Thermo Scientific

SkanIt™ Automation
Interface
User Manual
API Version 2.0
Cat. No. N19215 Rev. 2.0 2018
© 2018 Thermo Fisher Scientific Inc. All rights reserved.

Manufacturer:

Thermo Fisher Scientific Oy

Ratastie 2, P.O. Box 100

FI-01621 Vantaa

Finland

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
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The contents of this document are subject to change without notice. All technical information in this
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Sale shall govern all conflicting information between the two documents.

These are the original instructions.

For Research Use Only. Not for use in diagnostic procedures.

 P

Preface

About this guide

This user manual has been written for the software engineer planning to integrate a Thermo Fisher
Scientific Microplate Reader into an automation environment. It provides information about the setup
and usage of the Automation Interface, as well as technical advice for the integration as part of an
existing automation software. The SkanIt Automation Interface (hereinafter Automation Interface)
supports the following devices: Varioskan LUX, Multiskan Sky, Multiskan GO, Multiskan FC,
Fluoroskan, Fluoroskan FL, and Luminoskan.

In this document, Automation Interface refers to the complete software package found on the
installation media of SkanIt Software for Microplate Readers, Research Edition, containing both the
automation server and the sample client.

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Preface

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Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
About this guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
SiLA Compliance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Contents of the Automation Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
User Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Automation Server (AI Server) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Automation Client (AI Tester). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Chapter 2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Setting up the Automation Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Testing the AI Server with the AI Tester . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Chapter 3 Configuration Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

AIServer.exe.config . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Section <applicationSettings> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Section <services> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Section <system.diagnostics> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
AITester.config . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Section <client> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Section <services> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Section <system.diagnostics> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Chapter 4 API Commands and Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

SiLA mandatory commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Required commands for SiLA "Reader/Imager" device class . . . . . . . . . . . . . . . 10
Optional SiLA commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Custom commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Command return values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Deviations from the SiLA Standard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Breaking changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Chapter 5 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

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 1

Introduction
The Automation Interface provides high-level control for Thermo Fisher Scientific microplate
instruments in automation environments. Setting up an automation environment requires:
• robotics or a microplate stacker to handle the microplates
• hardware to integrate the instrument with the robotics, and
• automation master software (commonly called Process Management System or PMS for short) to
control the instrument.

The user can implement these components or acquire them from a third-party automation provider.
The Automation Interface provides a web-service based server (hereinafter AI Server), which enables
instrument control for the integrator's automation management software (hereinafter AI Client) via
web service calls. The AI Server is implemented with Microsoft's WCF technology but the choice of
technology for the AI Client is free as long as it allows web service communication.

The Automation Interface is a part of the SkanIt Software for Microplate Readers, Research Edition
release (hereinafter SkanIt) which must be installed before using the Automation Interface. In the
normal work flow, the end-user creates a session (this includes layout definitions, measurement steps,
possible result steps etc.) using SkanIt. After this step, SkanIt is closed and not needed anymore. Only
basic measurements can be created through the Automation Interface bypassing SkanIt. Through web
service calls to the AI Server, the AI Client then takes control of the instrument, loads the desired plates
using robotics, and starts the session execution. The measurement results are returned as XML data
from the AI Server, and also internally stored in the resulting session file. Session files created through
the Automation Interface can be opened in SkanIt for further analysis. Full reports of the execution can
be generated on demand (PDF, Excel, TXT, XML), including all calculation results, if calculation steps
had been defined in the session.

The Automation Interface 2.0 as described here and included in SkanIt Software 6.0 and later is not
compatible with Automation clients developed against version 1.0 (included in SkanIt Software
4.0-5.0). For a list of changes, see “Breaking changes” on page 13.

SiLA Compliance
The Automation Interface has been implemented to conform to the SiLA Device Class Interface
Design Guidelines Version 0.3 and the SiLA Device Control & Data Interface Version 1.3.08. The
Automation Interface provides an API according to the SiLA Command Dictionary Specification
Version 0.3 (herinafter the Standard) for an instrument of the SiLA Device Class "Reader / Imager".

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1 Introduction
Requirements

In terms used by the SiLA Standard, the AI Server is the SiLA Service Provider for a "Reader" device.
Any SiLA-compliant Process Management System (PMS) can access and control the device, therefore
acting as a SiLA Service Consumer.

