GEM-2 Short User Manual

GEM-2 Short User Manual
rev. 20181212(a)
1 Introduction ...................................................................................................................................2
1.1 The GEM-2 hardware and WinGEM software ......................................................................2
1.2 The three stages of a survey ...................................................................................................2
2 Before the survey ..........................................................................................................................3
1.1. Site survey.............................................................................................................................3
1.2. Select a frequency set (optional) ...........................................................................................3
3 Performing the survey ...................................................................................................................4
3.1 Preliminary checks .................................................................................................................4
3.2 Start WinGEM2 .....................................................................................................................5
3.3 Check the battery status .........................................................................................................5
3.4 Setting Bluetooth Connection ................................................................................................6
3.5 Getting started with WinGEM2 .............................................................................................7
3.6 Data collection .......................................................................................................................9
3.6.1 Performing a dead reckoning survey ..............................................................................9
3.6.2 Performing a GPS-based survey ...................................................................................11
4 After the survey...........................................................................................................................11
4.1 Exporting data from the Trimble Nomad.............................................................................11
4.1.1 Copying from the storage card ......................................................................................11
4.1.2 Using Windows Mobile Device Center ........................................................................11
4.2 Converting the .gbf survey files ...........................................................................................12
4.3 CSV file inspection ..............................................................................................................14
4.4 Compute conductivity/susceptibility (optional) ...................................................................16
4.5 Plotting the data as an X-Y map ..........................................................................................17
4.5.1 Other plotting methods .................................................................................................20
GEM-2_Short_User_Manual20181212(A).docx page 1 of 22
1 Introduction
1.1 The GEM-2 hardware and WinGEM software

The Gem-2 is the handheld instrument which is used to collect data during a survey. The sensor
can measure apparent electrical conductivities and magnetic susceptibilities at multiple user-
selected frequencies. It consists of the ski and its electronics console, a carrying strap, and other
accessories. The GEM-2 does not store any of the collected data; instead it sends out the data as
a serial bit stream to be recorded in real time by a separate data logging computer; the data link
uses either Bluetooth or a hard-wired RS-232 connection.
Data logging is performed by a Windows computer running the WinGEM software. WinGEM is
Geophex‟s proprietary software for running the GEM-2. The logging computer can be either:
 a Trimble Nomad or equivalent handheld computer, running the Windows Mobile
operating system (OS), with the Mobile version of WinGEM (download Trimble manual
from http://www.trimble.com/globalTRLTAB.asp?Nav=Collection-62860 )
OR
 A laptop or desktop computer running a recent Windows OS, with the desktop version of
WinGEM.
Most users will use a handheld computer during the survey, but will use the desktop version of
WinGEM before and after the survey because of greater convenience (larger screen) and more
extensive features.
1.2 The three stages of a survey

Before the survey
 Charge the batteries and check the connections.
 If necessary, re-configure the GEM-2 for the specific survey conditions. Often, the
previous configuration, or the factory defaults are sufficient, so there is little to do.
During the survey

 Perform the survey while monitoring the screen to ensure that the data is good quality,
and that it is being recorded.
After the survey

 Export the data to a desktop computer using Geophex‟s EmExport program to produce a
CSV (comma separated values) file.
 Perform additional post-processing as desired, such filtering or inversion, then 2-D maps.
2 Before the survey
1.1. Site survey
Before the survey, have someone visit the site to answer the questions:
 How flat is the ground?
 How irregular is the surface?
 What obstacles are there?
 Are there hazards such as holes or trip wires?
 How difficult would it be to walk the site while keeping the GEM-2 at a uniform height
and level?
 If there are plants or bushes that will make the survey more difficult, can they be mowed
ahead of time? It is usually worth the cost of clearing the field to get better survey results,
keeping in mind the cost of the survey itself, and the importance of the results.
 What kind of cart or sled would be useful for improving the quality of the data? It is
usually worth the cost of building a cart to improve the survey results.
1.2. Select a frequency set (optional)

