the template file in Oxysoft in Menu  View at the tab “Template
file” to the new template file.

Add more templates to a template file by creating more measurements

(with different names) in the project.

Figure 7-5. Program options – template file

The extinction coefficient table of this project can be selected by clicking on

“Browse” (Figure 7-6). The extinction coefficient tables are saved in a *.xml
format in the Oxysoft installation directory in the folder “Tables”. You can
also add your own table. The default table is from Cope [Cope 1991].

The DPF (differential pathlength factor) table can be used to correct the
DPF for its wavelength dependency. The table can be selected by clicking
on “Browse”. The DPF tables are saved as “DPF_*.xml” file in the Oxysoft
directory in the folder “Tables”. The default table is “no correction”, which
we recommend for most applications.

Figure 7-6. Program options – default coefficient tables

60
This chapter describes how to do a measurement with Oxysoft and which
parameters are important during the measurement. Take care of the
measurement quality with the DAQ value. The last paragraph describes how to
calibrate an Oxymon, in the other paragraphs is assumed that the system is
calibrated.

Like in every scientific set-up you should, in advance, have an idea of the
questions you want to solve as it determines the design of the protocol.
Concerning NIRS measurements, it means that you must choose the task
(intervention), the anatomic area of interest, and decide whether you prefer
a qualitative or quantitative approach. Especially the latter has distinct
consequences for the protocol as it can only be done under specific
conditions.

Good preparation before data acquisition will save time and increase the
accuracy of the measurements. We advise to create all desired graphs
(paragraph 9.3) and to add all necessary traces (Paragraph 9.4) to the
graphs before you start the measurement. Graphs and traces can also be
made during and after the measurement. For instance, when you program
your expected and possible unexpected occurrences (e.g. “movement
artifact”) prior to the measurement, you will have the hands and mind free
to react to other things that come up. Accurate and frequent instructions
for the subject are also essential for a good result. Especially instructions
when not to move can be very important for the determination of
quantitative variables afterwards, e.g. at the start or after cessation of an
occlusion. Movement artifacts can easily obscure the data and rule out the
possibility of quantitative calculation, but can mostly be avoided with
adequate instruction.

A measurement can be accomplished in the following way. First, be sure

that the system is fully installed (see chapter 5) and calibrated (see
paragraph 8.9).

1. Put the power supply cable into the Oxymon(s) (paragraph 6.1).
2. If necessary: Connect the Oxymon to other Oxymons (paragraph 6.2)
3. Put the USB cable to the USB port of the Oxymon (paragraph 6.1). If an
AD box is used, see paragraph 5.4 how to connect the Oxymon in
combination with an AD box.
4. If applicable: Connect the AD cables to the AD board or box (paragraph
6.3)
 5. Connect the optical fibers to the Oxymon(s) (paragraph 8.2)
6. Connect the optical fibers to the optode holder(s) (paragraph 8.2).
Measure the distance between the optodes of each holder to
determine the source-detector distances.
7. Turn the Oxymon(s) on by the main switch (paragraph 6.1). Wait until
the status lamp is green (paragraph 6.1).
8. Start and create a measurement in Oxysoft (paragraph 8.2) and set
DPF, D(mm), (delta d(mm), h and k for TSI templates) and appropriate
sample rate
9. Warm up the machine for about 20 minutes for a TSI calibration (if
applicable) (paragraph 12.5)
10. Make graphs (paragraph 9.3) with traces.
11. Fixate the optode holder to the subject (paragraph 8.3)
12. Fixate the optical fibers to the subject and the environment
13. Start the data acquisition (paragraph 8.4). Check the ‘Measure’ lamp at
the Oxymon (paragraph 6.1).
14. Check the DAQ status view before the start of the experiment
(paragraph 8.5)
15. If necessary, adjust the gain settings in Oxysoft to get a good
measurement quality (paragraph 8.7)

16. If all settings are set right, bias the traces and start recording.
17. Indicate the start of the measurement with an event (paragraph 10.1)
for two reasons. 1: to indicate the start, 2: to be sure the data is being
recorded. If the event cannot be inserted, make sure you have started
the recording (paragraph 10.1.2).
18. Check the DAQ value view or Template DAQ state during the
measurement to keep a good measurement quality (paragraph 8.7)
19. Insert events during the measurement if needed(paragraph 10.1)
20. End the data acquisition (paragraph 8.4)
21. Analyze the data (chapter 10)

During the measurement:

- Watch the device status in the DAQ value view (Paragraph 8.7)
- Watch the light level in the DAQ status view (Paragraph 8.8)
- Change the settings if a DAQ value field is red (paragraph 8.7)

8.1.2.1 Problems
If no changes are visible during the DAQ in the traces, the traces are flat,
zero or gone, there can be several reasons behind this observation. If
analyzing data make sure that there is:
- attached a data file with data (check the file information (paragraph
9.2.3))
- the ‘measure’- lamp at the Oxymon is turned on (paragraph 6.1). If not,
restart Oxysoft, connect to the Oxymon and start the measurement

62
 NOT by pressing the recording button, but the green start button or via
the data collection measurement wizard.
- filled in the correct inter-optode distance and DPF (paragraph 9.2.4)
- the correct light source-to-optode assignment (paragraph 9.2.4)
- a correct graph scale and zoom or set to auto scale (paragraph 9.4 and
9.3.17)
- done ‘bias all traces in measurement’ to get better offsets (paragraph
9.4.6)
- non-filtered traces (paragraph 10.5)

If this is observed during a measurement, please make sure that:

- The experimental setup is all correct, and all transmitting and receiving
fibers and optodes are well attached
- Enough light is received by checking Menu  View  DAQ value view and
look at all the signals of interest. If the received signal is too low, higher
the power level or higher the gain of the receiver if possible (paragraph
8.7)
- Try a one-channel measurement. Notice the trace properties. It shows
different tabs, one of them being channel A. Make sure to click on the
white circle between Tx1 and Rx1, this selects the channel
- If data is visible, but not as expected, take a few steps back and check
the experimental setup. Please never underestimate the simplest one-
channel measurement for piloting (trial and error!)

Using devices FROM OTHER suppliers:

Warning: never mix up the data files of the two systems!
They can have the same extensions as the data files of the Oxymon!

The optical fibers have to be connected to the Oxymon to perform a

measurement. The fibers with the blue stickers on the endings are the
receiver fibers, fibers with yellow stickers are transmitter or laser fibers.
Plug the connectors of the receiver fibers in the receiver holes. Put the
connectors of the transmitter fibers in the transmitter holes and fasten the
screws of the connectors (Figure 8-1) to connect the transmitter fibers. The
two connectors of a fiber are equal.

In Figure 8-2 it is illustrated how the fibers should be connected if only two
wavelengths are available in the device. Connect the first fiber to both
lasers of Tx1; connect the second fiber to both lasers of Tx2, etc. Usually,
an Oxymon has two wavelengths about 850 nm and 760 nm. The lasers of
850 nm are the upper lasers; the lasers of 760 nm are the lower lasers.
Two lasers with each a different wavelength form a transmitter and have to
be combined into one fiber. If the Oxymon has three or four wavelengths,
the lasers will be arranged in a different way. In this case, the three or four
lasers with each a different wavelength forms a transmitter and will be
connected to one fiber. Two lasers above each other form a transmitter

63
block, which is equal to a transmitter if just two wavelengths are available in
the Oxymon. Both lasers concerning to one transmitter block have to be
connected to an optical fiber before the lasers can be enabled.

Figure 8-1. Connector of the transmitter optical fiber

Figure 8-2. How to connect the fibers to the Oxymon. Connect both connectors of a fiber to one
transmitter block!

It is also possible to connect the fibers in other ways, but only do this if you
have more than two wavelengths (see below) or if you are sure that it is
right. Please contact Artinis before you do this! If you have connected the
fibers in the wrong way during a measurement, the data of the
measurement might be useless. Always check (and change) the lasers to
optode mapping in the measurement properties if you are using another
way of fiber connecting.

If three different wavelengths are used for one transmitter, an optical fiber
with three connectors and an empty connector (a connector without the
fiber) has to be used. This empty connector is necessary because the
transmitter blocks only emit light if both lasers are connected. The first two
wavelengths at the first transmitter block (Tx1) are enabled by making the
connection to the three-ending fiber. The third laser at the second
transmitter block (Tx2) is not enabled by connecting the three-ending fiber,
because the fourth laser is not connected to a fiber. To enable the third
laser, connect the empty connector to the fourth laser and fasten the
screw. If four different wavelengths are used for one transmitter, use an
optical fiber with four connectors and connect those to the lasers.

If three or four wavelengths are available, also only two wavelengths can be
used for a measurement. If both desired wavelengths are at one

64
 transmitter block, connect these lasers to an optical fiber with two
connectors. If the desired wavelengths are at two different transmitter
blocks, connect the desired lasers to the optical fiber with two connectors
and connect the other lasers to empty screws.

Take care: optical fibers can break easily

- Do not over bend the fibers.
- Do not pull the fibers.
- Place nothing on the fibers.
- Fixate the optical fibers during the measurement to the subject and the
environment (table, bike, ceil) to reduce artifacts and to protect the
optical fibers.

Screw Optode
(holes) holes

Fixation
frames

Figure 8-3. One Channel optode holder. The optodes stick out a bit at the lower side of the holder

For different optode configurations different optode holders are available.

With the Oxymon delivery, also one or more optode holders are delivered
depending on what kind of system is ordered. The simplest optode holder
is a 1-channel optode holder, see Figure 8-3. Each optode holder has
optode holes to put in the optodes, screw holes with screws to fixate the
optodes in the optode holes and fixation frames to fixate the optode
holder to the subject.

The fixation of the optode holder can be done just before starting the data
acquisition. Prepare the optode holder in the following way:
1. In case of hair on the skin:
2. A little hair will not influence your measurement.
3. Shave the skin if the fixation with tape is a problem or use the straps.
4. Dark and much hair between the skin and the optode can diminish the
measurement quality. Part the hair if necessary and place the optodes
at the parting.

65
5. Determine which optode holder is necessary for the optode
configuration (or optode holders)
6. Clean the optodes, the holder and the skin with alcohol
7. Determine the optode distance between the receiver and transmitter
optodes and choose applicable holes for the optodes
8. Stick the double-sided electrode stickers around the chosen holes at
lower side of the holder and place it at the region of interest (Figure 8-4
left). We advise to use extra (medical) tape for better skin contact
(Figure 8-4 right).
9. Put the optodes in the chosen holes of the holder. Notice the distance
between the optodes. To get a good skin contact when applying the
holder to the skin, it is better that the optodes stick out a little bit from
the holder at the lower side. Light leaking between the optode and the
skin will cause undesired reflections and light lose. If the optodes stick
out too far, it will hurt the subject.
10. Fasten the screws (in the screw holes) in the optode holder with a small
screwdriver until the optodes are fixated.

Figure 8-4. Apply optode holder to the skin using e.g. double sided sticky discs. Apply extra
medical tape for better skin contact

11. The holder (and optodes) should not move during the measurement.
However, a too tight fixation of the holder can hurt the subject or
obstruct the blood flow. Especially during exercise, caution has to be
taken that no friction on optode-skin contact arises because of
movements of the fibers. Avoid movement of the measurement volume
by accurate support of optical fibers. The optical fibers can be fixated
to the environment (like a table, chair or bike) with tape and to the
clothing of the subject with the supplied clip to prevent for movement
artifacts. Weight of the fibers on the holder itself can be reduced by
making a strain release with extra tape (Figure 8-5)

66
Caution should be taken with the placement of optical fibers and body
parts under investigation, in order to obtain sound results. Take care that
circulation is not impaired due to incorrect positioning of the subject. For
instance, in case of lower arm or lower leg, avoid contact of the
measurement site with the ground to prevent circulatory obstructions
other than those which are controlled (e.g. occlusion). Avoid venous pooling
of the blood in the limb, possibly by placing the limb at heart level and in an
o
upward angle of ±30 .

More general: take care that the subject is comfortable in his/her position
and able to relax, as unwanted muscle tonus must be avoided as much as
possible.

Covering of the optode holder from environmental light may improve the
measurement quality (especially when measuring TSI).

Figure 8-5. Apply a strain release (in top) to reduce effect of movement of the fibers on the
holder.

The lasers are firing by clicking on the green start button in the toolbar or
by Menu  Data Collection  start device. Data is recorded automatically or
by clicking on or by Menu  Data Collection  start recording. If the
lasers are firing, the measure lamp at the Oxymon will blink red. The data

67
acquisition ends by clicking on or by Menu  Data Collection  stop
device.

If “Data Collection measurement wizard” is used to create the

measurement, the program can enable the lasers after finishing the wizard
automatically. For security purposes, the message shown in Figure 8-6
comes up before the lasers are enabled. Press “Yes” to start the device,
press “No” to not start the device.

Figure 8-6. Security warning before the lasers start to fire

Watch the device status of all devices during the measurement (open by
Menu  View  DAQ status view, Figure 7.7). If an error or warning occurs,
try to find out what causes this error or warning. If the cause is unclear,
contact Artinis Medical Systems and do not continue the measurements. The
warning “TX 2/3/4 Fiber not connected” is a normal warning and means that
no optical fiber is connected to this transmitter block.

The clock as shown in Figure 8-7 displays the duration of the recording
(00:50, min:sec). The file size is the size of the saved *.oxy3 file. “00:23 since
A” means that 4 seconds are expired since the last event, which was event
“A”.

Figure 8-7. Data Collection status view

68
The Template DAQ State shows the used optode template belonging to the
devices and warns with red marks if one of the optode combinations
receives too less (See Rx1 - Tx4 and Rx2 – Tx4 in Figure 8-8).

Figure 8-8. Template DAQ state showing the used optode template with optode combinations
out of range (Rx1 - Tx4 and Rx2 - Tx4)

Monitor the DAQ value view (open by Menu  View  DAQ value view,
Figure 8-9) during the measurement to control the percentage of received
light. The value view describes:
- the percentage of received light per optode combination
- the wavelength of each laser
- the used laser output level (dimmed or standard)
- the used receiver gains (low or high)
The DAQ value view shows all possible optode combinations, independent
from the chosen optode template and belonging optode combinations.

The first row shows the corresponding device. For one stack of Oxymons
the device numbers are shown in the order of master, slave 1, slave 2 and
slave 3.

The second row shows the wavelengths of the Oxymon per laser. The
wavelengths can be a little bit different from the ordered wavelengths. In
case a stack of Oxymons are used, the lasers of the slaves are numbered
successive to the master lasers.

69
Figure 8-9. Data Collection value view. All laser outputs are set to standard. Receiver 1 is used
with high gain, receiver 2 with low gain. The light of L1 to L4 is not received by R2, the value view
warns with red fields. If light is not received, but is also not included in the measurement
template, the will not turn red (L5 to L8 for R2). Switch between gains (“low” and “high”) by clicking
on the gain field per receiver-laser combination above the DAQ value or for all lasers for one
receiver by clicking on the ‘select’. The laser output power (“off”, “dimmed” and “standard” can be
changed in the same way by clicking on the power field.

The third row shows the power level of the lasers, which are all set to
“standard” in Figure 8-9. Switch the power level of a laser to “off” or
“dimmed” (for less laser power if “standard” saturates the receiver) by
clicking on the belonging power field in the DAQ value view.

The fourth row shows the gain of receiver 1 (R1) for each laser, which are all
“high” in Figure 8-9. Switch the gain of a receiver to “low” by clicking on the
belonging gain field in the DAQ value view. The sixth row shows the gain of
receiver 2 (R2) for each laser, which are “low”. In case a stack of Oxymons is
used, the receivers of the slaves are numbered successive to the master
receivers (R3, R4, etc.).

The fifth row shows the percentage of received light in percentages for the
optode combinations belonging to receiver 1. The percentage of received
light is displayed in percentage (“Perc”) or in AD counts (“Raw”); switching
between those can be done by clicking in the left field of the first line of the
DAQ value view (in Figure 8-9 “Perc”). The percentage is between 0-100%
and the counts between 0 and 65535, where 65535 counts equals to
100%. If a DAQ value field is red-colored, the percentage of light is out of
range, it is too low or too high to get a high quality measurement. Set the
limits for out of range in the program options the limits for out of range
(paragraph 7.6).

If the percentage is close to 100%, the receiver probably measures

environmental light. During a normal measurement, the percentages will be
lower. Check the fixation of the optode holder and fibers. Cover the optode
holder from environmental light. To check how much environmental light is
received, set all powers to “off”. The percentages will show only the received
environmental light, because the light sources are powered off.

If the percentage is higher than 75% the DAQ value field becomes red.
When the percentages get higher than this value the measurement is
unreliable due to non-linearity.

If the percentage is close to 0%, the tissue absorbs (almost) all light. Try to
remove dark hair. Most probable the light of one transmitter is completely

70
 absorbed. Check if you can see the heart beat in the signals or something
else you are expecting, see paragraph 8.7 for more information.

The seventh row shows the percentage of received light in percentages for
the optode combinations of receiver 2.

The settings during data acquisition are important for the quality of the
measurement. An important factor for the quality is the percentage of
received light. If a field in the DAQ value view is red, the measured signal is
out of range. Change the settings to improve the signal and the
measurement quality as described in the next paragraphs. The device
settings are the sample rate, the light source power level and the receiver
gain. The sample rate cannot be changed during the measurement. The
right settings are dependent to the individual subject, measurement and
need. Therefore, these have to be set for each measurement. It is handy to
insert an event after adjustment of the settings. However, we advise to
choose the settings before the start of the experiment to have a good
quality during the whole experiment!

The laser output level is set to "off" or on to "dimmed" or to “standard”

during creation of the measurement. The chosen level is displayed in the
DAQ value view (Figure 8-9). The power level can be changed per laser
during the data acquisition, but we recommend setting the powers before
the actual measurement. The level can be changed by clicking in the DAQ
value view on the power, which has to be changed, and selection of the
desired laser output level or by Menu  Data Collection  Laser power and
selection of the desired laser output level.

The gain defines the degree of amplification of the received signal and can
be “low” and “high”. Older systems have also a “medium” gain setting. The
gain of the system can be changed per optode combination.

8.8.2.1 Auto gain

If Oxysoft is set to auto gain, the program will choose the best gain for each
optode combination. We recommend this option not to use during the data
acquisition, but to use it just for help to set the gain. Despite of calibration,
during the gain adjustment the signal can show a “spike”.

8.8.2.2 Which gain should I use?

To decide which gain is the best for a measurement, check the percentage
of received light in the DAQ value view (see Figure 8-9).

71
The effect of using a low or high gain is shown by an example. Using the
low gain, the percentage of received light is 4% (Figure 8-10), which is about
2600 counts. This is a good value for measuring; the values should be
between 150 and 50000 counts. If the counts are too low, the DAQ value
view will warn you by a red field. The counts can be increased by using high
gain. This results in an increase of the percentage (to 34% and 35%), as
illustrated in Figure 8-11. This figure shows the same measurement as
Figure 8-10.

However, the concentrations measured with low and high gain are equal!
The system compensates for the gains by using the calibration information.
The adjustment to the high gain takes some time, which gives the short
spike at 24 sec in Figure 8-11. Because of this spike and the “never-perfect”
calibration, we advise to set the gain before the start of the measurement
and not changing it during the measurement. For the same reason, we
advise to use the auto-gain function only before the measurement to see
what the best gain is for the measurement.

Care should be taken when using the highest gain setting: if environmental
light comes onto the optical probes or detector, this may increase the
detected intensity value. This will only be problem if the signal measured is
very weak, for example when a large source-detector distance is used in
brain measurements. It might help to reduce the ambient light in the
measurement area, and to shield the fiber of the transmitter.

Figure 8-10. Example of using low gain at a 1 channel measurement (Rx1- Tx1). Receiver 1
receives 4% of the transmitted light of laser 1 and laser 2. Laser 3 and 4 are not used.

72
 Figure 8-11. High Gain, same measurement as Figure 8-10. The gain is switched from low to high
around 24 seconds, which is visible by a short peak. This short peak is because of the adjustment
to the high gain takes some time. Receiver 1 receives 34% and 35% of the light of respectively
laser 1 and laser 2.

