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Introduction

The OMERO.insight client is a Java based desktop application that runs on Windows, Mac and Unix/Linux. There are a number of ways the client can be configured to improve or extend its functionality.


Note

Configuring your client application depends on the operating system and the client used. Also note that this guide does not cover OMERO.web, which uses a different, server-based, configuration.



Adding third-party JARs to OMERO.insight

OMERO comes bundled with a number of standard Java Archives (JARs). However, functionality can be extended by adding JARs to OMERO.insight and OMERO.server.

An example of this is where some proprietary file formats require additional readers to enable OMERO to open and read the files. These readers can be provided by the owners of the formats as JARs, which need to be added to OMERO to enable the functionality.

Download the third-party JAR from the appropriate source.


Note

If third-party JARs are related to the Bio-Formats import reader, they will also need to be added to the OMERO.server by your OMERO systems administrator. There is no need to do this if they are simply OMERO.insight update JARs.

The appropriate Bio-Formats version required by the third-party JAR, indicated by the provider, will also need to be installed on your OMERO.server by the administrator.




OMERO.insight on OS X


  1. Locate the OMERO.insight.app in Finder and right-click (or control-click) on it.

    Choose Show Package Contents from the contextual menu.


    ../images/configureClientPackage.jpg

  2. Navigate to the Contents folder.

    Select the Java folder.

    Drag and drop, or copy, the third-party .jar file into the Java folder.


    ../images/configureClientJava.jpg


  3. Restart OMERO.insight to enable the new JAR’s functionality.


OMERO.insight on Windows


  1. Locate the OMERO.insight.app in Explorer.

    Open the libs directory.

    Drag and drop, or copy, the third-party .jar file into the libs folder.


    ../images/configureClientWindows.jpg


  2. Restart OMERO.insight to enable the new JAR’s functionality.


OMERO.insight on Unix/Linux


  1. Locate the directory that contains the OMERO.insight.jar.

    Open the libs directory.

    Drag and drop, or copy, the third-party .jar file into the libs folder.


    ../images/configureClientLinux.jpg


  2. Restart OMERO.insight to enable the new JAR’s functionality.



Increasing OMERO.insight memory allocation

By default, the OMERO desktop clients allocate a certain amount of memory for themselves during the start-up process which should be sufficient for most uses.

However, you may encounter out of memory exceptions while trying to import or display very large images. In these situations, it is beneficial to increase the memory allocation to the clients as outlined below.



OMERO.insight on OS X

  1. Locate the OMERO.insight.app in Finder and right-click (or control-click) on it.

    Choose Show Package Contents from the contextual menu.


    ../images/configureClientPackage.jpg

  2. Navigate to the Contents folder.

    Right-click on the Info.plist file, and select to open it in either Xcode (if installed) or your default text editor.


    ../images/configureClientPlist.jpg



  3. Within Xcode, click and open the JVMDefaultOptions node.

    Under Xmx, you will see a value such as:    -Xmx1024M     indicating you currently have 1024 Megabytes reserved for the application to use.

    Increase this to the amount of memory you wish to allocate, -Xmx2048M if you wish to allocate 2048 Megabytes of memory, for example.

    Viewing the file in a text editor, line 54, has the value set as:    <string>-Xmx1024M</string> .

    Edit the value to:    <string>-Xmx2048M</string>     to increase the allocated memory to 2048 Megabytes.

    The minimum memory allocation, the -Xms value, should not be changed.

    Save the file and close.

    Restart OMERO.insight to load the new setting.


    ../images/configureClientEdit.jpg



OMERO.insight on Windows

To alter the memory allocation of the Windows clients, you must add an optional parameter file to the same folder as the application.

Create a file called OMERO.insight.vmoptions in the same directory as your OMERO.insight_64.exe or OMERO.insight.exe file and insert a value such as -Xmx2048M, as described in OMERO.insight on OS X above.



OMERO.insight on Unix/Linux

Changing OMERO.insight memory allocation under Unix requires you to edit the start-up script file, OMEROinsight_unix.sh located with the clients.

In the OMEROinsight_unix.sh file, edit the maximum value for allocated memory (-Xmx) in the line java -Xms256000000 -Xmx1024000000 -jar omero.insight.jar with a new maximum memory value.

See the Java online documentation for a full description of these options.




All Tutorial Material is available on line at: help.openmicroscopy.org

The Main OME website is at: www.openmicroscopy.org