The SiLA compliance is implemented on the software level, i.e. the controlled devices themselves are
not SiLA-aware. The Automation Server hosts its own Web Service so it can be run either on the same
PC as the PMS, or on a separate PC. Thus the automation interface fulfills the SiLA integration level
2.

Due to the nature of the supported instruments, not all parts of the Standard are implemented.
Exceptions to the standard are listed in “Deviations from the SiLA Standard” on page 13.

For more information, visit the web page of the SiLA Standard at: http://www.sila-standard.org/.

Requirements
The Automation Interface requires the installation of the SkanIt Software for Microplate Readers,
Research Edition on the PC hosting the automation web service. For its system requirements, refer to
the SkanIt™ Software for Microplate Readers User Manual.
Note The Automation Interface is not supported for the Drug Discovery Edition (DDE) version of
SkanIt Software.

It is highly recommended to thoroughly familiarize yourself with the SiLA Standard, especially its
architecture and the SiLA state machine, prior to developing your own client.

Some basic knowledge about Microsoft WCF services is recommended, especially if you need to tweak
the AI Server configurations.

Contents of the Automation Interface

The Automation Interface for SkanIt consists of the following components.

User Manual
This document.

Automation Server (AI Server)

All files necessary to set up the AI Server: a web server providing access to a connected device using
standard SOAP web service calls as required in the SiLA Standard (see “SiLA Compliance” on page 1).
Can be executed as standard .NET application, or as a Windows Service.
Note Only one instance of the AI Server can be running at a time.

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 1 Introduction
Contents of the Automation Interface

Automation Client (AI Tester)

A .NET/WCF sample application that acts as a client to connect to the AI Server. The integrator has to
implement its own version of an AI Client, the AI Tester is only meant for initial testing. However, it
contains access to all commands that are provided by the Automation API. The AI Tester is
implemented as SiLA PMS, therefore it encapsulates both the SiLA Service Consumer and the SiLA
Event Receiver. Only one AI Tester can be connected to an AI Server at a time.
Note The AI Tester sample application is provided as is, it has not been fully tested for stability and
may malfunction when used in an unexpected way.

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Contents of the Automation Interface

4 Thermo Scientific SkanIt™ Automation Interface Thermo Fisher Scientific

 2

Installation

Setting up the Automation Server

1. Install the SkanIt Software. It is recommended to at least start SkanIt once before using the AI
Server.
2. Locate the "AI"-folder on your SkanIt Software installation media. Copy all files to your SkanIt
installation folder.
3. Optional: Open AIServer.exe.config from the installation folder and define the instrument to
connect to. As default, the simulator for Multiskan Sky has been defined.
4. Execute the AIServer.exe with administrator rights.

Testing the AI Server with the AI Tester

1. Locate the AITester-folder on your PC, see “Automation Client (AI Tester)” on page 3.
2. Start the AITester.exe with administrator rights.

This is the fastest way to get started. However, it is recommended to go through the configuration files
as described in “Configuration Files” on page 7.

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2 Installation
Testing the AI Server with the AI Tester

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 3

Configuration Files
The Automation Interface consists of two configuration files that are used to set up the automation
environment, both AI Server and AI Client. All parts that the integrator might have to edit are listed
below, all other sections shall be kept unchanged unless the user is fully aware about their meaning.
Most WCF-specific settings are left at their default values.

AIServer.exe.config
This configuration file is needed for correctly setting up the AI Server. It is located in the SkanIt
installation folder alongside the main AIServer.exe executable.

Section <applicationSettings>
This section configures the device parameters.
Table 1. Device parameters.
Parameter Description
<add key="consoleApp" value="true" /> When set to "true", the server is running as a Windows console
application, on "false", the server is running as a Windows
Service. See comments in the configuration file for more details.
<add key="statusEventTimer" value="30000" /> Defines how often the server sends basic instrument status events
(e.g. temperature). The value is time in milliseconds.
<add key="aiDevice" value="1234-1234" /> Configures the device that shall be controlled. The value is the
device's serial number. Initially, there is a device simulator
defined so you can startup the AI Server without connecting a
real instrument. Only one device can be connected at a time. See
comments in the configuration file for more details about using a
device simulator.