Another phenomenon may occur when there is too much light on the
detector from the lasers at the highest gain. Saturation in this gain setting
may cause compression of the detected signal, resulting in a lower value
than could be expected. If suspicious, lower the gain to see what happens.
If nothing changes in whatever channel it is best to restart the Oxymon and
the Oxysoft.

8.8.2.3 Change gain

The gain can be changed by clicking in the DAQ value view on the gain field,
which has to be changed, and selection of the desired gain (Figure 8-9) and
by Menu  Data Collection  Rx Gain and selection of the desired gain. All
gains can be set at once by Menu  Data Collection  All Rx gain and
selection of the desired gain.

During the gain switch it is possible to get a spike in the signals, therefore it
is recommend to switch not gains during the (important parts of the)
measurement.

Watch during the whole measurement the DAQ value view (paragraph 8.7)
to see if the percentage of received light is not out of range. If the
percentage of received light is too low or too high, try the following:
- Check the power level of the laser. The power for every laser has to be
set to off (no output), dimmed (low output) or standard (high output).

73
 - Check the gain. The gain of the receiver can be set at low gain and high
gain (older systems have also the option medium gain). High gain
amplifies the received light more than low (or medium) gain.
- Check the fixation of the fibers to the skin. Are all fibers connected in
the right way? Is the optode holder still fixated? Are the optodes or is
the skin polluted? Is there hair between the optodes and the skin?
- Are all fibers still in the machine?
- Diminish or increase the source-detector distance in the optode
holder. A smaller distance will increase the percentage of received light.
- Dark skin and hair color can diminish the percentage of light received.

8.8.3.1 Beep when out of range

When the system is out of range, a beep can be given by the computer. To
play a beep when the system is out of range, check Menu  Data Collection
 Beep when out of range. The default of playing a beep or not when out of
range can be changed by the program settings (paragraph 7.6).

A system calibration is necessary to compensate for the different powers

and gains of the Oxymon in Oxysoft. The Oxymon is already calibrated
when it is delivered and has to be calibrated once a year. The calibration
file is saved in C:\Users\Public\Documents\Artinis Medical Systems
BV\common\device as *.xml file. A new calibration will not overwrite the old
file, but the new calibration information is added to it. Oxysoft will always
take the newest calibration information. A new calibration is needed if the
stack (combination of Oxymons) has changed in order (switching slaves or
the master and a slave).

The date of the last calibration is in the calibration file. Go to the Oxysoft
installation directory, Folder “Device” and open the calibration file. Open it
with internet explorer; the calibration date is marked as “timestamp”.

If a single Oxymon is used, just follow the instructions below to calibrate

the Oxymon. If multiple Oxymons are used, first connect the Oxymons as
described in paragraph 6.2 and follow the instructions below. The
calibration file will be saved as a calibration file for the master Oxymon. For
single use of the Oxymons, it is necessary to calibrate the systems one by
one! Take care that the calibration of the master Oxymon is done for single
OR master-slave use.

When using an AD Box in combination with the Oxymon, connect the

Oxymon to the computer without the AD Box and perform the calibration.
Subsequently, make the setup with the AD Box and the Oxymon.

The calibration procedure has to be accomplished as described below:

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- Connect an optical fiber to receiver 1 and connect a fiber to laser 1.
(Laser 1 only transmits light if laser 2 also is connected to an optical
fiber.)
- Take the calibration tool (Figure 8-12). The receiver and a transmitter
optical fiber can be plugged in the two openings at the endings of the
tool. Use the small screws to fasten the optical fibers in the calibration
tool.
- Connect the Oxymon by USB to the PC and start the Oxymon.
- Start Oxysoft. Go to Menu  Data Collection  Calibration. Follow the
procedure of the calibration as described in the window. The large
screws of the calibration tools can change the percentage of received
light.
- Save the results when the calibration is ready! The calibration file is
saved in the Oxysoft directory in the folder “device” as *.xml file.

Small screw

Large screw

Figure 8-12. Calibration tool

13

75
This chapter describes how to manage your data in Oxysoft: How to make a
new measurement and how to display, save and export the measured data.
There are examples available in the folder “Data Examples” in the installation
folder.

In Oxysoft, the measurements are ordered in projects. Each project is a

certain set of measurements belonging to for instance one study. A
measurement contains the data and graphs. The measured raw data is
saved in *.oxy3 files (or *.oxy and *.evt for older versions) in optical
densities. The (transformed) data is displayed in the graphs by traces. The
data saved in the *.oxy3 files is the raw data (in Optical Densities or OD).
This means that after completion of the measurement, all measurement
properties can be adjusted (optode template, source detector distance,
optode mapping, etc.). The relative concentrations will be recalculated after
changing a property. The properties cannot be adjusted during a
measurement. Only the device settings cannot be changed afterwards
(sample frequency, light source power and gains). The unit of the relative
concentrations is µM (micro Molar or micromole / liter tissue) and the unit
of the TSI is percentage (%).

A project is a set of measurements belonging to each other. In the project

file all information is saved about the measurements, graphs, traces and
the measurement settings. The recorded data is not saved in the project
file, but in the *.oxy3 file.

Open a new project by Menu  File  New project file. The project view will
refresh and show the new project. The name of the project is automatically
set to “New Project”. It can be changed by saving the project under another
name. The first time that Oxysoft is used, a new project without any
measurements is shown in the project view.

Open an existing project by Menu  File  Open project file. Project files
have the extension *.oxyproj. Measurements can be added and changed.
Use Menu  File to quickly select the last used projects.
 Figure 9-1. Project properties

Save a project by Menu  File  Save Project file as or Menu  File  Save
Project File. The latter will overwrite the last saved version of the current
project. If the project is not saved before closing Oxysoft, the project
settings will be lost. In that case, the measured data is not lost, because it is
always saved in the *.oxy3 files.

Show the properties of the project (Figure 9-1) by Menu  File  Project
Properties or by right mouse clicking on the project in the project view and
selection of “Project properties” or by double clicking at the project in the
project view, or by selection of the project in the project view and clicking
on the toolbar button . The project properties define the used
coefficients: extinction coefficient table, the DPF table and the project
settings.

9.1.4.1 Coefficients
The extinction coefficient table of this project can be selected by clicking on
“Browse”. The extinction coefficient tables are saved in a *.xml format in the
Oxysoft installation directory in the folder “Tables”. You can also add your
own table. The default table is from Cope [Cope 1991]. The default used
tables can be selected in the program options (paragraph 7.6).

The DPF (differential pathlength factor) table can be used to correct the
DPF for its wavelength dependency. The table can be selected by clicking
on “Browse”. The DPF tables are saved as “DPF_*.xml” file in the Oxysoft
directory in the folder “Tables”. The default table is “no correction”, which
we recommend for most applications.

9.1.4.2 Project settings

Project settings have the option to select the use of relative file paths.
Using relative data file paths, data files are saved with a relative path to the
project, which is handy for instance for making a data CD/USB or when
moving to another computer for analysis. With this setting it is possible to
copy all files without problems with incorrect links to the *.oxy3 files.

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 Close a project by Menu  File  Close Project File

In Oxysoft, the measurements are ordered in projects. Each project can

contain a certain set of measurements belonging to for instance one study.
There are several ways to make a new measurement:

- The easiest way: go to the Menu  Measurement  Create measurement

and start DAQ measurement (wizard) (paragraph 9.2.2).
- Open an existing data file (*.oxy3 file), use Menu  Measurement 
Create offline measurement (paragraph 9.2.3).
- Copy settings from an existing measurement: Menu  Measurement 
Duplicate measurement (paragraph 9.2.6), or choose in the DAQ
measurement wizard to copy settings from another measurement
(paragraph 9.2.2).
- Existing measurements can be reused for data acquisition: Menu 
Measurement  Properties, check “Open for data acquisition”. Data
cannot be overwritten.

Open the wizard by Menu  Measurement  Create measurement and start

DAQ measurement (wizard), or clicking or to do an online
measurement (Figure 9-2). All measurement settings can be changed after
the measurement, because the raw data is always saved in the *.oxy3 file.
The best is to use the correct settings while recording, so you are sure the
displayed data is right during the recording. The settings are saved in the
*.oxy3 file as well. Always check all available parameters in the DAQ
measurement wizard to be correct for the specific measurement!

If the ‘DAQ measurement wizard’ is not available, check the following:

- A measurement is already opened for data acquisition. Open this
measurement and disable “Open for data acquisition”.
- The drivers are not working correctly and need to be (re-) installed.
These drivers are needed for the computer to be able to communicate
with the Oxymon.

9.2.2.1 Create a measurement

The settings in this tab (Figure 9-2) affect the name of measurement, the
location of the data file and secondary data. Be sure that the Oxymon is
connected to the computer and it is turned on by the main switch of the
Oxymon.

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Figure 9-2. Create new measurement

Name
This specifies the name of the measurement. This name is for own
reference and will be shown in the project view.

Data file
This specifies the data file and the saving location. The file (*.oxy3 or the
older *.oxy/*.evt combination) is the primary source of data for all graphs
and calculations accomplished in this measurement. A standard name is
given as the copy of the measurement name. The field itself is not editable,
but can be changed by pressing the browse button that opens the file
browse dialog. Click on browse, search a location to save and type a name
for your file. Older files cannot be overwritten.

We strongly advise to save the data to the local computer. Oxysoft does not
warn for lost data if the data is lost during transmission over a network to
save the data at another computer.

Copy settings from

This copies the settings (e.g. graphs and template settings) from an earlier
accomplished measurement or from a template. Click on the field to select
a measurement.

Description
The description field is a free text field reserved for your own comments.

Quick start
This will skip the next screens if you are sure that no other settings needs
to be adjusted, compared with the copied settings. After selecting the
device (Figure 9-3) the device will be ready to start the measurement.

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 Next, Oxysoft will try to make a connection to the device(s) (Figure 9-3).
Enable the system you want to use. If only one system is present, it will
automatically connect. It is possible to connect multiple systems (also
Oxymon and portable systems) up to a maximum of 8 receivers or 7
portable systems. Right mouse click will give the question to deselect all.
“Save Selection” will save the selected devices for a following connection.
New devices can be added in the file in C:\Users\Public\Documents\Artinis
Medical Systems BV\common\PortaSoft.ini by copying another (similar)
system and change the number and Bluetooth address of the wireless
devices.

Figure 9-3. Connect to a device screen. Enable the system you want to use. If only one system is
present, it will automatically connect.

9.2.2.2 Optode Template

This screen specifies the optode template to be used (Figure 9-4) per
device. Set the template per system. One stack of Oxymons all connected
via one USB cable is considered as one system. These settings are essential
to create the correct graphs and to calculate the concentrations from
optical densities. For more information about optode templates see
chapter 11. The optode template picture at the right side of the window will
adjust to the chosen settings.

Optode template
This specifies the predefined optode template to use for this
measurement. The choices of templates may be simplified by filtering the
list. If the desired template cannot be found, make sure that the category is
not already filtered out. The selected optode template is shown in the
figure on the right.

Filter
When clicked, a dialog pops up that allows filtering the list of optode
templates by category: single channel, multichannel, TSI, PortaMon and
PortaLite.

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Subtemplate
The subtemplate data grid is designed to define parameters for calculating
concentrations per subtemplate. A template may consist of several
independent subtemplates. Each subtemplate is parameterized
individually. The following parameters can be set:
- DPF: Differential pathlength factor. Choose DPF according to literature.
DPF can be changed before and after the data has been recorded and
it will influence the graphical data representation of the concentration
changes. Some reference values can be found in Table 4.2.
- d (mm): source-detector distance or nominal distance of the template
grid. Change d by clicking on the “35” and choosing another value or
typing in that field. Measure the distance at the optode holder. The
value for source-detector distance can be changed before and after the
measurement.

Calculate DPF from Age (Brain)

This activates a dialog for calculating the DPF from age (Figure 9-5). The DPF
is calculated as

𝐷𝑃𝐹 = 4.99 + 0.067 ∗ 𝐴𝑔𝑒 0.814

Figure 9-4. Optode template

Figure 9-5. Calculate DPF from age

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 This formula is valid for measurements on BRAIN tissue for 17-50 year old
human subjects, derived from the data of Duncan et al. [1996]. Fill in the
age, click on “Copy to Clipboard” and “Return”. The window will close. Paste
the DPF in the DPF field by right mouse clicking in the field and “Paste”.

Restore
This function will restore the measurement and optode template settings
to the settings used during recording.

Use H2O correction

This option only is applicable for TSI measurements. This will give you the
option to fill in the percentage of water in the tissue. Set to zero, or disable
to compare your data with older measurements or measurements done
with other systems without this correction.
For example if assumed that 70% of the tissue consists of water, this
corresponds to 38.9 M H2O. Absorption is now defined as:

𝜇𝑎 (𝑙)/ ln 10 = 𝜀𝐻𝑏𝑂2 (𝑙)𝑐𝐻𝑏𝑂2 + 𝜀𝐻𝐻𝑏 (𝑙)𝑐𝐻𝐻𝑏 + 𝜀𝐻2𝑂 (𝑙)𝑐𝐻2𝑂

With 𝜇𝑎 , the total absorption coefficient. Next to absorption by HbO2 and

HHb, also H2O is included. The concentration is known by the filled in
concentration and the extinction coefficients can be found in the extinction
table (together with the HbO2 and HHb extinction coefficients).

After filling in all fields, for all devices, click on “Next”.

9.2.2.3 Light source to optode mapping

In this tab, light sources can be assigned to optodes (Figure 9-6) for each
device. This mapping is performed automatically, but may be overruled
here. The view shows all transmitting optodes used by the selected optode
template for each device. Per optode, zero, one or more light source can
be assigned to it. The assigned light source (Lx) are depicted as leaves on
the optode. The mapping can be changed by drag and drop the laser
leaves. When not assigned to an optode, a laser is assigned to the 'Ø' node.
Using standard configurations (see paragraph 8.2), you should not change
this mapping!

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 Figure 9-6. Laser to optode mapping

Figure 9-7. Device settings

Laser 1 and 2 are in transmitter block 1 (Tx1 at the Oxymon), laser 3 and 4
are in transmitter block 2 (Tx2 at the Oxymon), laser 5 and 6 in transmitter
block 3, laser 7 and 8 in transmitter block 4, laser 9 and laser 10 in
transmitter block 1 of the second Oxymon (Tx1 at the second Oxymon), etc.

If you have to change the mapping, make sure you have connected the
optical fibers in the same way as you configure this mapping (see
paragraph 8.2)!
After choosing the right optode mapping, click on “Next”.

9.2.2.4 Device settings

This tab defines the sample rate and laser output level settings (Figure 9-7).

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Sample rate
This specifies the available sample rates of the system. The system can
measure at, 1, 2, 5, 10, 25 and 50, which is called the sample rate or
frequency. If the system is designed for 250 Hz, it is possible to measure at
125 and 250 Hz as well.

Power
This specifies all the laser output level of system. A laser can be turned
"off", "standard" or "dimmed” which is using about half of the laser power.
Please be aware that split fibers can only emit one output power, so do not
use different powers one different subtemplates with the same split
transmitters.

For a measurement with TSI, it is strongly recommended to use the same

power levels on ALL lasers. If dimmed levels are going to be used, select all
dimmed power levels BEFORE performing the absolute calibration! The
same goes for “standard”, if standard power levels are going to be used. If
possible, use standard power for TSI measurements to receive as much
light as possible.

Figure 9-8. Further options

Subtemplate
The laser output levels are selected for all lasers arranged according to the
subtemplates.

Optode
The power levels are selected for all lasers arranged according to the
optodes.

Laser
The power levels are selected according to a single laser.

After choosing the device settings, click on “Next” to get further options
(Figure 9-8). If the measurement has to start after finishing the wizard,
select “Start measurement after finishing wizard”. If the measurement has
to start later, select “Do not … for data-acquisition”. Finish the wizard by
clicking on “Finish”.

Next, Figure 9-9 will come up to help you to create some graphs
automatically. It will create graphs for all measurement channels with the

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selected traces. For more information about graphs and traces, see
paragraph 9.3 and 9.4. After finishing the wizard, the new created
measurement (and graphs) is available in the project view.

Figure 9-9. Create all graphs

The function Menu  Measurement  Create offline measurement creates a

measurement folder. First you are given the option (Figure 9-10) to choose
a predefined measurement setting (paragraph 7.6). Second window is the
“measurement properties”. This can be used to visualize the data from an
already obtained *.oxy3 file but also a connection can be made to create a
new file. All tabs are equal to the wizard, but they do need to be used in the
same order as with the wizard. An additional tab “Device settings” is only
available if there is a connection to a device. This can be done by clicking on
the button (Figure 9-11):

Figure 9-10. The option to use predefined settings

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Figure 9-11. Create a measurement

To open an existing *.oxy3, click on the “browse” button to open (Browse

will ‘save’ data if there is a connection to a device).

If you have very old or downloaded (from portable Artinis systems) *.oxy
files Click on drop down menu to switch between *.oxy3 and *.oxy, select
the file and click on “Open”. Press “Apply” to transform the data of an *.oxy
file to *.oxy3 file and to see the data file info as described below. Click on
“OK” to close the window and make graphs to display the data. The *.oxy3
file made by transformation of an *.oxy file will be named like the *.oxy file.
Opening an *.oxy file with the same name as an existing *.oxy3 file (in the
same folder) will open the already existing *.oxy3 file instead of the *.oxy
file. To open the *.oxy file, rename the *.oxy file (and the *.evt file) or the
existing *.oxy3 file or move it to another folder.

Figure 9-12. Data file info – what about AD Channel names?

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9.2.3.1 Data file info
This is a read only field with information about the data recording stored in
the data file (*.oxy3). The available information is the used version of
Oxysoft, name of the data file, recording date, system information,
measurement settings and the used wavelengths (Figure 9-12). Clicking on
“Apply” will refresh the information.

Show the measurement properties (Figure 9-11) by Menu  Measurement

 Properties, by right mouse clicking on the measurement in the project
view and selection of “Measurement properties”, by double clicking on the
measurement in the project view or by selection of the measurement in the
project view and clicking on the toolbar button . The measurement
properties have the same tabs as the function “Create measurement”. All
parameters are explained in paragraph 9.2.4.

Rename a measurement by Menu  Measurement  Rename measurement

or by right-mouse clicking in the project view on the measurement and
selection of “Rename measurement” or change the name field in the
measurement properties.

Duplicate a measurement by Menu  Measurement  Duplicate

measurement or by right-mouse clicking in the project view on the
measurement and selection of “Duplicate measurement”. Measurement
duplication can be useful to copy all settings from the measurement to a
new measurement. Warning: The duplicate is linked to the same *.oxy3 file
as the original measurement!

To remove a measurement, select the measurement in the project view; go

to Menu  Measurement  Remove measurement or by right-mouse clicking
in the project view on the measurement and selection of “Remove
measurement”. The measurement is removed from the current project, but
the *.oxy3 file is still available for later analysis.

Oxysoft features a 3D plugin for neuroscientific research, which enables

advanced graph viewmodes (see paragraph 9.3.4). There are two
possibilities to specify positions of the optodes for these view modes. You

87
 can either use a Polhemus digitizer, or you can manually determine the
optode positions using a 2D topographic plot.

9.2.8.1 Digitizing optode positions using a Polhemus digitizer

A Polhemus digitizer is a 3D digitizer allowing to measure points in a 3D-

Space relative to a predefined source location. Polhemus devices can be
acquired through Artinis Medical Systems.

After having installed the Polhemus digitizer according to the Polhemus

instructions (see X), you can proceed to using the built-in digitizing and
coregistration feature of the Polhemus digitizer by clicking on
“Measurement”->“Digitize optode positions” and then selecting “Polhemus
digitizer”. As described in paragraph 9.3.4, the digitized positions will be
used to coregister the participants head with the well-known MNI ICBM 152
brain template of the Montreal Neurological Institute 1. After having done
so, the positions of the individual subtemplates for the different 3D
viewmodes are directly taken over from the digitized and coregistered
positions.