In many cases, the factory settings, or the settings left over from a previous survey are sufficient
and there is very little to configure. It is a good idea to charge batteries and verify that the GEM-
2 connection (Bluetooth or cable) works.
The GEM-2 configuration is stored in non-volatile flash memory, so it remains between surveys.
The Trimble Nomad uses a battery-backed configuration; we recommend re-charging the
Trimble batteries at least once a month if they are not being used; this can avoid a lot of
configuration work the next time they are needed.
The GEM-2 comes pre-configured with 4 standard frequency sets.
The standard configuration files
Approximate
Config file Notes
frequencies used (Hz)
450, 1.53 k, 5.31 k, Default: covers a wide frequency range,
GEM2-xxx-C5
18.33 k, 63.03 k good for most surveys
Includes lower frequencies for conductive areas
GEM2-xxx-L3 450, 2.85 k, 18.33 k
and geological characterization
Useful for mapping shallow soil
GEM2-xxx-H3 18.33 k, 38.31 k, 80.01 k
conductivity variations
GEM2-xxx-W3 2.43 k, 12.39 k, 63.03 k Wide range with limited frequencies
To choose a frequency set in the hand-held version of WinGEM2, click the Cfg menu at the
bottom, and then click on Set GEM from file. Choose the appropriate file from the list based on
the file name. The GEM-2 will be reconfigured for the new frequency set.
3 Performing the survey

3.1 Preliminary checks
Check that the GEM-2 battery is charged. There is a button on the battery itself that turns on a
charge indicator. Also ensure that the Trimble Nomad is charged.
Turn on the GEM-2 before starting the WinGEM2 program.
3.2 Start WinGEM2
Press the power button and wait for Windows logo to clear
and for the main screen to appear. It should look like this:
If necessary, click on any Unlock buttons that may appear.
Note: If the WinGEM2 button does not appear on the main screen, this is not a problem; you
can always start it from the Start menu (at top left). To make the WinGEM button appear on the
main screen, do the following:
1. On the Start menu, click Settings (on the Personal tab)
2. In the Settings menu, click Today (on the Personal tab)
3. At the bottom, select the Items tab, wait for the list to appear
4. Scroll to the bottom of the list, find the WinGEM2 item
5. If the box is not checked, check it. If the box is already checked, un-check it, then re-
check it.
6. At the top right, click OK twice to exit. Wait for the main screen to appear. The
WinGEM2 button should be present.
3.3 Check the battery status
The battery icon provides a basic battery status.
You can click on the battery icon for more information.

Click OK when done.
3.4 Setting Bluetooth Connection
The Bluetooth icon provides the status.
If the status is Off, click the Bluetooth icon itself. In the

following screen, click the Bluetooth icon to turn it ON, then
click Done at the bottom left. It should now be On.
To initially set up the Trimble Nomad for connecting GEM-2 via Bluetooth:
1. Power on Trimble and GEM-2
2. Click on the Bluetooth Icon on the desktop. This takes you to the Wireless
Manager screen.
3. If necessary, turn on Bluetooth by clicking on the large Bluetooth button.
4. While still in Wireless Manager, click on Menu,, then Bluetooth Settings at the
bottom right.
5. If necessary, select the Devices tab at the bottom, then select Bluetooth settings
6. Click on Add new device...
7. Wait for Bluetooth to search and find devices. You are looking for something called
GEM--xxx, where xxx is the serial number of your GEM-2. [Note: if other devices
are installed, we recommend you delete them to increase the reliability of your
Bluetooth connection.]
8. Select your GEM-2 (GEM2-xxx) when found, then click on Next.
9. When prompted, enter the passcode as "1234", then click on Next.
10. Select the COM Ports tab at the bottom, click on New Outgoing Port, highlight
the entry for your GEM-2, then click on Next.
11. Make a note of the COM number (usually COM8), uncheck the Secure Connection
checkbox, then click on Finish. You will see your GEM-2 listed with its COM port
number.
12. Select the Modes tab at the bottom, and check both Turn on Bluetooth and Make
this device visible… checkboxes.
13. Select the Power tab at the bottom, and un-check the Maintain Bluetooth
connections ... checkbox.
14. In the top right corner, click ok.
15. Back in Wireless Manager, click Done at the bottom left to finish.
3.5 Getting started with WinGEM2
Turn on the GEM-2 itself and wait a few seconds (approx. 5-10) so it is ready to connect to the
WinGEM2 program.
Note: If you start WinGEM2 before the GEM-2 is

ready, you will see one or both of these error messages.
In this case, quit WinGEM2, and then restart it.
These are the error messages you will see whenever the
WinGEM2 program loses communication with the
GEM-2. This could happen with Bluetooth if they are
too far apart.
Note: Depending on the version of Windows Mobile

operating system, you may get this error screen at
startup.
This is not a problem, just click on Don’t Send at the

bottom to make it go away
Here is the main WinGEM2 screen.
The title bar shows which configuration file is loaded.