Section <services>
This section configures how the automation server is accessible to incoming connections. Here only
the row for setting up the address and port has to be considered:

<add baseAddress="http://localhost:8733/MIP/Reader" />

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3 Configuration Files
AITester.config

Section <system.diagnostics>
This section configures the server's logging. It is implemented according to Microsoft WCF
recommendations. The log is created to the path as specified in the <sharedListeners> element. All log
entries with "AISiLATrace" are created by the automation server's own code, everything else by the
underlying WCF framework.

AITester.config
The AI Tester is a sample AI Client that connects to the AI Server and uses the services the AI Server
provides. As it is implemented as a SiLA Service Consumer, it has a separate EventHandler (where the
AI Server sends events) which is a web server on its own. Therefore two addresses have to be defined in
the AI Tester config:
• the address and port of the server it connects to, and
• the address of the AI Tester and the port on which it is listening to incoming requests from the AI
Server.

Section <client>
This section contains the information about the automation server. Only the value of the parameter
"address" has to be edited. The value shall be the same address as described in Section <services> for
AIServer.exe.config above.

Section <services>
This section contains the information about the AI Tester (i.e. its event receiver). Can be "localhost"
only when both the server and client reside on the same machine. Otherwise, the correct IP has to be
used. Only the value of the parameter "baseAddress" has to be edited.

Section <system.diagnostics>
See Section <system.diagnostics> for AIServer.exe.config above.

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 4

API Commands and Events

The following lists the commands that are available in the Automation Interface. The API contains
commands required by the SiLA "Reader/Imager" device class as well as some custom commands.
Only short descriptions are given here. For more details, see the SiLA Command Dictionary
Specification Version 0.3.

SiLA mandatory commands

Table 2. SiLA mandatory commands.

Command
Abort (int requestId, string lockId)
GetDeviceIdentification (int requestId, string lockId,
out SiLADeviceIdentification deviceDescription)
GetStatus (int requestId, out string deviceId, out State
state, out SiLACommandDescription[] subStates, out
bool locked, out string PMSId, out DateTime
currentTime)
Initialize (int requestId, string lockId)
LockDevice (int requestId, string lockId, string
lockTimeout, string eventReceiverURI, string PMSId)
Reset (int requestId, string lockId, string deviceId, string This command is used to reset the Service Provider at
eventReceiverURI, string PMSId, string
errorHandlingTimeout, bool simulationMode)
UnlockDevice(int requestId, string lockId)
Description
This command aborts the execution.
This command reports on details of the instrument.
This command reports the status of the instrument.
This command initializes the instrument.
This command locks the instrument by using lockId key.
If you lock the AI Server with some key, you have to use
the same key with every command to be able to execute
the command.
any time from any state.
This command unlocks the instrument. Parameter
lockId is the key that has been previously used to lock
the device.

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4 API Commands and Events
Required commands for SiLA "Reader/Imager" device class

Required commands for SiLA "Reader/Imager" device class

Table 3. Required commands for SiLA “Reader/Imager” device class

Command Description
GetParameters (int requestId, string lockId) This command is used to retrieve the available
parameters which can be set by using the SetParameters
command. This command returns all configurable
parameters in XML format which is part of the
SiLAReturnValue. The same XML format is used to set
those parameters with the SetParameters command. You
can use the AITester application's GetSetParameters
button to see what GetParameters returns and what will
be sent with the SetParameters command.

For the values that can be set, see Table “Values for the
GetParameters command.” on page 10.
PrepareForInput (int requestId, string lockId, int This command puts the instrument into a state where it
position) is ready to accept new labware, i.e. the same as the
CloseDoor command.
PrepareForOutput (int requestId, string lockId, int This command puts the instrument into a state to release
position) the processed labware, i.e. the same as the OpenDoor
command.
SetParameters (int requestId, string lockId, string This command is used to send new parameter values to
paramsXML) the instrument. The format of the paramsXML can be
retrieved by using the GetParameters command. You can
use the AITester application's GetSetParameters button
to see what GetParameters returns and what will be sent
with the SetParameters command.

Table 4. Values for the GetParameters command.