Figure 9.9-13 Built-in 3D digitization and coregistration procedure.

After having established a connection with the Polhemus digitizer, a 3D

glasshead representation will be shown to the left, alongside with
instructions to the right (see Figure 9.9-13). The goal of the initial
digitization is to determine the rough size and shape of the participant’s
head. For this, five well-defined anatomical landmarks, so called fiducials,
must be digitized. The anatomical landmarks are called nasion, inion, left
and right pre-auricular points and the vertex. See Figure 9.9-14 for a
description and visual representation of these fiducial points.

1
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

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Figure 9.9-14 The five anatomical landmarks (fiducial points) on the human head used in Oxysoft
for digitization and coregistration. The nasion is defined as the valley on the nasal bone. The
inion can be located by searching for the occipital skull bone at the back of the head and using
the lower bulging of this bone. The left and right preauricular points are located just above the
upper end of the tragus of the ears. The vertex is located right exactly in the center of the
circumferential line between nasion and inion and in the center of the circumferential line of the
two preauricular points.

After successful digitization of the fiducial points, the coregistration

procedure can begin. For this, the digitized coordinates of the optodes of
the selected optodetemplate is required. To the right of the 3D view, the to-
be-digitized optode will be highlighted in green. After digitizing an optode,
the coordinate will immediately be coregistered to the brain atlas and is
visualized in the 3D view. See Figure 9.9-15 for an example. During the co-
registration, a second sensor can be attached to a headband, which the
participant is wearing. This will make account for small head movements of
the participant.

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Figure 9.9-15 Digitization and coregistration procedure of the an OctaMon optode template. Rx1
has already been digitized and the view automatically rotated to the digitized position. Next, Rx2
has to be digitized, as it is the highlighted optode in green on the right in the optodetemplate.

After having digitized all optodes of the optodetemplate, all 3D topo views
of that measurement will use these digitized and co-registered optode
positions. If such digitized 3D positions are available, an inverse
transformation and projection will be performed to calculate the 2D
positions in the 2D topo view (for more information on different view
modes, see paragraph 9.3.4). This is done by coregistering the 3D fiducial
points to the fiducial positions of the standard 10-20 system2. Note that
due to the use of an anatomical template model, the shown locations of
activation do not allow for any conclusive statements about the true
location of brain activity during the measurement.

Some advise for troubleshooting:

 The Polhemus digitizer work by creating a weak electromagnetic
field. Please do not use in patients with a pacemaker or deep brain
electrodes, or similar apparatus sensitive to electromagnetic fields.
 Make sure that the source of the Polhemus device is relatively
close, but stays under the to-be-digitized positions. The source has
to stand straight up!
 The digitization has to take place in a room with as few metallic
objects as possible, as metal can distort the electromagnetic field.
 Under no circumstances move the source during the digitization
process, as this will distort the measurements!
 If the fiducial digitizing fails, please check above points and maybe
relocate the sensor. A quick test whether the setup can work
successfully can be done using the Polhemus program “PiMgr”.
Start the program, connect to the Polhemus digitizer and put on
the continuous mode (by clicking on the green arrow). Put the
stylus directly on top of the source and rotate it around. If the first

2
Jasper, HH (1958). "Report of the committee on methods of clinical examination in
electroencephalography: 1957”. Electroencephalography and Clinical Neurophysiology 10
(2): 370–375. doi:10.1016/0013-4694(58)90053-1

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 three coordinates that the program shows change significantly, the
current setup is not working well, and the position of the source
has be changed.

9.2.8.2 Digitizing optode positions manually

As an alternative to using a Polhemus, for example if the device is currently

not available, optode positions can be manually digitized. This is done by
clicking on “Measurement”->“Digitize optode positions” and then selecting
“Manual digitization”. A view will open, showing a 2D topo view to the left
and a 3D scalp view to the right. The optodes in the 2D view can be
translated or rotated, and the changed position is taken over to the 3D
view. For moving (translation) of the subtemplate position, click and hold
the left mouse button in the enclosed area of the respective subtemplate
and drag it to the desired location. The same can be done for single
optodes by clicking on the optode and dragging it to the desired location.
For changing the orientation of the subtemplate (rotation), click and hold
the CTRL key on the keyboard, and then click and hold left mouse button
on the respective template and move the mouse to the left or right (or up
and down) until the desired orientation is shown.

As the translation and rotation takes place in 2D, a co-registration

procedure is performed to obtain 3D coordinates for the 3D views. The
procedure is alike to the inverse procedure of the 3D to 2D projection and
coregistration (see paragraph 9.2.8.1). First, the individual optode positions
are transformed to a three-dimensional space according to a modified,
equidistant Lambert-azimuthal transformation. This special transformation
is optimized to retain distances between individual optodes as well as
possible during the transition from 2D to 3D. In a second step, the 3D
coordinates are then further transformed by a transformation matrix
obtained from a coregistration procedure with predefined anatomical
landmarks (the nasion, the inion, the left and right preauricular points and
the vertex) of the 10-20 system in 2D, and 3D positions measured by Artinis
Medical Systems. Finally, the optodes are projected to the nearest scalp
location in 3D. Note that this procedure in combination with the manual
subtemplate positioning and the use of a 3D template model, this will only
give a rough estimate of the real location of optodes. The estimated
location therefore do not allow for any conclusive statements about the
true location of brain activity.

Graphs show the measured data by traces. The graph is the window; the
trace is for instance the O2Hb concentration measured by one optode
combination. The available graphs are:
- (regular) Graph: Time view (paragraph 9.3.1)
- Topo Graph: Spatial view (paragraph 9.3.4)

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- Spectrum Graph: Frequency spectrum (paragraph 9.3.5)
- Indicator view: Numerical view (paragraph 9.3.6)

A regular graph is a time view of the measured data. The time is plotted
along the x-axis in seconds and the measured signal is plotted along the y-
axis. The scroll bar in the graph can be used to show the concentrations
over time. Graphs with the icon are regular graphs. A regular graph can
be created in several ways:
- Menu  Graph Create graph or Create All Graphs or Create graphs
from Optode Template.
- Right-mouse clicking the project view on the measurement and select
“Create Graph”, “Create All Graphs” or “Create graphs from
Measurement Template”.
- Via “Create all graphs” at the end of the DAQ measurement wizard.

The function “Create Graph” creates an empty graph without traces. “Create
all graphs” creates graphs for the optode template with traces for the
desired concentrations according to the optode template (chapter 11).
“Create Graph from a template” creates graphs from a measurement
template (paragraph 7.6.3). This measurement template shows the data in
a clarifying way.

This paragraph describes how to create a graph with the function “Create
Graph” (Figure 9-16).

Figure 9-16. Graph properties

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9.3.1.1 Graph properties
The properties in this tab affect the name of graph, event display mode,
coloring and comments. More graph properties can be found in Menu 
View  Options, tab “Graph Options”.

Graph Name
This specifies the name of the graph.

Show events
To show events in the graph, set this to 'show events'. For more
information about events, see paragraph 10.1. In case of cyclic data the list
of options is expanded with traces based on cyclic data (paragraph 10.3).
Selecting one of these, events will be projected on the timeline of that
trace. To show/hide events as default in any graphs, use the program
options use the program options (paragraph 7.6).

Show Legend
When checked, a legend of traces is shown to the right of the graph (Figure
7-1). To show/hide as default the legend in all graphs, use the program
options (paragraph 7.6).

Background color
This button changes the background color of the graph. To change the
default background color, use the program options (paragraph 7.6).

Text color
Click on this button to change the text color of the graph. To change the
default text color, use the program options (paragraph 7.6).

Comments
The comments field is a free text field reserved for extra information.

Figure 9-17. Graph properties – the x-axes

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9.3.1.2 X-axis
The properties in this tab affect scaling settings of the time axis (Figure
9-17. Graph properties – the x-axes). During data acquisition the x-axis is
set by the time span settings in the program options.

Auto scale
If checked, the time scale is set to automatically: the axis will start at the
minimum time of traces and end at the maximum time.

Manual scale
When checked the manual scale settings are used instead. The scale is set
by:
- Minimum: The axis will start at the minimum value entered here. Fill in
the minimum.
- Time: “1”, “10”, etc. The axis will start at 1 or 10 seconds.
- A unique event label: “A1”, “B2”, etc. The axis will start at event “A1”
or “B2”.
- An event label: “A”, “B”, etc. The axis will start at the first event “A” or
“B”.
- A combination of time and event labels: “A+10”, “B-10”, etc. The axis
will start 10 seconds after event A1 or 10 seconds before event B1.
(Warning: “10+A” does not work). The code “<” smaller than and “>”
bigger than: “A>100”, “B<500”. The periods will start with the first
event A after 100 seconds or event B before 500 seconds (handy to
define the maximum of the x-axis).

Figure 9-18. Graph properties – the y-axis

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 - The code “|” OR: “A1|A3”. The axis will start at the first of A1 and A3.
The input “A1|A3>100” will start at the first of A1 and A3 which is larger
than 100.
- The “!” operator subtracts the given set from the set containing all
events. For example: !U2 takes all events except U2 or !U2 & !U4 takes
all events except U2 and U4 Note the equivalent is !(U2|U4).
- Maximum: The axis will end at the maximum value entered in this field.
The maximum should be larger than the minimum. See the minimum
for how to define the maximum.
- Ticks: Enter the axis-tick interval in this field. Leave 0 to let the program
decide for a reasonable value.

9.3.1.3 Y axis
The properties in this tab (Figure 9-18) affect scaling settings of the value
axis

Common auto scale

If checked, the value scale is set automatically to the same for all available
graphs in the measurement also set to “Common auto scale”. The axis will
start at the minimum value of traces and end at the maximum value and
some margin will be included. During data acquisition, the scaling will adapt
the y-axis dynamically in order to show the current values.

Auto scale
If checked, the value scale is set to automatically: the axis will start at the
minimum value of traces and end at the maximum value and some margin
will be included. During data acquisition, the scaling will adapt the y-axis
dynamically in order to show the current values. The minimum range of the
scale can be set by:
- Minimum range: When in auto scale mode, the range of the scale will
not be smaller than this value.

Manual scale
When checked the manual scale settings are used instead. The scale can
be set by:
- Minimum: The axis will start at the minimum value entered.
- Maximum: The axis will end at the maximum value entered. The
maximum should be larger than the minimum.
- Ticks: Enter the axis-tick interval. Leave “0” to let the program choose
for a reasonable value.
- Unit: Enter the unit of the y-axis. This unit will be shown along the y-axis
-6
and when the y-axis value is reported: Relative concentration (µM, 10
mol/l), AD Input Voltage (Volt), TSI (%)

Suppress Scale Factorization

The values shown along the y-axis are scaled in order to limit the number
of digits used. For example: if the minimum value is 0, and the maximum
value .01, then (with steps) values from 0.0 through 10.0 are shown and
before the unit 1e-3 is displayed as scale factor. When this option is

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 checked, the factorization is suppressed and the values are shown in an
unscaled way, at the expense of a wider space reserved for the y-axis
numbers. To suppress scale factorization in all graphs, change the program
options (paragraph 7.6).

9.3.1.4 Gridlines
This tab defines if any gridlines is to be shown in the graph (Figure 9-19)

Gridlines X-axis/Y-axis
If checked, gridlines on the x-axis/y-axis are shown.

Figure 9-19. Graph properties – gridlines

The function “Create all graphs” is called by Menu  Measurement  Create

all graphs, by right mouse clicking in the project view at the current
measurement and selection of “Create all graphs” or in the last window of
DAQ measurement wizard. “Create all graphs” creates graphs for all optode
combination of the optode template with traces for the desired
concentrations (O2Hb, HHb, tHb and HbDiff). The graphs are arranged as
the optode template.

This function will remove all earlier created graphs from the measurement.
Therefore, a warning (Figure 9-20) is given.

Figure 9-20. Warning after automatic graph creation

A measurement template can be used to create graphs containing all

necessary data arranged in a clarifying way. One template is currently
available, the “PortaMon TSI” template. The graphs can be created from the
template by Menu  Graph  Create Graphs from Optode Template, by right

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clicking in the project view on the measurement and selection of “Create
graphs from a template”. This function will remove all earlier created graphs
from the measurement. Therefore, a warning (Figure 9-20) is given.

To change the template file used to make graphical templates or to create

own templates, see paragraph 7.6.3.

A topo graph is a spatial or topographic time view of the measured data

showing the measured concentrations by a color scale (Figure 9-21). A topo
graph can only be made of mapping measurements, which are
measurements with a 2D optode template like the “4 channel square”
template. The topo graph uses automatically all optode combinations;
therefore no traces can be added to this graph. Graphs with the icon are
topo graphs. The scroll bar in the graph can be used to show the
concentrations over time.

The 3D/Neuro license allows for topographic plotting on a 2D projection of

a head or a 3D model of a head or a 3D model of the brain. The 3D models
are created from the MNI ICBM 152 brain template obtained from
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009. For using
the 3D/Neuro license the correct USB dongle is needed. You can contact
Artinis Medical Systems directly to obtain such a license
(askforinfo@artinis.com).

A nice example is in the folder “Sample” in the Oxysoft directory. Open the
project “Measurement examples.oxyproj” and open the available
measurement.

A topo graph can be created by Menu  Measurement  Create Topo Graph

or by right mouse clicking on the measurement in the project view and
selection of “Create Topo Graph”. The window shown in Figure 9-23 will
open.

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Figure 9-21. Topo graph for a 4 channel square template measurement

In 2D Plain mode, positions of optodes are based on the chosen

optodetemplate. Using the 3D/Neuro license, additional view modes
become available. In 2D Topograph mode, the optodetemplates is placed in
a 2D projection of a head with a radius of 10.0 cm. The position of the
individual subtemplates can either registered with a 3D Polhemus digitizer
or set manually by moving and rotating the subtemplate in digitize mode
(see 9.2.8).

There are three 3D view models available. The 3D Scalp Projection

viewmode shows the optode activity as projected on a 3D scalp model. The
3D Cortical Mesh viewmode estimates the illuminated cortical surface based
on an oblate spheroid (an ellipsoid with equal semi-diameters), centered in
the middle of the transmitter and receiver, with the semi-diameters defined
by the distance between transmitter and receiver. In 3D Glasshead+Cortex
viewmode, both viewmodes are combined while the scalp view is made
transparent. See Figure 9.19 for an example.

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Figure 9.9-22 Example of a 3D glasshead view of an n-back task using the Octamon.

Figure 9-23. Topo graph properties – graph properties

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 Figure 9-24. Topo graph properties – color scale

9.3.4.1 Graph properties

The properties in this tab affect the name of the graph, legends, labels and
comments. For explanation about the graph name, legend and comments
see paragraph 9.3.1.

Show Labels
When checked, labels are shown in the graph. The o in a topo graph shows
the used optode combination points, which can be labeled by using this
option.

Show sensors
When checked, indicates the optode positions in the topo graph.

Show channel positions

When checked, indicates the center location of receiver-transmitter
combinations.

Show 10-20 locations

Only for 2D topo graphs: Shows the sensor locations of the standardized
EEG 10-20 system.

9.3.4.2 Transformation A
The properties in this tab are identical with defining a regular trace
(paragraph 9.3.1).

9.3.4.3 Color scale

The properties in this tab (Figure 9-24) affect the color settings of the topo
graph.

Color Axis: Auto scale

If checked, the value scale is set to automatically: the axis will start at the
minimum value of traces and end at the maximum value and some margin

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 will be included. During DAQ, the scaling will adapt the y-axis dynamically in
order to show the current values.

Color Axis: Manual scale

When checked the manual scale settings are used instead. The scale is set
by:
- Minimum: The axis will start at the minimum value entered here.
- Maximum: The axis will end at the maximum value entered in this field.
The maximum should be larger than the minimum.
- Unit: Enter the unit of the y-axis. This unit will be shown along the y-axis
and when the y-axis values are reported.

Color mapping
This defines the color mapping of the topo graph. The options are:
- Linear color mapping: defines the color scale of the topo graph by going
linear in the sRGB color space, from the selected minimum color to the
selected maximum (see below).
- Hue: is an attribute, which defines an element in the color wheel (which
starts with red, orange, yellow... and then comes back to red again).
Positive hue means the color mapping will follow the color wheel in
positive direction from the selected minimum color to the selected
maximum (see below), and negative hue in negative direction. RGB and
hue are standard tools to describe perceived color in color spaces.
The scale can be set by:
- Minimum: The color mapping will start at the minimum value entered
here. Select by clicking on the color box.
- Maximum: The color mapping will start at the maximum value entered
here. Select by clicking on the color box.

9.3.4.4 Play recorded data

Recorded mapping data can be played with Menu  Playback  Play,
Record and Stop. The toolbar buttons are also used to play the
data. First make a topo graph of the measured data. The play speed can be
adjusted with Menu  Playback  Speed.

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 Figure 9-25. Create movie

9.3.4.5 Movie
The topo graphs can be exported to a movie by Menu  Playback  Movie
capture. A window shown in Figure 9-25 will open. Recording a movie is only
possible in plain 2D mode.

Source graphs and period

Select one or two graphs at “Graph A” and “Graph B”. The start and the end
are defined in seconds or as events.

Movie specification
Choose a file name by browse. The window size specifies the size of the
windows of the movie. Small sizes can result in a cut off legend, but require
less space to save. To add two graphs, choose a window size with A and B!
The frame rate specifies number of frames per seconds (fps). A high frame
rate gives more detail, a low frame rate requires less space. The frame rate
is restricted to the sample rate of the measurement; higher frame rates
give a frame rate equal to the sample rate. The movie duration defines the
duration of the movie; a three-hour measurement of can be reduced to a
ten-minute movie.

The graphs have scrollbars if the complete measurement does not fit in the
screen, which are also used to review data. Use the zoom buttons to look
at details.

A spectrum graph is a plot of the data in the frequency domain (Figure

9-26). The measured data is transformed to the frequency domain by

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Figure 9-26. Spectrum graph

Fourier transformation. The frequency is plotted along the x-axis and the
amplitude along the y-axis. Graphs with the icon are spectrum graphs. A
spectrum graph can be opened by Menu  Measurement  Create
Spectrum Graph or right mouse clicking at the measurement in the project
view and selection of “Create Spectrum Graph”.

During the measurement, the frequency spectrum of the currently

measured data is displayed in the graph, after the measurement the
spectrum of the whole measurement is displayed in the graph. To plot the
spectrum over a period, select a period in a regular graph as described in
paragraph 10.2.

These graphs can be a useful help to select filters (paragraph 10.5),

however it is currently not possible to add filtered traces to spectrum
graphs. Traces with a cyclic operator can be added to the spectrum graph;
however, only “cyclic” is available as operator, because of the other cyclic
operators give the same result as “cyclic”.

The properties are identical with a regular graph (paragraph 9.3.1).

An indicator view is a graph containing a number and a bar, displaying the

current measured value (Figure 9-27). Graphs with the icon are indicator
views. The properties in the tabs are almost identical with defining a regular
graph (paragraph 9.3.1). There is an extra option to display the numerical
bars horizontally or vertically. Notice that you can add multiple traces to
this graph. An indicator view opens by Menu  Graph  Create indicator
view or right mouse clicking at the measurement in the project view and
selection of “create indicator view”. Enabling “show legend” will show labels
to the indicator view.

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 Figure 9-27. Indicator view with two traces and legend, horizontal bars and vertical bars.

Show graph properties by Menu  Graph  Properties, by right mouse

clicking on the graph in the project view and selection of “Graph
properties”, by double clicking on the graph in the project view or by
selection of the graph in the project view and clicking on the toolbar button
. The windows concerning to the graph properties are equal to the
windows of the graph creation (paragraph 9.3.1).

