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OMERO Clients

Show or hide the answer What are the official OMERO clients?

The OMERO team develops clients to manage, view, analyse data stored in an OMERO server. View the feature list for more information. The official clients are:

  • OMERO.importer (Java Client)
  • OMERO.insight (Java Client) with integrated OMERO.editor
  • OMERO.web (Web Client)
  • OMERO.editor as a standalone Java application
If you use the Java clients, you will need to use Java 1.5 or higher ( Java Download)

Show or hide the answer Is there a browser version of the OMERO client?

Yes there is: OMERO.web. However in order to fully evaluate the application OMERO rich clients must be used as certain functionality is not available in OMERO.web. This is predominantly:

  • Data import
  • Region of interest creation and manipulation
  • Measurement
Show or hide the answer What do I need to connect to an OMERO server?

You will need:

  • The address of the server e.g. test.openmicroscopy.org.uk
  • A user name
  • A password
If you use the Java clients, near the text field where you enter the address, you will notice the number 4064. This indicates the port used, you should not modify it unless told to do so by your administrator. To connect using the web client, go to http://server-name/webclint, e.g. http://test.openmicroscopy.org.uk/webclient, and log in with your user name and password.



The connection is always secured. You can also choose to transfer all data in a secure manner.
Show or hide the answer Can I open an image stored in OMERO in ImageJ?

Yes, an OMERO ImageJ plugin is available. Visit our download page Downloads

Show or hide the answer Can I still use OMERO.editor as a standalone application?

Yes. OMERO.editor has been integrated to OMERO.insight to offer more functionalities. Nevertheless, OMERO.editor can still be used as a standalone application.

Show or hide the answer On which platform can I use the Java clients?

The OMERO Java clients work on Windows, Mac OS X or Linux. You will require Java 1.5 or higher

Show or hide the answer The client crashed, what to do?

If the application crashed, a window should pop up. You can submit the error without entering any details by pressing the Submit button.

To help tackling the problem, we recommend that you indicate what you were doing when the application crashed. If desired, you can also add your e-mail address, which will allow the feedback system to keep you notified of the status of your feedback. See the QA site for more information.

Show or hide the answer Can I modify the Acquisition metadata?

No, not yet. The acquisition metadata e.g. Objective, Detector are READ-ONLY.

Show or hide the answer What is Shoola?

Shoola was the name of our first Java client, used to connect to an OME-Perl server. That version is no longer maintained, but we've kept the name around after migrating Shoola to OMERO.insight.

Now, why Shoola?

Ok, this goes back a ways. In 2004, the OME team met at Don Shula's Steak House in Baltimore, MD (their meeting rooms were cheap, and yes, we bought our coffee at the neighboring Starbuck's). Our meeting room was plastered with pictures of Don Shula, who successfully coached the Miami Dolphins during the 1970's and 1980's. At this meeting, we decided to begin developing our first Java client application. We code-named the project "Shoola". What else could we do after 3 days surround by Don's glory days? The name stuck.

Show or hide the answer Why is my image so small?

Images in OMERO should be EXACTLY the same size as the image that was imported.

Have you imported the thumbnail from the file?

Some file formats contain two images: the full size one and a smaller version used as a thumbnail by the original application. It can be impossible for us to tell these apart so we may have either imported both or only the first one we found in the file.

Show or hide the answer Can I combine multiple files into channels?

No, not yet.  We are certainly working on this.

Show or hide the answer Can I export an image out of OMERO?

You can export images from OMERO as OME-TIFF (all image planes are exported and some metadata is included as OME-XML). Other formats for export include jpeg, png and movies (.avi).

Show or hide the answer Can I make a movie from an image?

Since 4.1.x, a make-movie utility has been added to OMERO. You will be able to make MPEG or QuickTime movie. See the Feature List for a screencast about how to make your own movie.

Show or hide the answer I cannot connect because I am blocked by a proxy server. Can I configure it?

Please be aware that will only happen if your site blocks outgoing connections to port 4063 and 4064, otherwise connection should be handled automatically.

Currently we do not provide any functionality to configure a proxy and you will not be able to connect to the OMERO server. Please contact your local IT support staff and ask them to open port 4063 and 4064.

See Security for more information.

Show or hide the answer Are the OMERO java clients proxy aware?

OMERO java clients do not use HTTP and are not SOCKS proxy compatible. It will not inherit default IE LAN settings to use the proxy/PAC.

Information on the TCP ports that OMERO rich clients use as well as a security briefing is available here:

http://www.openmicroscopy.org/site/support/omero4/server/security

Show or hide the answer How do I add my own agent to OMERO.insight?

See the following page: How to Build an Agent.

Show or hide the answer Does OMERO support the Leica file format?

Since version 4.1 there has been significant improvements in the way OMERO and Bio-Formats supports the various Leica file formats. This includes more reliable imports for edge-case files, better meta-data support, color channel display improvements, and support for the archiving/retrieval of all the original files imported.