In this picture it is GEM2-XXX-C5.
The drop-down box at the top right selects the display

mode.
 Spectrum displays instantaneous Inphase and
Quadrature data for each frequency.
 Stripchart displays the Inphase and
Quadrature data for a selected frequency. This
is usually the most common choice during
surveys.
 Table shows a table of numerical values
 Contour displays real time 2D painting of the
selected data. This is complicated to set up and
only recommended for expert users.
Above the main graph:
 The BAT icon provides a basic battery status. As you survey, check that the battery does
not go below 10%.
 The GPS icon provides the GPS status (see below).
 The LINE icon shows the line number during a „dead reckoning‟ survey (see below).
The menus along the bottom are usually not used during a survey.
Understanding GPS status
8 satellites are visible, no fix
9 satellites are visible, standard fix achieved
+ means the PPS (pulse per second) is being received,

standard fix achieved
Receiving PPS, differential fix achieved, now receiving

WAS data. Blue background indicates that GPS is
ready for use.
What are ppm units?
WinGEM displays and records ppm (part per million) values.
PPM is a relative, rather than absolute unit. It is the ratio of the received field
strength, relative to the transmitted field strength. If there are variations in the
strength of the transmit field, due to heat or low battery, the ppm value remains
constant.
Later, when the PPM values are exported, they can be converted to resistivity and
susceptibility values.
3.6 Data collection
3.6.1 Performing a dead reckoning survey
What is a dead reckoning survey?
A low cost GPS is not very accurate, with errors of as much as a

several meters. Also, GPS signals can be lost due to local
interference from trees, buildings, etc. Often a more reliable
alternative is a dead reckoning survey.
In a dead reckoning survey, the survey area is marked with parallel

lines, using paint or string. In this photo, the lines run vertically.
(The definition of horizontal and vertical is arbitrary, but it may be
easier if “vertical” is approx. North-South) The line spacing is
always the same, for example 1 meter. So the X position = line
spacing * line number.
The length of the lines is also the same, say 15 meters.

Perpendicular markings define the start and end of each line. When
doing the survey, the operator „marks‟ the start and end of each line
as they walk by. The mark defines the start and end of the lines. If
the start is at 0 meters, then the end will be at 15 meters; if walking
in the other direction, the start is at 15 meters, then the end will be at
0 meters.
Note: It is still helpful to connect a low cost GPS to the GEM-2

during a dead reckoning survey. The GPS will provide very reliable
time stamps for logging the data. Also, the GPS position
information will be recorded and may be useful to supplement the
dead reckoning position estimates.
The steps to perform a dead reckoning survey are:
 Start the transmitter in WinGEM2. The TX button will light
up (figure 1 at right).
 Press the Log button as you walk by the start of the first
line; the Log button will light up and the LINE box will
show the first line number, which is 0. (Note: while logging,
the TX button disappears, but it is still transmitting) ( figure
2)
 When you get to the end of the line, press the Log button
again. The Log button will dim and the LINE box will stay
at the same line number. Recording of log data is
temporarily stopped. ( figure 3).
 Get positioned to start the next line and press the Log button
to start the next line ( figure 4).
 Walk all the remaining lines in the same way.
 After all the lines have been logged, end the survey and save
the data by clicking Run in the bottom left corner, then
Close survey.
Note: Two keys on the front of the Trimble