9.3.7.1 Common graph properties

The graph properties of all graphs in one measurement can be changed by
the common graph properties. Right click on the measurement in the
project view and select “Common graph properties” or via Menu  Graph 
Common Graph Properties. The window shown in Figure 9-28 will open. The
tabs “Graph”, “X Axis”, “Y axis” and “Gridlines” are equal to the regular graph
properties (paragraph 9.3.1), with exception of the checkbox “Modify”. After
changing a property, “Modify” is checked to apply it to all graphs in the
measurement. The tab “Filter/transform” is similar to the “Transformation A”
of trace properties (paragraph 9.4.3). If a property is selected to change, it
will change for all traces in the measurement.

Figure 9-28. Common graph properties

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A closed graph can be opened by selection of the graph in the project view,
Menu  Graph  Open Graph, by right mouse clicking in the project view at
the graph and selection of “Open Graph” or double clicking in the project
view at the graph. If you cannot find the graph, it might be hidden behind
another graph or minimized.

All graphs of a measurement can be opened at once by Menu  Graph 

Open all graphs, the shortcut <F2> or by right mouse clicking on the
measurement in the project view and selection of “Open All Graphs”. The
button on the toolbar will also open all graphs.

A graph can be renamed by right-mouse clicking in the project view on the

graph and selection of “Rename Graph” or change the name in the graph
properties.

A graph can be duplicated by Menu  Graph  Duplicate graph or by right-

mouse clicking in the project view on the graph and selection of “Duplicate
Graph”. Graph duplication can be useful to copy all settings from the graph
to a new graph. Graphs can only be duplicated within in a measurement.

Clear a graph during the measurement by clicking on in the toolbar or

by Menu  View  Clear Graphs or by the shortcut <F7>. The measured
data is not deleted, only the graph is cleared. This function can be handy to
make nice screenshots during the measurements. You can also use <F6>
or the button to bias and clear the graph (paragraph 9.4.6).

Figure 9-29. Menu Window

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A graph can be frozen/de-frozen during the measurement by clicking on
in the toolbar or by Menu  View  Freeze Graphs or by the shortcut <F8>.
The measurement continues recording during the freeze period, only the
graph is frozen. This function can be handy to make nice screenshots
during the measurements.

Arrange graphs by Menu  Window as “Cascade”, “Tile”, “optode template”

or “measurement template”. “Cascade” will arrange the opened graphs as a
cascade; “Tile” will place the opened graphs in such way that all graphs fit
on the screen; “Arrange graphs as optode template” will position the graphs
like the used optode template. “Restore graph lay-out to measurement
template” arranges the graphs back to the original format of the
measurement template (if used). The button on the toolbar will also
arrange the graphs to the measurement template.

In Menu  Window all opened graphs are shown, it is possible to switch

between the graphs by selecting another graph in this menu or just by
selection of an opened graph on the screen (Figure 9-29).

An open graph can be closed by right mouse clicking in the project view at
the graph and selection of “Close Graph” or at the exit cross in the upper
right corner.

All graphs of a measurement close at once by Menu  Graph  Close All

Graphs, the shortcut <F3>, by right mouse clicking on the measurement in
the project view and selection of “Close All Graphs” or by the button .
The opened graphs of all measurements can be close at once by Menu 
Windows  Close all graphs.

To remove a graph, select the graph in the project view; go to Menu 

Graph  Remove graph or by right-mouse clicking in the project view on the
graph and selection of “Remove graph”.

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Figure 9-30. Toolbar – zoom

A graph can be printed by Menu  File  Print. Only the selected graph will
be printed. Choose Menu  File  Print preview to preview the printed
graph. Select Menu  File  Print setup to change the print settings.
Copy a graph to another program by right clicking in the graph and
selection of “Copy to Clipboard” or use Ctrl+C.

To see more or less detail in graphs, it is possible to zoom in and out.

Zooming is done by clicking on the toolbar at the zoom buttons (see Figure
9-30) ) or by right mouse clicking in the graph and selection of “Zoom to
default”, “Zoom in X”, “Zoom in Y”, “Zoom out X” or “Zoom out Y”. These
options are also available at Menu  View. In addition, the axis scale in the
graph properties can be adjusted to make a standard zoom window
(paragraph 9.3.17). During a measurement it might be handy to freeze the
graphs (paragraph 9.3.12) before zooming in or to change the (default) time
span via the program options (paragraph 7.6).

The used time span can be switched to another time span (rollover mode
and trend view) by Menu  Data Collection  Toggle graph(s) to trend mode
or clicking on in the toolbar. The trend mode has a longer time span
then the rollover mode. The duration of spans can be changed by the
program options (paragraph 7.6).

With Menu  View  Zoom/scroll Synchronized and the toolbar button

the zoom and scroll of all graphs of the same measurement can be
synchronized if it is checked. When not checked, the zooming is only
applied to the currently selected graph.

A trace is a line or number displaying the measured data. A trace displays

only data from one optode channel or AD Channel. Create traces

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 automatically by creating graphs from a template or by the function “create
all graphs”. Add traces to a graph by the function “create trace” or “create
all traces”. The first creates a trace without specifications. The second
creates traces belonging to the optode template. Traces can be created in
regular graphs, indicator views and spectrum graphs.

A trace can be created in a graph if the graph is selected in the project view,
Menu  Trace  Create trace or by right-mouse clicking the project view on
the graph and select “Add trace”. The window shown in Figure 9-31 will
come up. Trace coordinates are shown by moving the mouse over the
trace. A trace can be selected by clicking on it in the graph or in the project
tree.

A topo graph uses all optode combinations of the subtemplate available, no

traces can be added to this graph type.

9.4.1.1 Channel A
The properties in this tab specify the name of trace, and the primary source
of data.

Label
This specifies the name of the trace. This name is automatically generated
from the source and the transformation applied. Overrule this by
deselecting “Auto” checkbox and enter an alternative name. The label is for
own reference and will be shown in the project view.

Figure 9-31. Trace properties – channel A

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 Figure 9-32. TSI optode template

Type source
Choose the type of data source. This option list will show “optode
combination”, the available AD Channels and external data file sources. If
an external data file source is added, select one of the defined data
columns in “column” (see paragraph 9.5.3).

Channel
If the optode combination is selected as type source, select one of the
optode combinations available in the optode template as data source. In
Figure 9-31 the white circles in the optode template are representing valid
optode combinations. Select a channel by clicking on one of these
combinations in the graphical display. To show the relative concentrations,
choose “Rx1-Tx1”, “Rx1-Tx2” or “Rx1-Tx3” as source channel. Each shows
the measured concentrations of that optode combination. The picture of a
TSI optode template has a square between the first and second channel
(two channel measurement) or behind the second channel (three channel
measurement), which is called the TSI combination source (Figure 9-32).
With selection of this square, you can show TSI or TSI Fit Factor and the
absolute concentrations calculated with the SRS method. Switch between
TSI and Tx2 by clicking again at the square.

9.4.1.2 Transformation A/B

The properties in this tab affect the transformed data, filters, scaling and
modifications that can be applied to a trace with channel A as data source
(Figure 9-33). If an AD Channel is selected as data source, the tab looks like
Figure 9-35.

Transformation
This defines which type of data to display. The available transformations
depend on the NIRS system and the selected data source at the “Channel
A” tab. The following transformations are explained:
- O2Hb, HHb, HbDiff and tHb are standard traces and display
concentration changes of oxygenated, de-oxygenated, difference
(O2Hb-HHb) and total (O2Hb+HHb) amount of hemoglobin and
Myoglobin [Mb]. These can be selected when an optode combination is
selected as source. ). If the TSI combination is selected as data source,
the estimated absolute concentrations are given.
- CtOx (or others) is available for Oxymons with a transmitter of three
wavelengths (or more) and can be selected when an optode
combination is selected as source. This trace displays concentration
changes of cytochrome oxidase.
- TSI% and TSI Fit Factor are absolute traces and display index of tissue
saturation in % and a figure for the Fit Factor. The Oxymon, setup and
channel must qualify for a spatially resolved spectroscopy

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 measurement. Select the TSI combination as source in at the Channel A
tab. For more information about TSI and the Fit Factor, see chapter 12.
- User defined transformation displays optical densities measured by the
Oxymon at a specific wavelength (and independent on DPF and source-
detector distance). Note that multiplication factors must be defined in
the entry box beside the available wavelength of interest, use “1” for
standard OD’s for one wavelength at the time and “0” for the other
wavelength (Figure 9-34). If the TSI combination is selected as data
source, the calculated absorption coefficient µa is displayed.
- User defined * 1/(dpf*dist) is the user defined transformation above, but
with the DPF and source-detector distance settings taken into account
(divided by these factors).

Wavelength entries
If “User defined” transformation is selected, a wavelength entry selects the
wavelength and multiplication factor. "O" means unselected, "1" means
selected and any positive number can be used for multiplication (Figure
9-34).
This defines the multiplication factor of the trace from an optode
combination. It can also be assigned negative values.

Figure 9-33. Trace properties – transformation A

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Figure 9-34. Trace properties - transformation A - User defined

Figure 9-35. Trace properties – transformation A with AD Channel

Scale
This defines the multiplication of a channel. This is standard set to 1.

Bias
This defines the offset y-value added to the entire trace from an optode
combination. For more information about the bias, see paragraph 9.4.6.
This parameter is automatically defined by the program when the ‘bias all
traces’ function is used or ‘bias traces at start’ is selected in the program
options (paragraph 7.6 but you can also type any number (positive and
negative)).

Filter
A filter can be applied to the trace. For more information, see paragraph
10.5.

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 Cyclic operator
Cyclic operators can be used to analyze repetitive measurements. For more
information about the cyclic operators, see paragraph 10.3.

Voltage
If an AD Channel is selected as “Channel A” data source, the voltage entries
will be available. Min Scale and Max Scale define the range of the input in
voltages, which should be specified by the input devices supplier or have to
be measured.

Scaled value
If an AD Channel or imported data file is selected as “Channel A” data
source, these scaled value entries will be available (Figure 9-35). Min Scale
and Max Scale define the (defined) scaling values. For example: If 0 Volt
should represent 10 bpm and 3 Volt should represent 80 bpm, then fill in
“0” for Min Scale of the Voltage, “3” for the Max Scale of the Voltage, “10” for
the Min Scale of the Scaled value and “80” for the Max Scale of the Scaled
value.

Delay (sec)
If AD Channel or imported data file is selected as “Channel A” data source,
these scaled value entries will be available. Fill in the delay of the AD
Channel signal in seconds.

9.4.1.3 Operator
The properties in this tab (Figure 9-36) affect the operator between the
primary source of data (Channel A) and secondary source (Channel B).

Figure 9-36. Trace properties – operator

Operator
This operator enables the combining of Channel A and Channel B source
into the same trace. By selecting no operator "None (Trace A only)" the
program only uses the defined settings of trace A. When an operator is
selected, also the properties of Channel B (next tab) need to be defined.
The available operator options are an addition (+), multiplication (*) and
division (/).

9.4.1.4 Channel B
This only seen if an operator is selected. The properties in this tab affect
the second source of data. These settings are only in use when an operator
is selected for combining Channel A and Channel B source into the same
trace.

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 The properties in the Channel B tab are identical with defining settings of
Channel A.

9.4.1.5 Transformation B
The properties in the transformation B tab are identical with defining
settings of transformation A.

9.4.1.6 Trace
The properties in this tab (Figure 9-37) affect the color and style of the
trace.

Color
This specifies the color of the trace. Select by clicking on the color box.
Style
This specifies the thickness of the trace. Select an available option from the
list.

Figure 9-37. Trace properties – trace

Figure 9-38. Create all traces – add traces to graph

By Menu  Trace  Add All Traces or by right mouse clicking in the project
view at the current graph and selection of “Create all traces” the traces to
show the concentrations (O2Hb, HHb, tHb, HbDiff, TSI and TSI Fit Factor)
can be created at once for an optode combination of the used optode
template. The window is shown in Figure 9-38.

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 Show the trace properties by Menu  Trace  Properties, by right mouse
clicking on the trace in the project view and selection of “Trace properties”,
by double clicking on the trace in the project view or by selecting of the
trace in the project view and clicking on the toolbar button . The
windows belonging to this function are equal to the windows belonging to
trace creation (paragraph 9.4.1).

A trace can be duplicated by Menu  Trace  Duplicate Trace or by right-

mouse clicking in the project view on the trace and selection of “Duplicate
trace”. Trace duplication can be useful to copy all settings from the trace to
a new trace. Traces can only be duplicated in a graph.

To remove a trace, select the trace in the project view; go to Menu  Trace
 Remove Trace or by right-mouse clicking in the project view on the trace
and selection of “Remove trace”.

9.4.6.1 Biasing
Biasing is setting a baseline of the data. Biasing all traces once in the
beginning of data acquisition is usually preferred, or to a point considered
as the baseline or reference of the measurement. Since we are always
looking into relative changes the starting point of a concentration value will
never matter, and the “Bias Trace” or “Bias All Traces …” is only for own
convenience and graphical displaying during the measurement or analysis.
The “biasing” will never affect the real recorded data and when afterwards
(off-line) traces can be biased to any point (for example in the “Trace
properties”). When using cyclic operator, the options with "detrend" will
bias traces to an average over a specified period, such as for example the
first 5 seconds.

Signals from the input AD Channels cannot be biased in this way. It is

possible to scale them and change the offset at the transformation A/B tab
of the trace properties.

9.4.6.2 Bias a trace

A selected trace can be biased (set the baseline) by Menu  Trace  Bias
Trace, by right clicking in the graph on the trace and selection of “Bias
trace”. Bias all traces in a graph at once by selection of “Bias All Traces in
Graph” and all traces in a measurement can be biased by selection of “Bias
All Traces in Measurement”. “Bias All Traces and Clear Graph”, the button

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 in the toolbar or <F6> is only available during measuring and will bias all
traces and clear the graphs at once. The trace(s) will be biased to the
selected data point.

9.4.6.3 Change a bias

The bias of a trace can be changed by biasing again or in the trace
properties, tab “transformation A/B” (paragraph 9.4.1.2). The bias of all
traces in a measurement can be changed by the common graph properties
(paragraph 9.3.7.1).

9.4.6.4 Bias traces at the start of a measurement

All traces can be biased at the start of a measurement by the program
options, Menu  View  Options, tab “DAQ”. Check “bias traces at start”. For
more information about program options, see paragraph 7.6.

The function Menu  Measurement Create offline measurement will open a

window which looks like the DAQ measurement wizard, and can be used to
open any *.oxy and *.oxy3 files. To open an *.oxy file, the belonging *.evt
should be in the same folder and have the same name. For more
information, see paragraph 9.2.3.

Import a measurement by Menu  Project  Import measurement or right-

click in the project view at the project. The measurement import window is
shown in Figure 9-39. Select the project file (*.oxyproj) in which the
measurement is by clicking on “Browse”. The available measurements will
be shown in the field “measurement”. Select the desired measurement.
Click “OK” to import the measurement including the belonging *.oxy3 file.

Import data files (*.txt) by Menu  Measurement  Add external file or right
click at the measurement folder in the project view and select “Add data
file”. The imported data file will be added to the current measurement in
the project view as shown in Figure 9-40. The data file import wizard is
shown in Figure 9-42. The result of importing the example (Figure 9-43)
with the settings from Figure 9-42 is shown in the graph of Figure 9-40.

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Figure 9-39. Import measurement

Figure 9-40. New data file

Name
Name shown in the project view for the added data file. In the example
(Figure 9-41) the name is “import file”.

File path
Select the *.txt file, which should be added, by clicking on “Browse”. The
example import file is called “import.txt” (Figure 9-43).

Type
This specifies the type of column separation:
- Fixed width: fixed width of the column (as in the example)
- Delimited: columns are separated by a delimiter:
- “,”
- “space”
- “tab”

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Figure 9-41. Import data file

Columns
This specifies the data columns in the data file:
- Name: Choose a name for the data column (“value” and “sample nr” in
the example).
- Start: start position of the data column in the data file (Fixed width).
- Width: Width of the data column (number of characters) in the data file
(Fixed width).
- Column number: number of the data column in the data file (Delimited).
The buttons “Add”, “Delete” and “Preview” also belong to this field
- Add: add an extra column.
- Delete: delete a column.
- Preview: give a preview of the imported data.

Time column
This field specifies the time column. The column names as specified at the
columns will be displayed. Select “row number” to use sample numbers.

Time scale
This field can be used to up or down sample the imported data to the same
frequency as your Oxysoft data. If the imported data is measured with 10
Hz the time scale value has to be set to 0.1.
Further it can be used to convert your time column data to seconds if it has
a different unit than seconds. Use for example a value of 0.001 to go from
ms to s.

Line of first row

This field specifies the line of the first data row. In the example, the first row
specifies the data types, so the data is imported from the second row.

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 Figure 9-42. Example file

Figure 9-43. Import data file - Add data to graphs

9.5.3.1 Add imported data to graphs

Add the imported data to graphs by adding a trace to a graph and to
specify at the trace properties, tab “Channel A”, as type the name of the
added file and as column a name of the data columns (Figure 9-44). The
result of importing the example (Figure 9-43) with the settings from Figure
9-42 is shown in Figure 9-40.

9.5.3.2 Properties
Change the properties of the imported data file by right mouse clicking in
the project view on the data file and select “Properties”.

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9.5.3.3 Duplicate imported data file
Duplicate an imported data file by right mouse clicking in the project view
on the data file and select “Duplicate”.

9.5.3.4 Rename imported data file

Rename an imported data file by right mouse clicking in the project view on
the data file and select “Rename”.

9.5.3.5 Remove imported data file

Remove the imported data file by right mouse clicking in the project view
on the data file and select “Remove”.

Data can be exported to other formats by Menu  Measurement Export

measurement or by the use of “calculate” and the function “graph data” (see
paragraph 10.4). When you use the first option, it will open the window
shown in Figure 9-44. The exported file contains all information about the
measurement, the used system and settings and the data including the
events.

If an error comes up during export, usually the amount of data is too big
for the program used to export to (usually MS Excel), or the file used to
export to is already opened in another program.

It is also possible to read the raw date (*.oxy3 files) with Matlab directly.
Contact Artinis for the m-files.

9.5.4.1 Export formats

Select the desired export format and click on next. The formats are:
- Text: export to a *.txt file format.
- MS Excel: export to Microsoft excel file (only possible if MS Excel is
installed).
- XML: export to a XML file.
- oxy/.evt file: exports to an *.oxy/*.evt file format, these formats can be
necessary for reopening files in older Artinis software.
- .oxy3 file: export to *.oxy3 file. Use this to select a part of the measured
data or to down sample the data for further analysis.

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Figure 9-44. Export – export type

Figure 9-45. Export – export file destination

Figure 9-46. Export – save as

120
9.5.4.2 Export file destination
The file name and destination of the exported file can be selected in the
next window, shown in Figure 9-45. Click on “Browse”, a new window will
open (Figure 9-46). Choose the file name and destination and click on
“Save” (Figure 9-46). Click on “Next” in the window of Figure 9-45.

9.5.4.3 Export options

The next window (Figure 9-48) will give the option to choose which data is
exported. This window is not available when exporting to an old *.oxy/*.evt
file format or to *.oxy3 file format, because the raw data will be exported
automatically.

Data transform
- Graph data of open graphs: exports concentrations and TSI shown in
the opened graphs. This can also export OD values and ADC voltages if
these are shown in an opened graph.
- OD values and ADC voltages: exports OD values and ADC voltages. This
can be used for (re)calculation and analysis.
- Raw data: gives an indication of the measured AD counts.
We recommend using only graph data of open graphs for normal
applications. This will export the measured concentrations and TSI. OD
values and ADC Voltages and Raw data is only useful for special applications.
Make sure you have all graphs with data open before you start the export.

Null field
separation of data (delimiter) fields can be specified by “Empty”, “Space”, “0”,
“-“ “*” or “NULL”.

Click on “Next”.

Figure 9-47. Export – export options

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 Figure 9-48. Export – export time span

9.5.4.4 Export time span

Time span (Figure 9-48)
- The export time span can be chosen in the next window by filling in:
- Start of export: the time coordinate or event where the export starts.
- End of export: the time coordinate or event where the export stops.
Empty fields will select the whole data set for export.