Value Description
UserActionTime Time to wait when the instrument needs user action (e.g. to change the
plate). You can give the time in seconds or in duration data type format.
EnableStatusEvent Enable/disable StatusEvent messages which are sent to the PMS. These
messages are e.g. periodical temperature messages and method execution
status messages.
GasAtmosphereO2 Set the oxygen level (only with Varioskan LUX).
GasAtmosphereCO2 Set the carbon dioxide level (only with Varioskan LUX).
MeasurementStep Set the step type which will be used with ReadPlate and ReadWell
commands. Values of this parameter are: 1: Absorbance, 2: Fluorescence, 3:
Luminescence, 4: AlphaScreen.

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 4 API Commands and Events
Optional SiLA commands

Table 4. Values for the GetParameters command.

Value Description
Wavelength1 The wavelength value is used with the ReadPlate and ReadWell commands.
This value is used in absorbance measurement with Varioskan LUX and
Multiskan GO, or as an excitation wavelength in fluorescence
measurement.
Wavelength2 The wavelength value is used with the ReadPlate and ReadWell commands.
This value is used in fluorescence measurement as an emission wavelength.
FilterPosition The filter position value is used with the ReadPlate and ReadWell
commands. This value is used in absorbance measurement with Multiskan
FC or in AlphaScreen measurement.
OutputSessionPath The full path of the session file that will be created as output of the
execution. This is mandatory when using ReadPlate() and ReadWell()
commands, otherwise an error will be returned. Set values are not saved and
have to be given before each execution. This parameter is optional when
using the ExecuteMethod() command, where the name and location of the
chosen method is used (adding a running number) if OutputSessionPath is
not defined.

Optional SiLA commands

Table 5. Optional SiLA commands.

Command
CloseDoor (int requestId, string lockId)
ExecuteMethod (int requestId, string methodName,
string lockId, int priority)
GetTemperature (int requestId, string lockId)
OpenDoor (int requestId, string lockId)
ReadPlate (int requestId, string lockId, int index)
Description
The CloseDoor command is used to close the door. This
is the same as command PrepareForInput.
The ExecuteMethod command is used to start a
previously defined method with the instrument. The
methodName parameter is the ID of the method which
can be retrieved by using the GetMethods command.
The GetTemperature command gets the set temperature
and the current temperature of the instrument.
The OpenDoor command is used to release the door.
This is the same as command PrepareForOutput.
The ReadPlate command creates a new method and
reads the current plate by using values defined via
SetParameters.

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4 API Commands and Events
Custom commands

Table 5. Optional SiLA commands.

Command
ReadWell (int requestId, string lockId, int index)
SetTemperature (int requestId, string lockId, double
temperature)
Description
The ReadWell command creates a new method and
reads one well defined in the index parameter by using
values defined via SetParameters.
This sets the temperature to the instrument. See the
instrument’s manual for details.

Custom commands

Table 6. Custom commands.

Command
GetReport (int requestId, string lockId, string filename)
GetErrors (int requestId, string lockId)
Description
The GetReport command generates a report of the
session and saves it to the given path.
The GetErrors command generates a report of
instrument errors. A list of the errors is returned in XML
format which is part of the SiLAReturnValue.

Note The GetErrors command is not supported by Fluoroskan, Fluoroskan FL and Luminoskan.

Command return values

Every command returns SiLAReturnValue which contains the following values:
• DeviceClass: This is always integer 4 (SiLA Reader/Imager).
• Duration: Duration of the command (see the Note below).
• Message: Human readable message or xml structure which uses SiLA Response schema
http://sila-standard.org/schemata/ResponseType_1.2.xsd.
• ReturnCode: The return code itself.
Note For all commands, the time given as the duration of the command is fixed to be always the
maximum possible time as defined in the SiLA Standard. This is simply because we cannot estimate
the execution time of complex sessions. Therefore, the "Duration" feature shall not be used for
scheduling or timeout handling.

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 4 API Commands and Events
Deviations from the SiLA Standard

Deviations from the SiLA Standard

Required command Delay() has been removed.

Mandatory commands Pause() and DoContinue() have been removed. Thus there is no state "Paused"
and no transition to or from such a state. Some instruments supported by SkanIt do not support
Pausing in between execution. Therefore the Automation Interface only supports functionality that is
also available in the SkanIt Software.

Breaking changes
Due to major redesign of the SkanIt Software in version 6.0, the API for the Automation Interface has
also changed and is not compatible with the previous version 1.0 (as included with SkanIt 4.0 to 5.0).
The following lists the breaking changes which have to be taken into account when updating AI
Clients from AI version 1.0 to 2.0.