Nomad can be used for the Log and Mark
functions. This may be easier than using the
stylus.
3.6.2 Performing a GPS-based survey
If a reliable and accurate GPS is available, a GPS survey is possible. The process is the same as
before, without the need to count the lines. The GPS also means that the survey does not need to
be laid out as straight lines, as long as the entire area gets covered.
As always, it is recommended to manually check the collected data before leaving the survey
site. See the section “CSV file inspection”, below.
4 After the survey
4.1 Exporting data from the Trimble Nomad
4.1.1 Copying from the storage card
The most convenient way to transfer files to a PC for analysis is a cable connection. However, it
may be difficult to install the required program on newer versions of Windows 10. If so, the data
card can be read directly instead.
There are 2 screw heads at the top of the Trimble Nomad. Turn
them ¼ turn only to remove the top cover. Carefully remove the
data card (Flash or SD) and plug into the local computer, using a
suitable adapter.
Refer to the next section for file and folder names.
4.1.2 Using Windows Mobile Device Center
The Trimble Nomad can be connected to a PC for file transfer with a USB cable. Unfortunately,
the files cannot simply be copied as if it was a USB memory. The data can only be transferred
using a Windows program called Windows Mobile Device Center.
These instructions assume that the Windows Mobile Device Center has already been installed on
the PC. (Note: for older versions of Windows, the program was called Active Sync.)
First, turn off the Trimble Nomad and plug it into the PC using a USB cable.
The Windows Mobile Device Center program should start

automatically. After a few moments, it will connect to the
device, and eventually the  Connected message will
appear at the bottom of the screen.
Click on Connect without setting up your device
On the next screen, choose
File Management
Browse the contents of your device
Select the correct Storage Card, and open the SDGemdata

folder. The data files are .gbf files.
In the example here, the date is May 24 (24My) and 03 is a

sequence number for that day (01, 02, 03 …).
(In the file name, the„d‟ means data file, 050 is a randomly
generated hex value.)
Users have reported many problems running Windows Mobile Device Center under
Windows10. Both Juniper Systems and Trimble Inc. have published workarounds. In December
2018, Juniper announced a new product called „Mobile Connect‟ as a solution; this has not been
tested yet by Geophex.
4.2 Converting the .gbf survey files

In order to keep the data files small, and to speed up data transfers, the data is stored in a
compact binary format. ( .gbf stands for GEM binary format). To convert .gbf files to a universal
data format, use a program called EMExport.
(Note: there is a version of EMExport on the mobile computer, but it usually makes more sense
to do the conversion after the files have been transferred.)
On the PC, run EMExport.
A File Open dialog pops up immediately. Browse to, and
select your survey file.
In the next screen, select the survey type by checking or un-

checking the GPS box. Depending on this choice, either the
upper or lower section of the screen will be active.
For GPS, the 2 other checkboxes are usually left un-checked.

Here is what they mean:
 Normally, the GPS lat/long data is converted by
EMExport into UTM coordinates, which is more
convenient because it provides distances in meters. If
the Pos. in Lat/Lon box is checked, the GPS Lat/Lon
values will pass through unmodified.
 Normally, any data points which cannot be located
because the GPS dropped out are omitted because the
location is unknown anyway. If the Export all box is
checked, all data points are passed through.
If the GPS box is un-checked, this indicates a dead reckoning survey. A dead reckoning survey
is explained below. Choose the parameters to reflect how the survey was laid out. Experiment
with clicking the various boxes and the picture will change to explain the choices. The 2 most
important factors are the Line Length and Line Spacing.
When ready, click Export. EMExport automatically creates 2 new files in .CSV format in the
same folder as the source file, and then closes.
The name of the new files is automatically created. If the name of the original file was xx-d-
yyyy-zzz_GEM.gbf, then the new data file will be xx-xr-yyyy-zzz_gem.csv.
EMExport also creates an additional file for reference, called xx-xr-yyyy-zzz_gps.csv; this
contains the raw GPS data and time stamps and is usually not necessary.
4.3 CSV file inspection
After export, the survey data is in a .csv file. The .csv file can be manually examined at this point
to make sure there are not any obvious problems with the survey data. If this is done before
leaving the survey site, it might save the trouble of having to travel back to the survey site to
repeat the survey.
Open the file in Excel (or equivalent), select one or more columns of frequency data, and insert a
line chart (graph) of the values. It might look like this: (2 columns shown)
Does it look like any data got collected? How noisy is the data? Also, are there targets visible?
Is there a systematic drift to the data? Are there any unexplained jumps in the data? Are there
data points that should be deleted?
You can also look in more detail at the data to decide if you want to apply some filtering or other
processing before continuing.
The .CSV file format
After export, the survey data is in a .csv file. The .csv (comma separated values) file format is a
very old and simple database file format, which is understood by many programs. A .csv file is a
text file. All the values for one data point are on a single line; with the values separated by
commas. The data values must NOT contain a comma, and if a field is missing, there would
appear 2 commas in a row because the commas are needed to keep track of the order of the
values.
In the terminology of databases, each line is a record, and each record is composed of fields
which are separated by commas.
The file can be opened in a text editor, but it is much clearer to open the file with a spreadsheet
program such as Excel or LibreOffice Calc. These programs understand the .CSV format and
can line up the field into columns. Depending on the PC you might be able to simply double-
click the .csv file, or start the spreadsheet program and do a File...Import or File...Open.
In the opening dialog choose the option that indicates the fields are separated by commas:
The columns (fields) in the lines are:

 Line: Line counter, gets incremented by a Log start and Log end; mainly for dead
reckoning surveys
 Sample: sequence number
 X: x position, in meters if using UTM coordinates
 Y: y position, in meters if using UTM coordinates
 Mark: increments each time the Mark button is WinGEM2 is pressed. Used to mark
specific points in a survey area
 Status: Error status code for WinGEM2, 0 is OK
 GPSStat: GPS status, 2 is minimum for receiving GPS position data
 GPSalt: GPS altitude, usually not very accurate
 Time [ms]: number of milliseconds after midnight
 Time[hhmmss.sss]: time code accurate to millisecond
 PowerLn: PPM reading at the power line frequency (50 or 60 Hz), a measure of ambient
power line noise
 I_nnHz: for each frequency, the inphase PPM value for that frequency
 Q_nnHz: for each frequency, the quadrature PPM value for that frequency
 I and Q pairs are repeated for each frequency
 Qsum: Sum of the Q values for all frequencies surveyed, a way to express all the
quadrature values as a single number
4.4 Compute conductivity/susceptibility (optional)
Inversion is a mathematical process of converting in-phase and quadrature readings into other
quantities. There are many types of inversions available as open-source and commercial products
for various applications. One source is the University of British Colombia in Canada
( https://gif.eos.ubc.ca/software ).
Geophex offers a simple free inversion program called Invertor, which uses I and Q survey data
to calculate equivalent values of electrical conductivity and magnetic susceptibility. Here is a
quick overview:
Start the Invertor program. On the first screen,

select the GEM2 instrument type and click on
Compute Conductivities
The default setting of Horizontal coplanar is

correct for a GEM-2 held horizontally. The coil
separation is 1.66 m is also correct for a GEM-2.
Sensor height can be adjusted as required, 1 meter
is typical.
Sometimes the lowest and highest frequencies are
much noisier that the others. The checkbox can be
used to omit them from the calculation.
Click OK. You will see a scrolling display as the

program moves through the data, and then the
program will close automatically.
The output is a new, additional .csv file in the same directory as the source, with an
automatically-created name. If the name of the original file was xxxxx_gem.csv, then the new
data file will be xxxxx_gem.EC.csv.
The output file is basically the same as the original .csv file, but with additional columns of
computed data appended on the right side. For survey with n frequencies, there will be 2n+1
additional columns added. The additional columns are:
 one column of electrical conductivity for each frequency (e.g. EC450Hz[mS/m] for
450 Hz)
 a single column of total conductivity TotalEC[mS/m]
 one column of magnetic susceptibility for each frequency (e.g. MSusc450Hz[1/1000]
for 450 Hz)
This data can be plotted like any other column in the spreadsheet.
4.5 Plotting the data as an X-Y map
Many programs are available for producing X-Y plots. For this example we will use Surfer 8, a
commercial product from Golden Software Inc. (www. Golden Software.com)
There are 2 stages to producing maps. First, each source of data (for example, one column of
data) is converted to a .grd (grid) file. So if we want to map both the in-phase and quadrature
response for 5 frequencies, 10 grid files are needed. It is important to name the files carefully to
avoid confusion.
Secondly, each .grd file can be used to produce a map.
Before starting, decide which *.csv file you want

to plot. Examine the file and note which 3
columns contain the X and Y position values, and
which column(s) holds the data to be plotted...
Start the Surfer program.
Use Grid, Data… to find and open the

appropriate .csv file.
Select the X, Y and data (Z) columns for the plot.
For the Gridding Method, choose Kriging.
Choose a useful name and location for the .grd