Use:
- Time: “1”, “10”, etc. The period will start or end at 1 or 10 seconds.
- An event label: “A1”, “B2”, etc. The period will start or end at event “A1”
or “B2”.
- An event label: “A”, “B”, etc. The period will start or end at events A1 or
B1. You cannot export different periods to one file by using multiple
events (A1, A2, etc.).
- The general code: ‘*’ instead of an event label, which will select any
existing event fulfilling the criteria.
- A combination of time and event labels: “A+10”, “B-10”, etc. The period
will start or end 10 seconds after event A1 or 10 seconds before event
B1. Warning: “10+A” does not work.

Down sample factor

Data can be exported with a lower sample rate by using a down sampling
factor. The factor is an integer (1, 2, 3 not 0.5 or 1.2) between 1 and 1000.
This way it is also possible to down sample a *.oxy3 file, by exporting the
file and use an appropriate down sample factor.

By example, a down sample factor “10” and a sample rate of 10 Hz will lead
to a new sample frequency of 1 Hz. A down sample factor “1” will leave the
sample rate to the sample rate during the measurement. The export
sample rate is shown at the right side of the field if filled in correctly.

Start Export
Click to start the export.

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The Ascii writer is a protocol that allows third party applications to receive
online data from OxySoft. Communication is through sockets.
The ASCII writer can be enabled in Portasoft.ini by adding in top of the file:

[Asciiwriter]
Enable=1
Port=7777

(7777 is the default port number when not specified)

This file is found in:

C:\Users\Public\Documents\Artinis Medical Systems BV\common

If the ASCII writer is enabled, it writes the sample data to a local TCP socket.
To connect to the ASCII writer a standard TCP socket can be opened to the
host computer on port 7777.

The datastream consists of '\n' terminated ascii lines.

In the client, connect to the socket. Upon connection, the server sends a
one line header with comma separated fields. The first field is always
"Samplenumber", the latter fields are the trace names given in OxySoft.
Consecutive lines are sent at the selected sample rate and contain comma
separated data values corresponding to the traces names given in the
header. Communication is stopped by closing the socket.

The ASCII writer writes the data in the following order:

Sample number, (RX1 - TX1), (RX1 - TX2), (RX2 - TX1), (RX2 - TX2) ...

The order of the data sent by the ASCII writer depends on the used
measurement template. For a split template, the data would be for
example:
Sample number, (RX1a - TX1), (RX1b - TX1), (RX1a - TX2), (RX1b - TX2) …

The data is always written as plain text (ASCII), and should be parsed by the
user as only raw values are given (relative changes should be calculated by
using a previous value as a starting point).

The FieldTrip buffer is an open source TCP/IP protocol, which allows clients
to write and read data from (for a more extensive description see
http://www.fieldtriptoolbox.org/development/realtime/buffer_overview).
The open source architecture allows a number of different systems to write

123
data to the shared memory segment, so that not only data from within
Oxysoft but also e.g. EMG or EEG data can be written to the buffer. The
FieldTrip buffer is platform and OS independent, thus all Windows, Mac and
Linux clients can connect to the buffer, and the software reading from or
writing to the buffer can be in any programming language. The original
buffer implementation is natively written in C and C++, but
implementations for reading and writing are freely available for Matlab. Java
and Python.

To activate the FieldTrip buffer, the following lines need to be added to the
portasoft.ini:

[FieldTrip]
Enable = 1
StartServer=1

This file is found in:

C:\Users\Public\Documents\Artinis Medical Systems BV\common

If the FieldTrip buffer is enabled, all recorded data in Oxysoft is written to

the buffer when a new measurement is started (i.e. as soon as data is
recorded). Oxysoft is always expecting the FieldTrip buffer port to be 1972.
If StartServer is set to 1, then a TCP socket is automatically opened at port
1972 upon starting Oxysoft. If a firewall is active, permissions to write to
and read from this port network-wide need to be set appropriately.

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This chapter describes how to work with events, periods, cyclic operators and
how to do a calculation or to apply a filter.

Use events to indicate the events during the measurement like the start
and end of an occlusion. Events will help to analyze measured data; they
are included in export files. Furthermore, they can be used for calculations,
to set the cyclic operator properties, to define the export period, to define
the period used for creation of a movie and adjustment of the x-axis. An
event is shown by a vertical line in the graph (Figure 10-1) and marked with
an event label (“E” in this example); however, it is only visible in trend
display mode and after the measurement is finished. The time since the
last event is marked in the DAQ status view.

The events made during online recording are defined by Menu  Analysis
 Event keys (Figure 10-2). The events are labeled by the keys, like “A”, “B”,
etc. Give an “event text” to describe the event as shown. It is possible to use
the same event label for multiple events. For instance, “A” indicates the
start of an exercise and “B” indicates the end. If the subject does the same
exercise twice in one measurement, the program will refer to the first start
event “A1” and the second “A2” and call the end events “B1” and “B2”. Using
the events to define a certain period for calculation, export, etc. call them
together as “A” and “B” and separate as “A1” and “A2”.

Meting 1 - Rx1 - Tx1

500
400 E
300
200
1e-3

100
0
-100
-200
-300
39.2 39.4 39.6 39.8 40.0 40.2 40.4 40.6 40.8 41.0 41.2 41.4 41.6
Figure 10-1. Graph with event E at 40.24 seconds

125
Figure 10-2. Define event keys

If recording is started, events can be inserted by Menu  Analysis  Insert

Event now or by the shortcut <F4> or simply pressing a key on the
keyboard. In the upcoming window (Figure 10-2), the event label can be
chosen by selection of “A”, “B”, etc. under “Key”. Events are inserted at the
moment you pressed the key or <F4>. If you have pressed “B” by mistake,
you can change this to by example to “A” by selection of another key or
remove it by pressing “cancel”. The “event text” can be used to describe the
event characteristics. The event is displayed as a green line (if the trend
display mode is used or if the data acquisition is ended). Look in the DAQ
Status View for the time since the last inserted event. Events inserted
during the measurement cannot be changed.

Inserting events after the measurement is possible by a right-mouse click in

the graph at any time coordinate. Select “Insert event” and the window
shown in Figure 10-3 will come up.

Figure 10-3. Insert event – event properties

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 The time coordinate of the event can be adjusted, also the event label and
the event text related to the event. The event is displayed as a blue vertical
line. Events inserted after the measurement are NOT saved in the *.oxy3
file but in the measurement. This can be done by using the export function
(8.5.d) and export to a new *.oxy3 file.

Events can be automatically generated by Menu  Analysis  Generate

events. This will open the window shown in Figure 10-4. The settings can be
set before and after the data acquisition, not during the acquisition. Two
modes are available, an absolute and relative mode. Both modes look for
changes in the data but in a different way.

10.1.4.1 Absolute
The absolute mode looks to the data values of one trace. An event will be
defined when the trace fulfills two conditions in a certain time span. The
event will be generated in the middle of the moments when the first
condition is fulfilled and the second condition is fulfilled. An example is
shown in Figure 10-4.

Select trace
Select a trace by clicking on it in the project view or in the graph and drag
this to the button. This trace will be used to generate events.

Event label
A, B, C, etc. labels the event. Previous defined events with the same label in
the measurement will be removed if “remove previous defined events with
this label” is checked.

Pre-event value-window
This defines the first condition. The trace has to be between the minimum
and maximum to fulfill to the first condition.

Post-event value-window
This defines the second condition. The trace has to be between the
minimum and maximum to fulfill to the second condition.

Width of test
This defines the time span wherein both conditions have to be fulfilled. The
width has to be specified in seconds.

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Figure 10-4. Generate events - absolute, see Figure 10-5 for the results

New Measurement - Rx1a - Tx1

8
7 C I C C I C C I C C I C
6
5
4
3
2
1
0
-1
0 15 30 45 60 75 90 105 120 135 150

Figure 10-5. Generated events with the parameters from Figure 10-4 (events C, where the data is
zero after the peak) and Figure 10-6 (events I, used to find only slopes with a steep slope).

Time offset
This adds a time offset to the event, it shifts the events forward in time. The
offset has to be specified in seconds.

Inhibit period
This defines the shortest possible time allowed between two events. The
period has to be defined in seconds.

Time between pre and post

This defines the time between end of pre and start of post in seconds.

128
 Figure 10-6. Generate events - relative

10.1.4.2 Relative
The relative mode looks to the slopes one of a trace. An event will be added
if the trace has a certain slope defined in the window as shown in Figure
10-6. Most properties are equal to the absolute mode, with exception of
“First derivate value window (unit/s)”.

First derivate value window (unit/s)

This defines the minimum and maximum value of the slope. The slope of
the trace has to be between these values to add an event.

The event properties can be shown by right clicking on the event in the
graph and selection of “Event properties”. It is only possible to see the
properties of events inserted after the measurement, because those can
be changed. To see properties of all the events, open the event list.

A list of the inserted events inserted to a measurement can be shown by

selection of the measurement, Menu  Analysis  Event list (Figure 10-7).
The information can be copied to the clipboard by clicking on “Copy to
Clipboard”. Adjusting the time, the event label and the description is

129
possible by typing in this window, but after closing the event list, the
adjusted information is not saved.

Figure 10-7. Event list

Figure 10-8. Remove an event

After the measurement change inserted events by right-mouse clicking on

the event and select the event properties. By selecting the event in the
graph, the event can be moved. Events generated/inserted during the
measurement cannot be moved. Remove the event and insert a
substituting event. Events can be removed during measuring by right-
mouse clicking at the event and selection of “remove event”. Figure 10-8 will
come up, click “Yes” to remove the event, click “No” to keep the event.

Take care: if an event is removed which was inserted during the

measurement, the event is removed definitely from the data file.

A period (or two) can be selected and used for calculation during an online
measurement or after each measurement or to make a spectrum graph
over a specified period. For a calculation, a period A can be used to define
the start and end of the calculation period (see paragraph 10.4). For the
compare function, also select a period B. After the measurement: use the
periods (period A) to make a spectrum graph over that period. Define the
periods by:

130
 - start of period A: Press or Menu  Analysis  Set start of period A.
- end of period A: Press or Menu  Analysis  Set end of period A.
- start of period B: Press or Menu  Analysis  Set start of period .B
- end of period B: Press or Menu  Analysis  Set end of period B.
Show/hide the period by pressing or Menu  Analysis  Show period.

The periods can be moved in the graph clicking at the middle of the grey
area (Figure 10-9) and drag the area to the desired time coordinate. It can
be enlarged or decreased by clicking at the start or end of the grey area
and drag the start or end of the area to the desired time coordinate. The
periods are not saved or transformed to events.

Blood flow measurement 2 - Rx1b - Tx2

8
B Grey area
4

-4

-8

-12
. 65 67 69 71 73 75 77 79 81 83 85 87 89 91 93

Period

Figure 10-9. Periods

Cyclic operators can be applied to a trace when analyzing for example a

periodic or repetitive task defined by events or time coordinates in the
software. An example is given in Figure 10-10.

To change the cyclic operator of a trace, select the trace and open the trace
properties (paragraph 9.4.3). Open the tab “Transformation A” and click on
“cyclic operator” (Figure 10-11). Choose an appropriate operator. The result
is equal if the operator is applied before, during or after a measurement.
However, during the measurement the trace is shown without the cyclic
operator. To remove the cyclic operator, select “No operation” as cyclic
operator.

The cyclic operators are:

- Cyclic: The operator will represent all cyclic traces from the selected
periods at once on a common scale according to the defined start and
end events/time coordinates.
- Detrend: the offsets of the cyclic traces will all be biased according to its
average value in the selected time window (defined in the detrend
period entry below).
- Front: selects the time window for bias in the front of the trace.
- Center: selects the time window for bias in the center of the trace.

131
- Average: the average of the cyclic traces will be displayed as one trace.
- SD: the standard deviation of the average trace will be displayed, in
another brighter color than the average trace.
And all combinations of these options.

First use only cyclic operators without averaging, look into the graph and
make sure the right cyclic periods and number of traces are present.

Cyclic mov ement - Concentrations

250

200

150

100

50

0
tHb
-50
HHb
-100 O2Hb

a. 0 15 30 45 60 75 90 105 120 135 150 165 180 195 210 225 240

Cyclic mov ement - Cyclic concentrations

250
200

150
100

50
0
tHb
-50
HHb
-100 O2Hb

b. 0 10 20 30 40 50 60
Figure 10-10. Example of cyclic measurements. a. measured concentrations (green tHb, red
O2Hb, blue HHb). b. Cyclic average of the measured concentrations with cyclic period is “60”
seconds, cyclic offset “0” and operator “cyclic average”.

132
Detrend front period (sec)
This defines the window in seconds if the “detrend front cyclic operator” is
selected.

Cyclic offset (sec)

This defines the time offset in seconds. It can only be used with a “time
coordinate” input in the cyclic period. For example, use “5” if the events are
known to be generated 5 seconds before the actual task start.

Cyclic period (sec)

This defines the duration of the cyclic period. The duration is defined in
seconds (10, 20, 60) and/or by events as a start and end of the cyclic period
separated by a comma: “,”. The events defining the period can be filled in
as:
- A unique event label: “A1”, “B2”, etc. The period will start or end at event
“A1” or “B2”.
- An event label: “A”, “B”, etc. including all events, which are present with
that label: “A1”, “A2”, etc. The periods will start or end at events A or B.
In this way, more periods can be defined at once.
- The general code: ‘*’ instead of an event label, which will select any
existing event fulfilling the criteria.
- A combination of time and event labels: “A+10”, “B-10”, etc. The period
will start 10 seconds after event A1 and end 10 seconds before event
B1. Warning: “10+A” does not work.
- The code “<” smaller than and “>” bigger than: “A>100”, “B<500”. The
periods will only start with events A after 100 seconds and end with
events B before 500 seconds.
- The code “|” OR: “A1|A3”. The period will start or end at A1 and A3. The
input “A1|A3>100” is actually “(A1|A3)>100”; if A1 or A3 is at least 100
seconds since the start of the measurement, it is used as start/end of
the period.
- The “!” operator subtracts the given set from the set containing all
events. For example: !U2 takes all events except U2 or !U2 & !U4 takes
all events except U2 and U4 Note the equivalent is !(U2|U4).

133
Figure 10-11. Trace properties – transformation A

Figure 10-12. Trace properties – transformation A

134
Oxysoft can apply several calculations to the data over a certain period or
more periods by the calculation function or by applying a cyclic operator to
the trace (paragraph 10.3). To open the calculation function, go to Menu 
Analysis  Calculate (Figure 10-13) press in the toolbar or use the
shortcut <F5>. Select a trace, a start and end of the calculation period, a
function and a channel to perform a measurement. After this, press
“Calculate”.

Trace
Add the trace to which the calculations have to be applied. It is not possible
to use traces from indicator views. Press the button and click in the project
view on the trace or drag-and-drop a trace from a graph. Select to apply
the calculation to the trace itself or the graph or traces in all opened graphs
of the measurement belonging to the selected trace in the field under
“Channel”.

Figure 10-13. Calculation.

Start and End

These define the start and end of the calculation period. Selection of a
period in a graph will fill in those fields automatically. Manually, the start
and end have to be specified in the fields as:
- Time: “1”, “10”, etc. The period will start or end at 1 or 10 seconds.
- An event label: “A1”, “B2”, etc. The period will start or end at event “A1”
or “B2”.

135
- An event label: “A”, “B”, etc. including all events, which are present with
that label (“A1”, “A2”, etc.). The periods will start or end at events A or B.
In this way, more periods can be defined at once.
- The general code: ‘*’ instead of an event label, which will select any
existing event fulfilling the criteria.
- A combination of time and event labels: “A+10”, “B-10”, etc. The period
will start or end 10 seconds after event A1 or 10 seconds before event
B1. Warning: “10+A” does not work.
- The code “<” smaller than and “>” bigger than: “A>100”, “B<500”. The
periods will only start or end with events A after 100 seconds or events
B before 500 seconds.
- The code “|” OR: “A1|A3”. The period will start or end at A1 and A3. The
input “A1|A3>100” is actual “(A1|A3)>100”; if A1 or A3 is after 100
seconds since the start of the measurement, it is used as start/end of
the period.
- The “!” operator subtracts the given set from the set containing all
events. For example: !U2 takes all events except U2 or !U2 & !U4 takes
all events except U2 and U4 Note the equivalent is !(U2|U4).

Select trace B
For the function “Compare” two traces are required or two periods of the
same trace. Press the button and click in the project view on the trace or
drag-and-drop a trace to the button. Define the start and end by using
period B or time and/or seconds like described at “Start and end”.

Function
The functions are the calculations, which can be applied to the data. The
functions are:
- Average: calculates average and standard deviation
- MinMax: calculates the minimum, maximum and the range (maximum
minus minimum).
- Average & MinMax: combination of Average and MinMax.
- Compare: compares two traces (or two periods of the same trace)
giving averages, standard deviations and the t-value of a student 2-
tailed paired t-test with the probability (prob) and alpha = 5%.
- Correlation: Select trace 1 and time period and choose trace 2, to value
calculate correlation with on same time period using Pearson
2
regression. Results are goodness of fit value: R , and it linear prediction
values with intercept and slope. The slope is the measure of
correlation.
- Regression: applies a linear regression to the data (y= a+bt). Results are
a, b, and r^2: a is the offset, b the slope and r^2 the fit quality ([0...1], 1
is a perfect linearity).
- Loglinear regression: applies a logarithmic linear regression to the data
(log10(y)=a+bt). Results are a, b, and r^2: a is the offset, b the slope and
r^2 the fit quality ([0...1], 1 is a perfect logarithmic linearity).
- VO2: volume consumed Oxygen, used for occlusion analysis; calculated
as the change of [O2Hb], [HHb] and [tHb] over time; “b” means the
slope from a regression fit (see regression). Both traces of O2Hb and

136
 HHb are needed for this (function cannot be used on ‘trace only’) so it
can also calculate a reliability factor according to RF= 100% * (1-abs(
b(tHb)/b(O2Hb) ) ). Note this function calculates the slope needed to
calculate VO2, not VO2 itself. More information about VO2 is found in
the thesis of Dr. M. van Beekvelt.
- Area: area under the trace. The area under the trace of a venous
occlusion is this equal to the blood flow (see chapter 4), arterial should
have no blood flow. Carefully notice is needed with biased traces.
- Graph data: no calculation, this gives the graph data in the specified
period.
- Harmonized graph data: resamples the specified period to your wishes.

If the function “compare” gives "0" as result, please make sure to open the
graphs, select the trace, drag-and-drop it to the correct button under
“Trace”. Both of the two buttons need to be updated with the correct
traces.

Channel
The calculations can be applied to more traces by specifying this field:
- Selected trace only.
- Selected graph only: the graph containing the selected trace.
- All opened graphs, non-cyclic traces.
- All opened graphs, cyclic traces only.
- All opened graphs.

Type
If the option “selected trace only” is not selected, this field is enabled. The
type data, which can be used for calculation, is specified here.

Calculate
Press to calculate. After finishing a calculation, just choose a new function,
trace or period and click on “calculate” to do a new calculation. If you have
selected “output to MS Excel file” it will write the output in the selected
sheet.

Save settings
Press to save the settings. The calculation is saved and can be reopened by
clicking in the project field on the calculation indicated with this icon .
The result of the calculation will be shown if the button “Calculate” is
pressed.

Copy to clipboard
This copies the result to the clipboard, which can be pasted in other
programs.

Output to MS Excel file

Check this to copy the output automatically to a MS Excel file. The file is
specified at the tab “MS Excel”. This option is only available if MS Excel is
installed to the computer! It writes the results to Excel when you press

137
 “Calculate”. Never have the Excel file already open. If an error comes up,
usually the amount of data is too big for the MS Excel program, or that the
file used to export to is already opened in MS Excel or by another program.

10.4.1.1 Format
This tab specifies the lay-out of the calculation results (Figure 10-14).

Figure 10-14. Calculation – Format

Figure 10-15. Calculation – MS Excel

10.4.1.2 MS Excel
This tab specifies the MS Excel file where the calculation results are saved
(Figure 10-15). This is only possible if MS Excel is installed to the computer
and the Excel file is not opened!