Show or hide the answer What protocols do the OMERO java client use?

The OMERO java clients use TCP/IP.

Show or hide the answer What external connections do the java clients make?

The OMERO java clients try to connect to our update server, to check if you have the latest software. The address of our update server is qa.openmicroscopy.org.uk and it is looked up using your DNS. The IP addresses is not used directly.

OMERO.editor has the option to load protocols and sample files from the internet. These either come from our site or from the URL specified by the user.

Other than that the only connections are to your OMERO server, the address for these is entered at login.

Show or hide the answer How do I use the Command Line Importer?

Information about how to use the command line importer can be found on the following support page: Command Line Import

Show or hide the answer My file failed to import. What should I do?

When a file import fails, it should provide you with an error in the importer's "error" tab. From here you can submit the error for correction. Most errors are usually corrected by the next major release.

To help fix the error, we recommend that you send us your original 'failed' file during this process, as well as indicate what you were doing when the application crashed. If desired, you can also add your e-mail address, which will allow the feedback system to keep you notified of the status of your feedback.

To read our documentation on submitting error reports in the importer, click here.

If your file has successfully imports but appears incorrect when viewed in OMERO.insight, please let us know about the problem by visiting our community forums.

Show or hide the answer What client/server versions are compatible?

Because we are constantly improving the OMERO system, its important to match up your client and server versions. So, if your administrator is currently running OMERO.server version 4.1.X, you should also be running version 4.1.X of the clients.

Sometimes, we release a 'minor' version of the client or server, which should still be compatible with other version in the same 'major' release. For example, the 4.1.0 server is still compatible with 4.1.3 of the clients.

Show or hide the answer How can I bulk import images using the command line importer?

The command line importer allows you to "bulk import" multiple files by passing in a top level directory containing several files rather then passing in a single file by itself. Please note: directory imports are recursive and will try to import all files found in all sub-directories as well.

For details on this function (and to see the full list of command line importer options), visit the CLI Importer page.

Show or hide the answer Can you upload non image related files?

A sample video showing how to attach documents to an images/projects/datasets can be found on the features page; this can include pdfs, word documents, protocols, results, etc.

The main steps are selecting the image/project/dataset you want to attach items to then clicking on the '+' button next to the word Attachment in the Annotation section of the right panel.

Show or hide the answer Where is the rendering history?

Due to a memory leak in Java, this feature has been disabled until we can resolve the leak by moving to a solution utilizing OpenGL

Show or hide the answer What are the supported Permissions in an OMERO Group?

Permissions in OMERO were all made private in version leading up to 4.1 because of various difficulties with the security system.

In order to allow group-sharing, a revamp of the permissions took place for 4.2. The intention is that all object graphs (e.g. Project/Dataset/Image) will belong to a single group, and all objects will have the same read permissions.

Mixing objects with different group-ownerships or different read-permissions will not be allowed. Further, a query will only ever return objects belonging to the currently selected group.

The various permissions levels are as follows:

  • Private: All data in this group is only visible to the user who owns it and the group owners. The group owner can view the data for other group members but not make any edits (same as read-only behaviour).

  • Collaborative - Read-only: Users in groups with this permission setting can view each others' data, but cannot edit or annotate another user's data. You can view another users' images but not comment, rate or tag their images.

  • Collaborative: Users in a collaborative group can view and annotate the data belonging to other users. You can tag another user's images or use their tags to annotate your own images. You can add comments to their images and save your own rendering settings for each image. However, you cannot edit the names of their images, projects, datasets, tags etc.

See also Permissions

Show or hide the answer Who can change the Permissions of a group?

It is possible for the group owner or server admin to change the permissions level on a group after it has been created and populated with data, with the following limitations:

  • It is not possible to 'reduce' permissions to 'Private'. Once links have been created in the database under 'Collaborative' (or Collaborative - Read-only) permissions, these cannot be severed. However, it is possible to 'promote' a Private group to be Collaborative or Read-only permissions.

See Permissions

Show or hide the answer What operations are allowed and restricted with a Collaborative Group?

As in 4.2.x version,

CAN DO:

  • Tagging:

    • You can add your tags to your images or another user's images
    • You can add another user's tags to your images, their images or another user's images
    • You can remove tags that you have added

  • Comments:

    • You can add comments to your images or another user's images

  • Rendering settings:

    • You can apply and save your own rendering settings to another user's images
    • This will not affect their rendering settings on their images

CANNOT DO:

  • You can't edit another user's Project, Dataset or Image names or descriptions

  • You can't remove Images from another user's Dataset, or remove Datasets (resp. Plate) from Projects (resp. Screen).

  • You can't add Images to another user's Dataset, or add Dataset (resp. Plate) to Project (resp. Screen)

  • You can't delete anything that belongs to another user

  • Tagging:

    • You can't remove a tag that another user has added, even if it is your tag on your own image
    • You can't edit another user's tag names or descriptions

  • Comments:

    • You can't edit any comments on any images. Comments are a historical record (same for all permissions levels).