file output. Click OK. Remember to use a new,
meaningful name for each data set; otherwise
Surfer will overwrite a previous file.
A dialog box will confirm the creation of

the .grd file.
The .grd files have been created, now let‟s make a

map.
On the menu bar, select Map, Image Map…,

then select one of your .grd files.
You might get something like this ...
Right-click on the map and choose Properties.
On the General tab, click on the Colors box.
The easiest way to define the color choices is to
select one of Surfer‟s pre-defined color schemes.
Click on the Load… button and select the
Rainbow.CLR file. (You may need to navigate to
Surfer8‟s Samples folder in Program Files folder
to find the .CLR files. Once you find them, you
can make copies in a more convenient location on
your hard drive.)
The map will now look something like this:
It can be helpful to overlay the path used to

collect the data.
On the menu bar, select Map, Post Map, New

Post Map…, then select the original .csv file that
was the source for the current map.
The initial result might look strange, no problem.
We just need to correctly define the X and Y

Coordinates.
Right click on the Post item in the left window
and choose Properties. Select the correct
columns for the X Coord. and Y Coord columns.
Click Apply or OK. The map now shows the

location of the data points.
Optionally, you can experiment with the

Frequency and Symbol Size parameters to make
the map less cluttered.
Finally, you can save your work using File, Save As… and choosing a suitable name and folder.
You can get a picture using File, Export…, and selecting name, folder and suitable file type.
GIF may be a good choice.
One of the problems with a back-and-forth dead

reckoning survey is that there may be a skew
between the odd and even numbered lines, due
to the delay at the start of each line.
To improve this, the original .csv file was

modified (with a new column) so that the X
value was increased by 1.6 meters for odd-
numbered lines only. Here is the result:
4.5.1 Other plotting methods
The website http://www.gpsvisualizer.com/ offers a free online tool for generating a .kmz file
from one of the data files. This can then be used in Google Earth to overlay a survey map on top
of satellite imagery.

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GEM-2 Short User Manual

1.1 The GEM-2 hardware and WinGEM software

1.2 The three stages of a survey

During the survey

After the survey

1.2. Select a frequency set (optional)

3 Performing the survey

Turn on the GEM-2 before starting the WinGEM2 program.

If necessary, click on any Unlock buttons that may appear.

3.3 Check the battery status

The battery icon provides a basic battery status.

You can click on the battery icon for more information.

The Bluetooth icon provides the status.

If the status is Off, click the Bluetooth icon itself. In the

Note: If you start WinGEM2 before the GEM-2 is

Note: Depending on the version of Windows Mobile

This is not a problem, just click on Don’t Send at the

The title bar shows which configuration file is loaded.

The drop-down box at the top right selects the display

8 satellites are visible, no fix

9 satellites are visible, standard fix achieved

+ means the PPS (pulse per second) is being received,

Receiving PPS, differential fix achieved, now receiving

What are ppm units?

WinGEM displays and records ppm (part per million) values.

3.6.1 Performing a dead reckoning survey

What is a dead reckoning survey?

A low cost GPS is not very accurate, with errors of as much as a

In a dead reckoning survey, the survey area is marked with parallel

The length of the lines is also the same, say 15 meters.

Note: It is still helpful to connect a low cost GPS to the GEM-2

Note: Two keys on the front of the Trimble

3.6.2 Performing a GPS-based survey

4.1 Exporting data from the Trimble Nomad

4.1.1 Copying from the storage card

Refer to the next section for file and folder names.

4.1.2 Using Windows Mobile Device Center

The Windows Mobile Device Center program should start

Click on Connect without setting up your device

Select the correct Storage Card, and open the SDGemdata

In the example here, the date is May 24 (24My) and 03 is a

4.2 Converting the .gbf survey files

On the PC, run EMExport.

In the next screen, select the survey type by checking or un-

For GPS, the 2 other checkboxes are usually left un-checked.

4.3 CSV file inspection

The .CSV file format

The columns (fields) in the lines are:

Start the Invertor program. On the first screen,

The default setting of Horizontal coplanar is

Click OK. You will see a scrolling display as the

4.5 Plotting the data as an X-Y map

Before starting, decide which *.csv file you want

Start the Surfer program.

Use Grid, Data… to find and open the

Choose a useful name and location for the .grd

A dialog box will confirm the creation of

The .grd files have been created, now let‟s make a