File
MS Excel file and location

Sheet
Sheet of the MS Excel file

138
On top of sheet/append to sheet
If the sheet already contains information, this information will be
overwritten by the calculation results if the first option is chosen. The
second option appends the data to the sheet.

Apply filters to reduce undesired parts of measured data, like noise or

trends. Oxysoft offers the possibility to filter data during and after the
measurement. Read this chapter carefully before application of any filter.
To become acquainted with the effect of filtering we advise to first do trials
measurement and to try several filters and cut-off frequencies by trial and
error.

Two main types of filters are available:

- Moving average filters can be applied to smoothen data measured with
a high frequency. The filter parameter is the filter width.
- FIR (Finite Impulse Response) filters attenuate specific frequency
components of the data. Which frequencies are present in the data can
be shown by making a spectrum graph (paragraph 9.3.5). The filter
parameters are the cut-off frequencies.

To add a filter to one trace, select the trace and open the trace properties
(paragraph 9.4.3). Open the tab “Transformation A” and click on “filter”.
Choose an appropriate filter. Fill in the filter width (seconds) or the cut-off
frequencies (Hertz). Click at “OK”. The program filters the data now. The
result of a filter is equal if the data is filtered before, during or after a
measurement. Filtering after measuring has as advantage that the effect of
the filter to the measured data will be clear. Applying a filter to a trace
before the measurement shows the result immediately.

To remove a filter from a trace, select the trace and open the trace
properties (paragraph 9.4.3). Open the tab “Transformation A” and click on
“filter”. Select “No filter” at “Filter”. Click at “OK” and the trace will be
unfiltered.

To add a filter to all traces of a measurement, right click on the

measurement in the project view and select “Common graph properties”.
Open the tab “Filter/transform”. Choose an appropriate filter. Fill in the filter

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 width or the cut-off frequencies. Check if “Modify” is selected for the filter
type and the filter width/cut-off frequencies. Click at “OK”. The program
filters all data of the measurement.

To remove a filter of all traces of a measurement, right click on the

measurement in the project view and select “Common graph properties”.
Open the tab “Filter/transform”. Select “No filter” at “Filter”. Click at “OK” and
the data of the measurement will be unfiltered.

10.5.6.1 Moving average

A moving average filter is a generic smoothing filter to reduce high
frequency noise. The filter width n has to be specified in seconds. The
moving average filter calculates the unweighted mean of the measured
data over the filter width from sample i-n/2 to sample i+n/2 (Figure 10-16).
As a result, the first n/2 and last n/2 seconds of data are lacking.
Gain Amplification H(f)

i t
n
Figure 10-16. Moving average filter with filter width (n) over time (t).

Figure 10-17. Measured O2Hb concentration (red) and filtered O2Hb concentration filtered by a
moving average filter with 0.3 seconds filter width (black).

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 Figure 10-18. Measured O2Hb concentration (red) and O2Hb concentration over time filtered by
a moving average filter with 10 seconds filter width (black).

Examples: to analyze the O2Hb concentration, it is possible to reduce the

high frequency noise from the O2Hb concentration by using the moving
average filter with a filter width of 0.3 seconds (Figure 10-17). If the interest
is the behavior of the O2Hb over time: reduced the pulse and the high
frequency noise at once by using the moving average filter with a filter
width of 10 seconds (Figure 10-18).

10.5.6.2 Moving Gaussian

The moving Gaussian (average) filter is also a generic smoothing filter to
reduce high frequency noise. The filter width n is specified in seconds. It
calculates the mean of measured data with a Gaussian filter window (Figure
10-19). The filter width n relates to the full width half maximum (FWHM) of
the Gaussian shaped peak by

1 FWHM
n , where fs is the sample frequency.
f s 2 2 ln( 2)

The advantage of the Moving Gaussian average filter compared to the

moving average filter is the weighted mean instead of the unweighted
mean, which gives a smoother result. Samples nearby the center of the
window have a larger weight in the calculation then samples further away
from the center. The disadvantage is that the Gaussian filter window is
wider in comparison to the moving average filter window; more samples
will be lacking at the beginning and the end of the trace.

Example: Figure 10-20 is the same as Figure 10-18, but the O2Hb
concentration is filtered with Moving Gaussian with a 0.3 s filter width
(blue). This filter result is much smoother compared to the filter result of
the moving average with the same filter width (black). Increasing the filter
width of the moving average still gives a less smooth result (green, filter
width is 0.8 s) compared to the Gaussian filter result, while the amplitudes
are equal.

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 Gain Amplification H(f)

i t
n
Figure 10-19. Moving Gaussian average filter with a Gaussian window with filter width (n) over
time (t).

Figure 10-20. measured O2Hb concentration (red), O2Hb concentration filtered by a moving
average filter with 0.3 seconds filter width (black), filtered by a moving Gaussian filter with 0.3
seconds filter width (blue) and filtered with a moving average filter width 0.8 seconds filter width
(green).

The low pass, high pass, band pass and band stop filters are filters which
attenuate a certain frequency component of the signal. The filters
parameters are estimated by the Parks-McClellan algorithm for FIR (Finite
Impulse Response) filter design. FIR filter designs need a certain amount of
samples for good characteristics, and this may result in "lack of data points"
in the beginning and end of the trace result. FIR filters are described by the
filter type, the gain, the band pass ripple, the transition band and the cut-
off frequencies. The cut-off frequencies are limited at 1/100 of the used
sample rate. If the cut-off frequency is too low, the error shown in Figure
10-21 will come up. If the cut-off frequency limit is reached, you can try to
downsample the data via the export function and use this downsampled
data for a lower cut-off frequency.

Figure 10-21. Search for filter parameters did not converge.

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 Which frequencies are present in the data can be shown by making a
spectrum graph (paragraph 9.3.5).

10.5.7.1 Low pass filter

Use a low pass filter to attenuate high frequency noise. The filter passes
through the low frequencies lower than the specified cut-off frequency, but
attenuates frequencies higher than the cut-off frequency. The cut-off
frequency (Lo. Freq) has to be specified in Hertz (Hz). The filter
characteristics (Figure 10-22) for attenuation is 30 dB, the band pass ripple
is 1 dB and the transition band is Lo Freq/4 Hz. The filter has a similar result
as the moving (Gaussian) average, but is more sophisticated. A moving
average filter is a simple form of a FIR filter. FIR filter designs need enough
samples for good characteristics, which result in "lack of data points" in the
beginning and end of the trace. This is more with a similar smoothing using
a moving average filter.

10.5.7.2 High pass filter

Use the high pass filter to attenuate slow changes of the measured data,
like trends or slow variations in data. The filter lets high frequencies pass,
but attenuates frequencies lower than the cutoff frequency. The high
frequency (Hi Freq) is the cutoff frequency in Hertz (Hz). The filter
characteristics (Figure 10-23) for the attenuation is 30 dB, the band pass
ripple is 1 dB and the transition band is Lo Freq/4 Hz. FIR filter designs need
enough samples for good characteristics, and this may result in "lack of
data points" in the beginning and end of the trace result. Cut-off frequency
is limited to 1/100 of the sample rate.

0
Gain [dB] 

-30

fL
fL/4

Figure 10-22. Low pass filter characteristics: attenuation is 30dB, band pass ripple is 1 dB and
transition band is Lo Freq/4 Hz

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 Gain [dB]  0

-30

fH
fH/4

Figure 10-23. High pass filter characteristics: attenuation is 30dB, band pass ripple is 1 dB and
transition band is Hi Freq/4 Hz

Figure 10-24. Measured O2Hb concentration (red) and high frequency O2Hb concentration
variations (black) filtered by a high pass filter, cut-off frequency =2 Hz

Example: To study the high frequency O2Hb concentration fluctuations, the

high pass filter with a cut-off frequency of 2 Hz. has reduced the slow
variations in the O2Hb concentration (Figure 10-24).

10.5.7.3 Band pass filter

Apply band pass filtering to attenuate both low and high frequencies. The
filter passes through frequencies inside the frequency band, but attenuates
frequencies outside the frequency band. The low cut-off frequency (Lo.
Freq.) and the high cut-off frequency (Hi. Freq) specify the frequency band.
The high cut-off frequency has to be larger than the low cut-off frequency.
The frequencies between these cut-off frequencies pass through. Band
pass filtering is a combination of low and high pass filtering. Figure 10-25
displays the filter characteristics. Notice that the cut-off frequency is limited
to 1/100 of the sample rate.

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 0

Gain [dB] 

-30

fL/4 fL fH fH/4

Figure 10-25. Band pass filter characteristics: attenuation is 30dB, band pass ripple is 1 dB, low
transition band is Lo Freq/4 Hz and high transition band is Hi Freq/4 Hz

Figure 10-26. Measured O2Hb concentration (red), O2Hb concentration without slow variations
(black) filtered by a high pass filter, cut-off frequency = 0.1 Hz, O2Hb concentration without slow
variations and high frequency noise (green) filtered by a band pass filter, low cut-off frequency =
0.1 Hz and high cut-off frequency= 0.9 Hz

Figure 10-27. Same as Figure 10-26, but enlarged.

Example: To reduce low frequent noise and high frequency noise of data, a
band pass filter is applied (Figure 10-26). The resulting data of the band
pass filter are the O2Hb concentrations fluctuations resulting from the
pulse. The picture is partly enlarged in Figure 10-27.

10.5.7.4 Band stop filter

Use band stop filtering to attenuate frequencies in a specified frequency
band. The filter passes frequencies outside the band, but attenuates
(reduces the amplitude of) frequencies inside the band. The band
frequencies have to be specified by a low cut-off frequency (Lo. Freq.) and a
high cut-off frequency (Hi. Freq). The high cut-off frequency has to be larger
than the low cut-off frequency. The amplitude of signals with frequencies
between these cut-off frequencies is reduced. The filter characteristics are
displayed in Figure 10-28. The attenuation is 30 dB, the band pass ripples
are 1 dB and the transition bands are Lo Freq/4 Hz and Hi Freq/4 Hz. FIR

145
 filter designs need a certain amount of samples for good characteristics,
and this may result in "lack of data points" in the beginning and end of the
trace result.

Example: To study the measured concentration without interest in the

pulse, a band-pass filter is applied (Figure 10-29), because the pulse is in a
frequency band.

0dB

-30dB

fL/4 fL fH fH/4

Figure 10-28. Band stop filter characteristics: The attenuation is 30dB, the band pass ripple is 1
dB, the low transition band is Lo Freq/4 Hz and the high transition band is Hi Freq/4 Hz

Figure 10-29. Measured O2Hb concentration (red), O2Hb concentration without fluctuations
resulting from the pulse (black) filtered by a band stop filter, low cut-off frequency = 0.1 Hz and
high cut-off frequency = 2 Hz.

10.5.7.5 RMS band pass filter

The RMS (Root Mean Square) Band pass filter describes the amplitude of a
signal by way of a band pass filter. The way of estimation of the amplitude is
comparable to estimation of the RMS or energy of a signal. The cut-off
frequencies specify the frequency band of the signal, which is used to
estimate the amplitude of the signal, and have to be specified by a low cut-
off frequency (Lo. Freq.) and a high cut-off frequency (Hi. Freq). The high
cut-off frequency has to be larger than the low cut-off frequency. The
frequencies between these cut-off frequencies are passed through. The

146
energy is equal to 1/2√2 * amplitude. The filter characteristics are equal to
a normal band pass filter, but with an extra application.

Example: An amplitude modified signal is shown in Figure 10-30 (blue). The

signal is RMS band pass filtered and results in a description of the
amplitude of the sinusoid (orange). This filter is handy for power estimation
of oxygenation changes resulting from a cyclic movement, like biking.

Figure 10-30. Amplitude modified sinus wave (blue), which is RMS band pass filtered (orange).

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This chapter gives information about the setup of optodes and optode
templates. The optode template describes the optode configuration.

Optode templates define the optode combination made by transmitter and

receiver optodes. The optode configuration, which is used during the
measurement, has to be specified in Oxysoft in the measurement
properties as optode template (paragraph 9.2.2). The optode templates are
essential to create the correct graphs and to calculate the concentrations
from optical densities.

The simplest optode template is the 1 channel, which consists of one

receiver (Rx) and one transmitter (Tx) (optode template: 1 channel). With
this 1 channel configuration, it is possible to measure concentrations at
one optode combination (Figure 11-1). It has one measurement point
(subtemplate) and one optode combination (channel). Each optode
template consists of one or more subtemplates; each can be used for a
different measurement location. A subtemplate is a part of the optode
template, which can have different source-detector distances and DPF.
Hence, one optode holder can be placed on a muscle and one can be
placed on the forehead with a 2 channel optode configuration.

Figure 11-1. 1 channel optode template and 4 channel square optode template using split
transmitter and receiver fibers. The square template is a used for mapping measurements.

Optode template “2x1 channel” is a two channel optode template with two
subtemplates and with each one channel. A 4 channel measurement can
be applied with four subtemplates (optode templates: 4x1 channel (split) I
and II), but also as a mapping measurement using one subtemplate
(optode templates: 4 channel cross and square). Mapping measurements
can be accomplished with two dimensional optode templates (see
paragraph 11.2.3 to 11.2.5) and can be displayed with a topo graph
(paragraph 9.3.4). Important for mapping measurements is an equal
source-detector distance between all transmitter and receiver optodes
forming an optode combination of the optode template.

The available optode templates in Oxysoft are shown in the measurement

properties at the tab “Optode template”. If a non-existent optode template
is needed, please contact Artinis. Artinis has several optode holders and
small elements to make special (flexible and rigid) designs.

How to connect optical fibers to the Oxymon and the optode holder is
described in the paragraph 8.2 and 8.3. Some examples of setups of
optode configurations are given in this chapter.

Figure 11-2. Schematic view of the setup of a 1 channel system with a one channel Oxymon
cabinet and the one channel optode configuration. Rx means receiver, Tx means transmitter. The
number “1” is the channel number.

The 1 channel system consists of one Oxymon cabinet with at least one
receiver and one transmitter as shown in Figure 11-2. The channel is
formed by the combination of the transmitter and the receiver optode. To
connect the optode holder to the Oxymon, two fibers are necessary: a
transmitter and receiver fiber. Connect both fibers to the Oxymon and
fixate the optodes in the optode holders. Measure the distance between
the optodes to determine the source-detector distance.

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Figure 11-3. Schematic view of the setup of a 2 channel system with a two channel Oxymon
cabinet and the two channel optode configuration. Rx means receiver, Tx means transmitter. The
number “1” and “2” are the channel numbers.

The 2 channel system consists of an Oxymon cabinet with at least one

receiver and two transmitters. The 2 channels are formed by the
combination of the two optodes of a split receiver fiber and the optodes a
two transmitter fibers (Figure 11-3). Put the receiver fiber in the Oxymon
and each optode of the receiver fiber in the optode holders. Screw both
transmitter fibers in the Oxymon and connect each to an optode holder.
Measure the distance between the optodes of both optode holders to
determine both source-detector distances.

Figure 11-4. Schematic view of the setup of a four channel square system with a four channel
Oxymon cabinet and the 4 channel optode configuration. Rx means receiver, Tx means
transmitter. The number 1-4 are the channel numbers.

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Table 11.1. The 4 channels will then be situated at the following receiver-transmitter pairs.

Tx1 Tx2
Rx1 1 2
Rx2 3 4

The 4 channel system consists of an Oxymon cabinet with at least two

receivers and two transmitters, or one receiver and four transmitters. A 4
channel can be used as four single measurement points (optode
templates: 4x1 channel (split) I and II), but also a mapping measurement
(optode templates: 4 channel cross and square). The given example is the 4
channel square. Use the measurement template “4 Channel square
mapping” to display the data.

The 4 channel square setup needs 2 receivers and 2 transmitters.

Transmitter 1 is combined with receiver 1 and receiver 2, forming two
channels. Also transmitter 2 is combined to these receivers, which gives in
total 4 channels. The optical fibers necessary for this optode configuration
are two unsplit transmitter fibers and two unsplit receiver fibers (Figure
11-4). The 4 channels will then be situated at the receiver-transmitter pairs
shown in Table 11.1.

The 8 channel system consists of a full Oxymon cabinet with two receivers
and four transmitters (Figure 11-5). All transmitter optodes are combined
with all receiver optodes, which makes in total 8 channels. In this setup the
receiver fibers are unsplit, the fibers of Tx1 and Tx2 are unsplit as well, and
the fibers of Tx3 and Tx4 are both split. The 8 channels will then be situated
at the receiver-transmitter pairs shown in Table 11.2. In terms of single
diodes and position in exported data files, the pairs are shown in Table
11.3. This optode template is called “8 channel split” in Oxysoft and can be
specified in the measurement properties.

Table 11.2. The 8 channels will then be situated at the following receiver-transmitter pairs.

Tx1 Tx2 Tx3a Tx3b Tx4a Tx4b

Rx1 3 4 2 1
Rx2 5 6 7 8

Table 11.3. The 8 channels will be filed the following way in terms of single diodes and position in
exported data files

Tx1 Tx2 Tx3 Tx4

Diode 1 2 3 4 5 6 7 8
nr
Rx1 1 (3) 2 (3) 3 (4) 4 (4) 5 (2) 6 (2) 7 (1) 8 (1)
Rx2 9 (5) 10 (5) 11 (6) 12 (6) 13 (7) 14 (7) 15 (8) 16 (8)

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Figure 11-5. Schematic view of the setup of an 8 channel system with an eight channel Oxymon
cabinet and an eight channel optode configuration. Rx means receiver, Tx means transmitter.
The number 1-8 are the channel numbers.

The 24 channel system consists of a 2 full Oxymon cabinets with each two
receivers and four transmitters (Figure 11-6). These cabinets have to
connect to each other as described in paragraph 6.2.2. The optode
configuration for the 24 channel setup is shown schematically in Figure
11-7. The fibers necessary for this setup are 8 unsplit transmitter fibers and
4 split receiver fibers. Take care that all fibers go to the right position on the
head setup. The 24 channels will then be situated at the receiver-
transmitter pairs shown in Table 11.4. In terms of single diodes and
position in exported data files, the pairs are shown in Table 11.5.

The 24 channel system is normally used for brain measurement. As a

practical tip for these measurements, try to remove as much hair as
possible by scratching through the hole of the optode holders before
connecting the fibers. Try to make sure there is some pressure, and thus a
good contact to the skin, of the fibers on the head. It can be handy to use
some sort of bandage around the head.

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Figure 11-6. 24 channel Oxymon cabinets with a master and a slave cabinet

Tx1 Rx2a
Rx1a 1 2 3
Tx2

4 5 6 7

8 9 10
Tx3 Rx4a
Tx4
Rx3a

11 12 13 14

15 16 17
Tx6
Rx4b
Tx5 Rx1b
18 19 20 21

22 23 24

Rx3b
Tx7 Rx2b Tx8
Figure 11-7. Schematic view of a 24 channel optode configuration. Rx means receiver, Tx means
transmitter. The number 1-24 are the channel numbers.