The biggest change is the removal of the database and thus the file-based handling of SkanIt session
files (*.skax).

Other changes:
• GetMethods() command has been removed.
• Get-/SetParamaters(): the parameter SessionName is now OutputSessionPath and defines the file
name and location of the resulting session file.
• Delay() command has been removed.
• DoContinue() command has been removed.
• Pause() command has been removed.
• ImportMethods() command has been removed.

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4 API Commands and Events
Breaking changes

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Troubleshooting
Table 7. Troubleshooting cases.
Case
AIServer as a Windows Service and
Startup type is Automatic (can be
reproduced at least with slower
machines)
When implementing the application
(PMS) to use AIServer, you have to
make sure that the maximum size of
messages is big enough.
Thermo Fisher Scientific
Issue
AIServer will not start automatically
and if starting it manually from
services.msc, it will give an error:
"Error 1053: The service did not
respond to the start or control
request in a timely fashion."
AIServer starts but it cannot connect 1. Change the service startup type to
to the defined instrument because
Windows has not recognized USB
devices, yet.
If you create this application by
using C# and basicHttpBinding,
then the default maximum size of the
message is 48 kb. This is really small
and you can execute only small
sessions without breaking this limit.
Thermo Scientific SkanIt™ Automation Interface
5
How to fix
1. Open the Registry Editor
(regedit.exe).
2. Create a new DWORD to
HKEY_LOCAL_MACHINE\SYST
EM\CurrentControlSet\Control.
Name it to "ServicesPipeTimeout"
and set its value e.g. to 60000 (60
seconds).
3. Restart the computer.
For more information about this, see:
https://support.microsoft.com/en-us
/kb/824344
“Automatic (Delayed Start)” instead
of “Automatic”.
It will take about 2 minutes until the
AIServer is started and it is enough
to make sure that all Windows
initializations are ready.
If you increase the maximum size to
e.g. 40 Mb, then it should be enough
for all possible cases. With smaller
sessions, a few megabytes should be
enough.
You can find more information
about this on the Internet by
searching with keywords:
basichttpbinding buffer size.
15
5 Troubleshooting
Table 7. Troubleshooting cases.
Case
Connection to server works when
the client and server reside on one
PC, but fails when on different PCs.
Possible error message: "There was
no endpoint listening at ... "
Starting up the AI Server does not
work. Error message contains: "Your
process does not have access rights to
this namespace..."
AI Tester starts up with error
messages in the EventHandler text
box.
Importing sessions does not work.
Importing completes with error
“Completed, there are no methods in
the given file to import”.
I'm encountering issues not covered
by this FAQ. Where do I find the log
files?
16 Thermo Scientific SkanIt™ Automation Interface
Issue
Sending a ping to the other machine Check your firewall settings and
(and vice versa) does not work.
Both PCs can ping each other but
still the client does not connect.
Importing command completes
without errors but the session is not
shown in the AI Tester.
How to fix
ensure incoming calls are not
blocked on private/domain
networks. Note that Windows 8/8.1
changed the default firewall settings,
so you might be able to connect to a
Windows 7 but not to a Windows 8
or 8.1.
Ensure the chosen ports are available.
Remember that the AI Client acts
also as a web server and thus needs a
separate port to receive events from
the AI Server. All ports smaller than
1024 are reserved for the system and
should not be used. See
https://en.wikipedia.org/wiki/List_of
_TCP_and_UDP_port_numbers
for further details.
You need to start the AI Server with
elevated rights. Right-click and select
"Run as administrator".
You need to start the AI Tester with
elevated rights. Right-click and select
"Run as administrator".
Click GetMethods to refresh the list.
Note that only the sessions that are
executable with the currently
connected device are shown.
Ensure that the user who is executing
the AI Server has at least once logged
into SkanIt prior to importing
sessions.
By default, AI’s logs go to the
%programdata%\Thermo\MIP\Rea
ders\<version>\Logs directory
(AI_Log.txt). If you want to get web
service logs (.svclog) which contain
more information, you can define its
folder by editing file
%programdata%\Thermo\MIP\Rea
ders\settings_ai.config.
Thermo Fisher Scientific