See Permissions

Show or hide the answer Can I move data between groups?

In the 4.2.x and 4.3.x series, it is NOT possible to move data graph between groups. All data a user imports and the work that is done is assigned to the current group and cannot be moved to another group.

See Permissions

Show or hide the answer What are the issues with Java 1.6?

Few bugs have been reported when some revisions of Java 1.6 are installed. Error reported on Windows opening a File chooser using Java 1.6.0_20, upgrading to revision (10/01/11 Java 1.6.0_23) should fix the problem (see http://netbeans.org/bugzilla/show_bug.cgi?id=186615): 

   java.lang.Exception: Abnormal termination due to an uncaught exception.
   java.lang.InternalError: Unable to bind C:footest
   at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source)
   at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source)
   at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown Source)
Error reported on Windows when browsing a plate using 1.6.0_13 
   java.lang.Exception: Abnormal termination due to an uncaught exception.
   java.lang.NullPointerException
   at java.awt.Component.getNormalShape(Unknown Source)
   at java.awt.Component.calculateCurrentShape(Unknown Source)
   at java.awt.Component.applyCurrentShape(Unknown Source)
   at java.awt.Component.mixOnReshaping(Unknown Source)
   at java.awt.Component.reshape(Unknown Source)
   at javax.swing.JComponent.reshape(Unknown Source)
   at java.awt.Component.setBounds(Unknown Source)
   at org.openmicroscopy.shoola.agents.dataBrowser.browser.CellDisplay.setBounds(CellDisplay.java:235)
Error reported on Windows while editing the name of an element e.g. a project, an image. 
   java.lang.ArrayIndexOutOfBoundsException: 15
   at sun.font.FontDesignMetrics.charsWidth(Unknown Source)
   at javax.swing.text.Utilities.getTabbedTextOffset(Unknown Source)
   at javax.swing.text.Utilities.getTabbedTextOffset(Unknown Source)
   at javax.swing.text.Utilities.getTabbedTextOffset(Unknown Source)
   at javax.swing.text.PlainView.viewToModel(Unknown Source)
   at javax.swing.plaf.basic.BasicTextUI$RootView.viewToModel(Unknown Source)
   at javax.swing.plaf.basic.BasicTextUI.viewToModel(Unknown Source)
   at javax.swing.text.DefaultCaret.positionCaret(Unknown Source)
   at javax.swing.text.DefaultCaret.adjustCaret(Unknown Source)
   at javax.swing.text.DefaultCaret.adjustCaretAndFocus(Unknown Source)
   at javax.swing.text.DefaultCaret.mousePressed(Unknown Source)
   at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
   at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)

Show or hide the answer Insight Encountered an Error while Zooming an Image

The following error has been reported while zooming in and out an image. The problem is due to a memory problem in Java. If you see the problem, you may want to try the OpenGL version of the Beta4.1.1 client. 

java.lang.OutOfMemoryError: Java heap space
at java.awt.image.DataBufferInt.<init>(Unknown Source)
at java.awt.image.Raster.createPackedRaster(Unknown Source)
at java.awt.image.DirectColorModel.createCompatibleWritableRaster(Unknown Source)
at java.awt.image.BufferedImage.<init>(Unknown Source)
at org.openmicroscopy.shoola.util.image.geom.Factory.magnifyImage(Factory.java:249)
at org.openmicroscopy.shoola.agents.imviewer.browser.BrowserModel.createDisplayedImage(BrowserModel.java:529)
Show or hide the answer What can cause slowdown and timeout in the clients?

Things to check:

  • Your network connection, are any other applications having a problem?
  • Are you running out of memory? Processing large datasets can cause problems
  • Is your server's HOME directory on a network share?

When performing some operations the clients make use of temporary file storage and log directories. By default these files are stored below the users HOME directory in $HOME/omero/tmp, $HOME/omero/log and $HOME/omero/sessions. If your home(~) directory $HOME is stored on a network, possibly NFS mounted (or similar), then these temporary files are being written and read over the network. This can slow access down.

The OMERO.server also accesses the $HOME/omero/tmp and $HOME/omero/log folders of the user the server process is running as. As the server makes heavier use of these folders than the clients, if the OMERO.server user's home(~) is stored on a network drive then slow performance can occur.

To resolve this issue for the OMERO.server you can define an OMERO_TEMPDIR environment variable pointing to a temporary directory located on the local file system (e.g. /tmp/).

Show or hide the answer I cannot connect, and I know that I do not have a proxy server. What do I do now?

First, please make sure that you have read through the Troubleshooting page, and that you are using the correct port, username, and password.

If you are still unable to log in using the OMERO clients, then please try clicking the lock symbol on the login window (it should now look like a closed lock).  See also the SSL section of the OMERO security page.

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