Table 11.4. The 24 channels will be filed with the following optode combinations

Tx1 Tx2 Tx3 Tx4 Tx5 Tx6 Tx7 Tx8

Rx1a 1 4
Rx1b 13 16 17 20
Rx2a 2 3 6
Rx2b 19 22 23
Rx3a 5 8 9 12
Rx3b 21 24
Rx4a 7 10 14
Rx4b 11 15 18

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Table 11.5. The 24 channels will be filed in terms of single diodes and position in data files as
shown in this table

Tx1 Tx2 Tx3 Tx4

Diode 1 2 3 4 5 6 7 8
Rx1 1 (1) 2 (1) 3 (-) 4 (-) 5 (4) 6 (4) 7 (13) 8 (13)
Rx2 17 (2) 18 (2) 19 (3) 20 (3) 21 (-) 22 (-) 23 (6) 24 (6)
Rx3 33 (5) 34 (5) 35 (-) 36 (-) 37 (8) 38 (8) 39 (9) 40 (9)
Rx4 49 (-) 50 (-) 51 (7) 52 (7) 53 54 55 56
(11) (11) (10) (10)

Tx5 Tx6 Tx7 Tx8

Diode 9 10 11 12 13 14 15 16
Rx1 9 (16) 10 11 12 13 (-) 14 (-) 15 16
(16) (17) (17) (20) (20)
Rx2 25 26 27 (-) 28 (-) 29 30 31 32
(19) (19) (22) (22) (23) (23)
Rx3 41 42 43 44 45 (-) 46 (-) 47 48
(12) (12) (21) (21) (24) (24)
Rx4 57 58 59 60 61 62 63 (-) 64 (-)
(15) (15) (14) (14) (18) (18)

The channels have the following positions:

Channel 1: 1 – 2 Channel 13: 7 – 8
Channel 2: 17 – 18 Channel 14: 59 – 60
Channel 3: 19 – 20 Channel 15: 57 – 58
Channel 4: 5 – 6 Channel 16: 9 – 10
Channel 5: 33 – 34 Channel 17: 11 – 12
Channel 6: 23 – 24 Channel 18: 61 – 62
Channel 7: 51 – 51 Channel 19: 25 – 26
Channel 8: 37 – 38 Channel 20: 15 – 16
Channel 9: 39 – 40 Channel 21: 43 – 44
Channel 10: 55 – 56 Channel 22: 13 – 14
Channel 11: 53 – 54 Channel 23: 31 – 32
Channel 12: 41 – 42 Channel 24: 47 – 48

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This chapter will help to set up a measurement for tissue saturation index (TSI)
in Oxysoft. Note that you need special TSI equipment for the Oxymon.

From the modified Lambert-Beer (MLB) law, values for concentration

changes of oxygenated and deoxygenated hemoglobin can be obtained.
Absolute concentrations can be obtained by using a different method:
spatial resolved spectroscopy (SRS). In SRS, the intensity of the light
reflected from the transmitter is measured as a function of the distance
from the transmitter. The shape of this function is related to the absorption
coefficient (μa) of the tissue, from which the absolute hemoglobin
concentrations [µM] and the tissue saturation index [%] can be calculated.

Figure 12-1. Schematic view of a TSI measurement: light through tissue with three transmitters,
rho, ua, us and absorbers

The propagation of photons in a highly scattering medium, like tissue, can

be approximated by the photon diffusion theory [Patterson et al. 1989].
The intensity of the light detected by a receiver is a function of the source-
detector distance and the absorption and scattering coefficient of the
tissue. The slope of the measured light attenuation versus source-detector
distance (𝛿OD/𝛿d) can be determined using at least two transmitters (see
Figure 12-1). From the slope, the absorption coefficient can be calculated.
The two main assumptions in this theory are that the measurement is
performed on homogeneous tissue and that the wavelength dependent
scattering coefficient of the tissue is constant during the measurement.

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The most significant absorbers in tissue that determine the absorption
coefficient are oxyhemoglobin, deoxyhemoglobin and water. The amount
of water in tissue is assumed to be constant and its value can be set in
Oxysoft. The correction for absorption due to water is as follows:

𝜇𝑎 () − 𝜀𝐻2𝑂 () 𝑐𝐻2𝑂 = 𝜀𝑂2𝐻𝑏 ()𝑐𝑂2𝐻𝑏 + 𝜀𝐻𝐻𝑏 ()𝑐𝐻𝐻𝑏

where 𝑐𝐻2𝑂 , 𝑐𝑂2𝐻𝑏 and 𝑐𝐻𝐻𝑏 are the absolute concentrations of water,
oxyhemoglobin and deoxyhemoglobin respectively. 𝜀𝐻2𝑂 (), 𝜀𝑂2𝐻𝑏 () and
𝜀𝐻𝐻𝑏 () are the extinction coefficients of water and the different types of
hemoglobin at the Oxymon wavelengths. Using two different wavelengths
enables you to distinguish between the oxygenated and deoxygenated
forms of hemoglobin. The tissue saturation index is an estimate of the
oxygen saturation of the tissue (StO2) and is defined as:

𝑐𝑂2𝐻𝑏 𝑐𝑂2𝐻𝑏
TSI [%] = × 100% = × 100%
𝑐𝑡𝐻𝑏 𝑐𝑂2𝐻𝑏 + 𝑐𝐻𝐻𝑏

In the calculation of the TSI, the scattering coefficient of the tissue is

needed. The reduced scattering coefficient 𝜇𝑠 is related to the distance that
the photons travel before being scattered. In tissue, 𝜇𝑠 is found to scale
linearly with the applied wavelength. The scattering coefficient is defined as
𝜇𝑠 = 𝑘(1 − ℎ 𝜆) and is measured on various kind of tissue by several
research groups. The values of 𝑘 and ℎ found by Matcher et al. (1997) are
given in Table 12.1. In Oxysoft, the scattering coefficient is approximated as
being constant over time and the values of 𝑘 and ℎ can be set.

Table 12.1. Example of scattering coefficient for three tissue types found by Matcher et al. (1997).

-1 -1
Tissue type 𝒌 [mm ] 𝒉 [nm ]
Forearm 1.1 4.6 ∙ 10−4
Head 1.45 4.5 ∙ 10−4
Calf 1.63 5.5 ∙ 10−4

The following parameters are needed in a TSI measurement and can be set
in Oxysoft in the optode template tab in the measurement properties
screen:

d – the average distance between transmitters and the detector

in the optode holder
delta d – the distance between two subsequent transmitters
𝑘 and – these constants determine the scattering coefficient
ℎ 𝜇𝑠 = 𝑘(1 − ℎ 𝜆). Predefined values as well as user defined
values can be used.
H 2O – assumed percentage of H2O in tissue. Disable if no correction
for light absorption due to water should be applied.

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Note that the DPF is not needed in the calculation of the TSI, but the DPF is
needed in the calculation of the concentration changes, so always set this
value as well.

Figure 12-2. Screenshot of tab Optode Template in measurement properties where all
parameters can be set.

The TSI is typically 60-80% in muscle tissue under normal conditions. Note
that the TSI theory will only be valid under certain conditions. Furthermore,
the Oxymon is assumed to be properly calibrated under the conditions it
will be used during measurement (power level, gain settings and fibers).
When the calculated TSI percentage is negative or larger than 100, it is
truncated to [0,100]. In that case the measurement does not fit into the
mathematical model.

A one channel TSI measurement can be performed by using two or three

transmitters in combination with one detector. A three channel
measurement provides you with an additional value: the TSI Fit factor. The
TSI Fit factor is determined by how well the measurement values fit the
theory and is a measure for the quality of your TSI measurement.
The TSI Fit factor can be increased by covering the optode during data
acquisition and by placing the optode on homogeneous tissue (e.g. no
moles). A TSI Fit factor of 100% means a perfect fit and TSI Fit factor of 99%
or higher will give you a good TSI measurement. Due to physiological
changes during exercise, this value may change during the measurement.
To set up a measurement with a TSI Fit Factor, use an optode template with
‘TSI Fit Factor’ in its name, like ‘1 channel TSI with error’.

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The TSI can be measured with an Oxymon containing at least two (we
advise three) transmitters and a special TSI optode holder with small fibers.
Figure 12-3 shows the special TSI optode holder. The average source-
detector distance can be adjusted from 3.5 to 5 cm. The shortest distances
are recommended for a TSI measurement.
The optode holder has a top plate which fixates the transmitting optical
fibers. It can be unscrewed if the fibers need to be replaced or changed to
a deeper/higher position. The position of the optode ends can be changed
to a deeper or higher position by replacing the small plate under or over
the optodes.

Tx3 Tx2 Tx1 top plate pin holes Rx

I I I

Figure 12-3. Top and bottom view of TSI optode holder.

The Oxymon has to be calibrated before measuring the TSI. Make sure the
system is calibrated (paragraph 8.9) and do a “System calibration” of the
device if needed. Besides the Oxymon calibration, also a TSI calibration is
necessary. The TSI calibration is preferably performed before every
experiment. When the fibers are re-attached to the machine or any other
condition has changed which will affect the relative light transmission
between Tx1, Tx2 (and Tx3), a new TSI calibration must be done.

1. In this paragraph is described how to perform a TSI calibration. The TSI

calibration basket (Figure 12-4) is used to calibrate the Oxymon. It can
also be used to investigate/compare the light transmission of both
transmitting and receiving optical fibers. Please keep the glass window
clean and intact; preferably cover it when not in use.
2. Turn the Oxymon on and wait for at least 20 minutes.
3. Connect the optical fibers to the Oxymon and connect the transmitter
fibers to the TSI optode holder. Place the receiver optical fiber in the
hole of the calibration tool and tighten with the screw if necessary

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4. Make sure the transmitter fibers are connected to the TSI holder in the
right order:
a. If you have three transmitter fibers, connect Tx1 to the hole
closest to the hinge of the optode holder, Tx2 to the next and
Tx3 to the last.
b. If you have two transmitter fibers, you can choose where to
connect the fibers, but always connect Tx1 closer to the hinge
of the optode holder than Tx2.
Place the holder at the top of the basket (Figure 12-5)
5. When a TSI measurement with split TSI fibers is performed, cover the
transmitting optodes which are not being calibrated with a black cloth.
6. Start Oxysoft, create a new measurement and set the device open for
data acquisition without turning on the lasers (do not start the
measurement).
7. Choose the optode template which will be used during the
measurement in the “Optode Template” tab of the “Measurement
properties” screen.
8. Special optode templates are designed for TSI measurements. For TSI
measurement with two transmitters in one holder select a template
with only “TSI” in its name and for TSI measurement with three
transmitters in one holder select a template with “TSI Fit Factor” in its
name.
9. It is recommended to pre-set the device settings that are going to be
used during measurement, such as the laser output levels and sample
rate. For a high signal to noise ratio, standard laser power and a low
sample rate (1 Hz) are recommend.
10. Start the TSI calibration via Menu  Data Collection  TSI Calibration
and follow the steps of the calibration procedure.

Figure 12-4. TSI calibration basket with mounted optical fibers

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Figure 12-5. Top view of the calibration basket with TSI optode holder in position

The following steps should be followed when doing a TSI measurement.

The Oxymon should be started at least 20 minutes before performing a
calibration or measurement.

1. Make sure the Oxymon is calibrated and do an “Oxymon calibration” if

needed. An Oxymon standard calibration is needed once a year. With
this calibration the normal fibers should be used and not the special
TSI transmitter fibers. This calibration should be performed before TSI
calibration.
2. Prepare the system for a TSI calibration by opening the data collection
in the “Measurement properties” screen. Choose the right TSI optode
template in the “Optode Template” tab and set the sample frequency
and power output in the “Device Settings” tab. The TSI parameters in
the “Optode Template” tab can be set as well.
3. Perform a “TSI Calibration”.
4. In the measurement folder, create the graphs and traces that you want
to see during your measurement. With your TSI setup you will be able
to plot the TSI and absolute concentrations, besides the concentrations
changes calculated from the MLB theory (see difference MLB and SRS
in Table 12.2). It is recommended to have a tracing or indicator of the
TSI (and TSI Fit Factor) available for each TSI channel, so that a check for
reasonable values can be done during the measurement. For a more
stable TSI fit factor indicator, choose a low sample rate and/or apply
averaging or filtering on the TSI trace.
5. Connect the receiver fiber to the TSI optode holder at the distance that
was set in the “Measurement properties” screen. Attach the TSI holder
with the fibers to the tissue. Assure good optode-skin contact, to avoid
motion artifacts during the measurement.
6. Check if proper light intensities are received on all channels.
7. Start the measurement. Note that it is recommended to keep the gain
and power settings during the measurement the same as the settings
that were used during the TSI calibration.

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 Table 12.2. Overview of MLB and SRS theories

Theory: Modified Lambert-Beer (MLB) Spatial resolved spectroscopy (SRS)*

Optodes: Combination of 1 Rx and 1 Tx Combination of 1 Rx and 2 Tx** or 1 Rx and 3 Tx

Measures: Hemoglobin concentration changes TSI, TSI Fit Factor and absolute hemoglobin
concentrations
Parameter Known: 𝜀𝑂2𝐻𝑏 , 𝜀𝐻𝐻𝑏 and d 𝜀𝑂2𝐻𝑏 , 𝜀𝐻𝐻𝑏 , d and Δd
s: Assumed: DPF 𝜇𝑠 () (ℎ and 𝑘) and 𝑐𝐻2𝑂
Channel selection for Select circle: Select square:
plotting: Example: Rx1 – Tx1 Example: Rx1 – Tx1, Tx2, Tx3

Measurement example Graph 1 (biased at start) Graph 1 – 3 calculated from the MLB law, graph 4
(Figure 12-6) and 5 calculated from the SRS theory

* Note that a TSI measurement will also provide you with the relative
concentrations calculated by the MLB theory as one TSI channel forms 2 or 3
normal channels. Therefore the DPF should also be set for TSI measurements.
** A TSI channel combination of 1 Rx and 2 Tx does not have the Fit Factor option

Figure 12-6. Measurement example: arterial occlusion

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1. What is Near InfraRed Spectroscopy (NIRS) based on?
NIRS is based on absorption of light by certain chromophores. When NIRS
is used on tissue the main absorbing chromophores are hemoglobin and
myoglobin. Both these chromophores have similar absorption spectra and
cannot be distinguished using NIRS. However, most important for NIRS are
the changes in oxygen binding to these chromophores. Very often only
hemoglobin is used to refer to both chromophores, as also by us.
Hemoglobin mainly exists in two forms, oxy- and deoxyhemoglobin. The
NIRS device measures changes in light absorption and uses the modified
Lambert Beer law to calculate changes in hemoglobin concentrations. Our
NIRS devices also have the possibility to calculate absolute concentrations
using spatially resolved spectroscopy. For more information you are
referred to the manual.

2. What values can I get from NIRS?

Of course, to start with, the changes in concentration of oxy- and
deoxyhemoglobin. If you add these up you will have the change in
concentration of total hemoglobin. Total hemoglobin can be used to
calculate blood volume and flow if the concentration of hemoglobin in
blood is given. With the high sampling frequency of our devices you can
accurately measure response time. Standard on the PortaMon and as an
option on the Oxymon, Tissue Saturation Index (TSI) is possible. TSI gives
you an absolute percentage of oxygenated hemoglobin. It is also possible
to have different wavelength so you can measure other chromophores.

3. At what depth can I measure?

General assumption is made based on Monte Carlo models that the
measurement depth is roughly half the distance between the receiver and
transmitter optode. It mainly depends on the tissue, power settings and the
fibers (split/unsplit, length) what the maximum distance is for your setup.
With ideal fibers, the maximum separation distance is approximately 5.5
cm. For the PortaMon the maximum distance is 4 cm.

4. How long do I need to get the system to warm up?

It is advised for both the PortaMon and the Oxymon to have the light
sources on for at least two minutes before you start the actual experiment.
If you use Tissue Saturation Index (TSI) with the Oxymon we advise to wait
for at least 20 minutes before you do the absolute calibration.

5. When do I need to calibrate?

Both the Oxymon and the PortaMon are calibrated before they are
delivered. We suggest doing a recalibration each year. For the Oxymon you

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can do this yourself and are referred to the manual for further instructions.
The PortaMon can be calibrated by us, please contact us at
askforinfo@artinis.com. If you use Tissue Saturation Index (TSI) with the
Oxymon, we advise to do the absolute/TSI calibration each time you use a
TSI.

6. I cannot get my AD box to work.

Please make sure that the AD box is connected as it should be; connect the
Oxymon as a slave and the output box as a master with the Master-slave
cable. Both need to be in the third UTP port (from the left). Connect the
USB to the AD box. Please be aware that the master-slave cable has two
ends (one is marked ‘m’ which is the master-end). Please make sure to turn
both devices on at the same time.

7. What is the effect of using split optical fibers?

Sometimes fibers are ‘split’, meaning that they have to ends on one end of
the fiber. With this fiber one receiver or transmitter unit can measure at
two independent areas at the same time. Please do notice that these
endings do need to make different combinations with the other
transmitters/receivers. So the advantage of splitting fibers is that you can
have more channels without adding receivers or transmitters, the
disadvantage of splitting fibers is a small loss of light intensity, resulting in a
smaller maximum distance between receiver and transmitter.

8. Where can I find relevant literature?

There are a vast number of publications on Near Infrared Spectroscopy. In
paragraph 4.11 some references to general publications are given. On our
website we present some of the general literature on NIRS, on specific
applications and literature utilizing the Oxymon and wireless
(PortaMon&PortaLite) systems. Please visit us at
http://www.artinis.com/product/oxymetry_publications.

9. Which Windows version is required for Oxysoft installation?

Oxysoft 2.0.49 and higher can be used on Windows 7 and 8. If you use
software version 2.1.6 or lower you need to contact Artinis at
askforinfo@artinis.com for additional drivers for Windows 7 and 8. Oxysoft
3.0.53 and higher is supported on Windows 7 and 8.

10. What rights do I need to run the software?

For Oxysoft version 2.1.6 and before you need to be administrator and
have to run the program with administrator rights. To store calibration data
you need to have set the security of” C:\Program Files\Artinis Medical
Systems BV” to full control for all users (right click on the Artinis folder, go
to properties, go to the tab ‘security’. Click ‘edit’ and select ‘full control’ for
all users).

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11. My license key does not work and software does not work.
- Try another USB port
- Make sure you are using the right key/USB dongle.
- The key should be plugged in before program start up and during
usage.
- Run the RocKey driver installation scripts on the Oxysoft CD/USB

12. Where can I find the latest version of Oxysoft?

Contact Artinis at askforinfo@artinis.com. You do not have to uninstall
previous versions from the computer. You can still run any of the installed
versions and the same projects and program settings can be used.

13. I lost my license key. How can I get a new one?

You can order a new key for 250 Euro if you lost it the first time. The
second time we have to charge the price of a new license.

14. I have an error “MSFLXGRD.OCX not installed”

Contact Artinis at askforinfo@artinis.com for additional files.

15. My data now looks different when I open it in different Oxysoft

versions
The data may look different in different versions of OxySoft, due to new
possibilities for correction. All added possibilities can be turned off. Contact
Artinis at askforinfo@artinis.com if you cannot find the difference in
settings.

16. What is the red USB key dongle/device for?

It is a license key for the Oxysoft program, which is necessary to run the
software. It looks like a normal USB memory stick, but you cannot open it
or use it to store any data files.

17. I cannot enable for data acquisition or connect with the machine in
the software?
First try to restart the computer. If this does not work, try the following;
Oxymon: If the ‘create new measurement wizard’ is not available, probably
your FTDI drivers are not working correctly and need to be (re-)installed.
You can find this driver in C:\Program Files\Artinis Medical Systems
BV\Oxysoft. If you have an Oxysoft version 2.1.6 or older, you will need a
new FTDI driver for Windows 7. Contact Artinis at askforinfo@artinis.com
for more information.
PortaMon: Try to connect first via the Bluetooth software. If this does not
work, make sure the Bluetooth dongle is inserted, the PortaMon is on and
try to make a new connection in the Bluetooth software with the PortaMon
and use the new COM port for connection.

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18. My Bluetooth connection of the PortaMon is very poor and gets
disconnected.
You might be too far from the computer. It depends on the type of antenna
you are using. Standard antennas go up to 100 meter, but we have
antennas which can go up to 1 km in the open field. If you have obstacles
between the PortaMon and laptop the distance will be less. Contact Artinis
at askforinfo@artinis.com for more information. The most likely cause is by
using the wrong (internal) Bluetooth module. This can be checked by
connecting to the PortaMon. While you are doing data acquisition, you
disconnect the USB Bluetooth module. If Oxysoft hangs you are using the
correct module. Please contact Artinis for further assistance. If Oxysoft is
still measuring you are using the internal Bluetooth module. To disable this,
go to ‘my computer’, go to ‘system properties’ and click on ‘device manager’.
Search for the internal Bluetooth module and disable it.

19. I do not know or do not remember all the steps to start my

measurement.
Use the “DAQ measurement wizard” in the Project menu. Check the
Oxysoft paper on “Basic instructions how to use the software” and OxySoft
instruction videos to learn more.

20. Where can I find manuals and information about NIRS, Oxymon or
Oxysoft?
Check the software CD/USB from the delivery of your Oxymon. You will find
various instruction videos, manuals and application notes. If you cannot
find it, please contact us.

21. Which DPF value should I use?

Choose your DPF according to literature. The DPF can be changed in your
measurement properties, also after the data has been recorded. It will
adjust the graphical data representation of the concentration changes.
Some reference values can be found in the Oxymon manual (Table 4.2).

For brain applications we suggest to use the software calculation button,

DPF= 4.99 + 0.067(Age^0.814). This formula is valid for ages 17-50 and
derived from data of Duncan et al.: Duncan A, Meek J H, Clemence M, Elwell
C E, Fallon P, Tyszczuk L, Cope M, Delpy D T, 1996. Measurement of cranial
optical pathlength as a function of age using phase resolved near infrared
spectroscopy. Pediatr. Res. 39, 889–894.

22. I do not want to start recording every time I start the data-
acquisition.
You can change this default setting in the “View” menu, select “Options...”. In
the “DAQ”-tab there is a check-box where you can enable/disable the
option to “Start recording manually”.

165
23. I cannot get the calculation function “compare” to work, or I only get
“0”.
Please make sure to open the graphs, select the trace you want to study,
drag-and-drop it to the correct button under “Trace”. Both of the two
buttons need to be updated with the correct traces.

24. When and how is an event generated?

Immediately when you press F4, or any letter on the keyboard, or select
“Insert event now…” in the analysis menu. After this you still have time to
enter the description. You can also generate events with certain criteria's
“Generate events”. Events can always be added later for analysis.

25. How can I change my events?

If you first click on the event to make it highlighted, then right click and
select “Remove event…” or go to the “Event properties”. But if the events
have been generated during a measurement in Oxydaq version 2.0.49 or
higher, they cannot be changed or deleted. For analysis or correction you
can add new events over the “old” ones. To check the exact time
coordinates of “old” events, right click on the measurement item of interest
and select “Event list”.

26. How can I select my events for a cyclic operator?

Select cyclic operator in the properties of a trace, the box entry called
“Cyclic period (sec)” is where you define the events. Separate the starting
events from the ending events by using “,”. You can use “<”, “>” or “|”, to pick
events fulfilling a certain criteria. You can either use a general ID letter “A”
which will include all A events you have (can be A1, A2, A3… and so on), or
you can select an unique event directly (for example “A2”) or use “*” which
means any existing event. A tip to check is first use only cyclic operators
without averaging look at the graph and make sure the cyclic periods and
number of traces present are the ones you intended to select.

27. Can I do regression on multiple events?

To calculate the regression you will have to give in the start and end of the
part of the data you are interested in calculation menu (under Analysis).
You can do this by filling in the time (in seconds), but you can also do this
with events. You can give events during your measurements by pressing F4
or any letter on your keyboard, or afterwards by right clicking on the time
where you would like to have an event. Now, if you give each start of each
event the same letter (e.g. A), and each end the same letter (e.g. B) you can
use these letters to fill in, in the calculation screen. In this screen you can fill
in A and B for start and end respectively to calculate them all at the same
time. You can use A1 and B1 for example, if you only want to measure the
first one.

28. When should the traces be biased?

Biasing all traces once before the beginning of your experiment is usually
to prefer. Since we are always looking at relative changes the starting point

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of a concentration value will never matter, and the “Bias trace” or “Bias all
traces…” is only for your own convenience and graphical displaying during
the measurement or analysis. The “biasing” will never affect the real
recorded data and when you look at recorded data afterwards (off-line)
traces can be biased to any point (for example in the “Trace properties”).

29. How do I export data to excel?

There are two options to do this; 1) via the file menu and 2) via calculations.
If you get an error, usually your amount of data is too big for your excel
program, or the file you are working with is already opened in excel or by
another program. 1) First make sure that you have created a measurement
with a data-file attached in the properties. By using export in the file menu,
you can export all OD values, AD voltages, raw or graph data. 2) Create
graphs and traces for the data you are interested in. By using calculation
functions you can get results you are interested in, and if the excel export is
enabled, the results will be saved to an excel file.

30. Why are my data traces only ‘flat’ or ‘zero’ or ‘gone’ or ‘wrong’?
There can be several reasons behind this observation. Make sure that you
have 1) attached a data file (.oxy3) with data (check the file information), 2)
filled in the correct optode distance and DPF, 3) the laser-to optode
assignment is correct, 4) that your graph scale and zoom is correctly set, 5)
do ‘bias all traces in measurement’ to get correct offsets. If you see this
while doing a measurement please make sure that 6) your experimental
setup is correct, and all transmitting and receiving fibers and optodes are
well attached (Oxymon), you still have a good Bluetooth connection
(PortaMon), 7) you receive enough light (signal %) by checking “View” menu,
select “DAQ value view” and look at all the signals you are using. If the
received signal is too low, set the power output or the gain settings of the
receiver to high (only possible with Oxymon).
If you see data, but not as expected, take a few steps back and check your
experimental setup. Please never underestimate the simplest 1 channel
measurement for piloting, trial and error!

31. My data or data file has changed or cannot be opened?

If you have downloaded a data file for example via ftp using text(ascii)-
mode or e-mailed a project file, data bytes can be changed and the most
secure way to send your data is first zip your files before sending them.
This can also be seen if you store or open data from a network drive.
Always open and store on local drive.

32. I have an out of memory error

This error is given when to loaded files is too large to handle with your
computer.
Installing the 64-bit version increases the use of the working memory.
Upgrading your computer with more working memory can reduce this

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error frequency. If upgrading is not a possibility, reducing your sampling
rate or recording time solves this issue too.

33. I cannot find my answers in this FAQ list?

If the manuals or instruction videos cannot help you, please contact us for
personal info in Dutch or English. To understand a specific problem related
to your data, please send us the available data files (.oxy
and .evt or .oxy3) and project files (.oxyproj) and a clear problem
description. We may also arrange personal visits, help via skype, msn or
remote desktop control if needed. Of course you can always expect a quick
response if you send an e-mail to askforinfo@artinis.com!

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In Oxysoft several shortcuts are available for quick handling of Oxysoft.

F1 help
F2 open all graphs
F3 close all graphs
F4 insert event now
F5 calculate
F6 bias all traces in a measurement and clear graphs
F7 clear graphs
F8 freeze graphs
F9 zoom in X
F10 zoom out X
Crtl+F9 zoom in Y
Ctrl+F10 zoom out Y
Crtl+N open a new project
Ctrl+C copy (graph)
Alt+Enter properties

169
These abbreviations are used in the manual and in Oxysoft

Abs absolute
AD analog/digital
Cyt cytochrome
Cyt.Ox cytochrome oxidase
DA digital/analog
DPF Differential pathlength factor
HHb de-oxyhemoglobin
Max maximum
Min minimum
NIRS Near Infrared Spectroscopy
O2Hb oxyhemoglobin
O2Mb oxymyoglobin
OD optical density
StO2 Tissue oxygen saturation
tHb total hemoglobin
TSI Tissue saturation index

170
Product Warranty
The warranty of Artinis Medical Systems products is one year from date of
delivery, except for optical fibers, which are fully excluded from warranty.
These warranties do not cover product abuse, modification, and failure to
adhere to product instructions, improper operations and/or misuse. Artinis
Medical Systems B.V. is not responsible for damage arising from failure to
follow instructions relating to the product’s intended use. Artinis Medical
Systems B.V. is not responsible for injury or loss caused by or associated
with the installation and/or use of equipment in any manner other than in
strict conformance with the instructions set in this manual. Artinis Medical
Systems B.V. does not warrant damages or defects to unauthorized
changes to one of the items or shipping damage (other than original
shipment from Artinis Medical Systems). The warranty is voided if the serial
number of the product is defaced, modified or missing. Software Products
are covered specifically for defective media or manuals only, and are
provided as is. The software license you acquired cannot under any
circumstance by transferred back to Artinis Medical Systems B.V. Artinis
Medical Systems B.V. does not warrant or represent that third-party
software or hardware will function error-free when used in conjunction
with its products.

Artinis Medical Systems devices are not intended to cure, treat, mitigate or
prevent any disease.

Warranty Repair
In the event that any Artinis Medical Systems product becomes defective in
material or workmanship during the warranty period, Artinis Medical
Systems B.V. will determine if the product defect is covered under
warranty. Artinis Medical Systems B.V., at its sole discretion, may replace or
repair the unit determined to be under warranty. The labor and material
costs associated with the repair of the product may be the responsibility of
Artinis Medical Systems if determined to be under warranty. You must
receive pre-approval by Artinis Medical Systems for the labor and material
costs prior to repair or replacement of warranty products. You must
contact Artinis Medical Systems to obtain a Return Material Authorization
(RMA) number. An RMA number may be obtained by contacting Artinis
Medical Systems B.V. online or by telephone. Performance of any repair or
replacement on product under warranty does not renew or extend the
warranty period. For repairs of products obtained via a reseller or
distributor, contact the reseller or distributor for warranty.

Non-Warranty Repair
You can return a product for repair that is not covered by warranty only if
you have received a preapproved RMA number from Artinis Medical

171
Systems. Labor costs and freight charges associated with non-warranty
repair will be the sole responsibility of the customer. For any product that is
repaired outside of the warranty period, extra costs for labor and materials
specific for the needed repair will be offered by Artinis Medical Systems BV
after receiving the product and has to be approved by the customer before
start of the repair. Repairs on products out of warranty carry a half year
warranty, but only for the repaired parts. The warranty becomes effective
the day that you receive the item after repair. For repairs of products
obtained via a reseller or distributor, contact the reseller or distributor for
warranty.

Non-Defective Products
You are notified if, after examining and testing a returned product, Artinis
Medical Systems concludes that the product is not defective. The product is
returned to you and you would be responsible for the freight charges
associated with the return.

172
absorption................................. 12, 15, 17, 98
AD box ........................................................ 43
AD Channel ....................... 37, 42, 97, 98, 110
board...................................................... 37
delay .................................................... 101
scaled value.......................................... 100
voltage ................................................. 100
air in- and outlet ................................... 24, 37
analog interface board.......... See AD Channel
Analog-Digital channels .........See AD Channel
arrange graph
as optode template .......................... 87, 94
cascade .................................................. 94
restore graph layout .............................. 94
tile .......................................................... 94
arterial occlusion ........................................ 17
arterial oxygen saturation........................... 13
asynchronous connector cable ............ 40, 41
average traces........................................... 120
axis
auto scale ............................. 52, 84, 85, 89
common auto scale ................................ 52
manual scale .............................. 52, 84, 89
ticks ........................................................ 85
unit ......................................................... 89
x-axis ...................................................... 84
y-axis ...................................................... 85
background color .................................. 51, 83
beep ..................................... See out of range
bias................ 44, 51, 100, 103, 104, 120, 160
blood flow ............................... 17, 18, 19, 124
blood volume ...................... 12, 13, 17, 18, 19
calculation........................... 73, 110, 113, 122
area ...................................................... 124
average ................................................ 124
compare ............................................... 124
graph data ............................................ 124
minmax ................................................ 124
regression ............................................ 124
VO2 ...................................................... 124
calibration ............................................. 41, 68
basket................................................... 150
calibration tool ....................................... 68
TSI150
channel ................... See optode combination
chromophore ........................................ 14, 15
clean ........................................................... 10
clock ............................................................ 62
concentration ....... 14, 19, 37, 81, 86, 98, 103
connect Oxymon ......................................... 73
connect OxyMon............................. 29, 44, 68
connection .................................................. 40
connector ................................................... 38
contact information ....................................49
copy (to clipboard) ................ 75, 95, 117, 125
173
cut-off frequency ...................... 126, 127, 130
cyclic operator .................... 83, 103, 113, 122
cyclic offset .......................................... 120
cyclic period ......................................... 120
detrend front period............................. 120
Cyt.Ox. .................................................. 13, 98
cytochrome................................... See Cyt.Ox.
cytochrome oxidase...................... See Cyt.Ox.
DAQ measurement wizard.................. 72, 104
DAQ status view.................................... 47, 62
DAQ value view ......................... 47, 57, 63, 67
data acquisition, open for ........................... 79
data file....................................... See oxy3 file
device settings ............................................ 77
Differential Pathlength Factor ........... See DPF
dongle ..................................... See license key
DPF.......................... 14, 17, 54, 71, 74, 75, 98
table ................................................. 54, 71
end-user license agreement .........See License
environmental light .................................... 64
event ........52, 62, 83, 111, 113, 119, 120, 160
change ................................................. 118
generate............................................... 115
insert .................................................... 114
label ..................................................... 115
list 117
properties .................................... 117, 118
remove ................................................. 118
evt file ........................................... 70, 73, 108
export ....................................... 108, 112, 113
down sample factor ............................. 111
options ................................................. 110
time span ............................................. 111
extinction coefficient ................ 14, 15, 54, 71
filter ...................................... 91, 92, 100, 126
add ....................................................... 127
band pass ............................................. 129
band pass filter .................................... 132
band stop ............................................. 129
band stop filter .................................... 133
FIR ................................................ 126, 130
high pass .............................................. 129
high pass filter...................................... 130
low pass ............................................... 129
low pass filter ....................................... 130
moving average ......................... 126, 127
moving Gaussian .......................... 126, 128
remove ................................................. 127
RMS band pass filter ............................ 133
width ............................................ 127, 128
FIR filters ................................................... 129
frequency
filter ......................................See filter, FIR
frequency domain....................................... 90
frequency spectrum .............................. 90, 92
gain ..........................................65, 66, 67, 149
auto gain................................................ 65
glass fibers .................................................. 38
graph .............................................. 55, 70, 81
arrange ................................... See arrange
clear ....................................................... 93
close ...................................................... 94
close all .................................................. 94 measurement quality ................................. 55
common auto scale ............................... 85
common graph properties ............. 92, 103
create .................................................... 82
create all .................................... 82, 86, 96
create from template ............................ 82
duplicate ................................................ 93
font ........................................................ 51
freeze..................................................... 94
gridlines ........................................... 86, 92
manual scale.......................................... 86
open ...................................................... 93
open all .................................................. 93
options .................................................. 51
properties ........................................ 83, 92
remove .................................................. 95
rename .................................................. 93
template ................................................ 87
ticks ....................................................... 86
unit ........................................................ 86 optode configuration ... See optode template
ground .................................................... 9, 37
hardware installation ................................. 23
hemoglobin ................... 12, 13, 15, 16, 19, 98
import
data files .............................................. 104
data to graph ............................... 101, 107
measurement .. See measurement; import
remove imported data ........................ 108
indicator view ................................. 47, 82, 92
interconnection board ............................... 37
inter-optode distanceSee source-detector distance subtemplate .......................................... 74
Lambert-Beer law ................................. 13, 14
laser .....................................17, 37, 38, 57, 61
laser module............. See transmitter module
laser power level .......................64, 65, 67, 77
legend................................................... 52, 83
license ............................................ 25, 49, 50
license key .................................................. 49
light source power level ............................ 65
local oxygen consumption .......................... 18
magnetic resonance imaging........................ 8
main switch .................................... 30, 37, 72
mapping ..................................................... 87
mapping measurement .................... 135, 138
high density ......................................... 143
master ................................. See master-slave
master-slave ........................ 37, 40, 41, 43, 68
cable ................................................ 37, 40
measure lamp....................................... 37, 61
measurement ............................................. 70
create .................................................... 72
duplicate ................................................ 81
174
import.................................................. 104
new ........................................................ 72
optode template ................................. 136
properties .............................................. 81
remove .................................................. 81
rename .................................................. 81
template ................................................ 73
menu .......................................................... 47
movie ................................................. 90, 113
myoglobin .................................................. 15
NIRS ...................................................... 12, 98
null field.................................................... 110
occlusion
arterial ................................................... 18
venous ................................................... 17
volume consumed Oxygen .................. 124
OD ............................. 14, 39, 74, 98, 110, 135
optical density ..................................... See OD
optical fiber ..................... 8, 10, 37, 38, 57, 58
split ........................................................ 39
optical pathlength ...................................... 14
optode .................................................. 38, 78
optode combination38, 39, 81, 87, 89, 97, 135
Optode combination
TSI combination............................... 97, 98
optode holder ...................................... 38, 59
optode mapping ......................................... 76
optode template39, 44, 51, 74, 75, 76, 97, 135
1 channel ..................................... 135, 136
12 channel ........................................... 139
2 channel ............................................. 137
24 channel ........................................... 140
2x24 channel ....................................... 143
4 channel ................................87, 135, 137
8 channel ............................................. 138
out of range......................... 51, 64, 65, 67, 68
oximetry .............................. 12, 13, 15, 18, 19
oxy file ...........................................70, 73, 108
open ...................................................... 80
oxy3 file ............... 62, 70, 71, 73, 81, 104, 108
open .............................................. 80, 104
oxygen consumption .................................. 17
OxySoft
about ..................................................... 49
close ...................................................... 49
directory ............................... 26, 54, 69, 71
start ....................................................... 48
pathlength correction factor ..............See DPF
period ................................................. 91, 118
periodic data ............................................ 119
power indicator .......................................... 39
power lamp .....................................30, 37, 43
power supply ......................... 9, 23, 37, 41, 43
information...................................... 23, 37
print............................................................ 95
program options.................... 50, 83, 100, 104
project......................................................... 70
close ....................................................... 72
new ........................................................ 70
open ....................................................... 70
properties .............................................. 71
save ........................................................ 71
project view .......................................... 47, 70
pulse oximetry ...................................... 13, 15
QCF ....................................................... 46, 98
radiation ..................................................... 14
incident radiation ...................................14
transmitted radiation ............................. 14
raw data .............................................. 70, 110
receiver ....................................................... 38
gain .............................................. See gain
receiver module .......................................... 37
receiver saturation...................................... 67
rollover mode ....................................... 51, 95
safety ...................................................... 8, 23
sample frequency ................. See sample rate
sample rate ................... 39, 77, 111, 130, 151
down samplingSee export; down sample factor
scale factorization ................................. 52, 86
scattering .............................................. 12, 14
service ......................................................... 10
slave ............................... 41, See master-slave
software installation ...................................24
source-detector distance ........ 38, 68, 75, 136
spectroscopy ..................................... See NIRS
spectrum graph................. 47, 82, 90, 92, 118
stack ...................................................... 40, 41
status bar .................................................... 47
status lamp ..................................... 37, 39, 43
subtemplate ................................................ 78
Template DAQ State ...................................62
template file See measurement: template file
templatefile ................................................ 53
175
text color ............................................... 51, 83
time span ...................... 51, 95, 111, 115, 116
time-of-flight............................................... 17
time-sequenced principle ........................... 38
tissue saturation index ........................See TSI
toolbar ........................................................ 47
topo graph ........................ 81, 87, 89, 96, 135
labels ...................................................... 89
properties .............................................. 88
transformation A.................................... 89
trace.......................................... 55, 56, 81, 87
bias................................................ See bias
channel A ......................... 43, 96, 100, 101
channel B .................. See trace, channel A
color ..................................................... 101
create ..................................................... 96
create all .............................................. 102
duplicate .............................................. 102
operator ............................................... 101
properties ........ 45, 92, 102, 103, 120, 127
remove ................................................. 103
style ............................................. 101, 102
transformation A45, 92, 98, 103, 120, 121, 127
transformation BSee trace,transformation A
transmitter............................................ 38, 57
transmitter block .................................. 38, 57
transmitter module .................................... 37
trend mode ........................................... 51, 95
TSI46, 60, 77, 87, 98, 110, 147
optode holder ...................................... 150
slope .................................................... 117
TSI QCF ............................................... See QCF
USB ..................................... 29, 37, 41, 43, 68
USB connection.................................. See USB
venous occlusion ........................................ 17
wavelength ................... 12, 21, 37, 38, 57, 98
zoom ............................................. 90, 95, 160