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OMERO

Questions about the OMERO platform

Show or hide the answer Why have you changed to ICE and what happened to JBOSS?

Though there was a transition period in which both Ice and JBoss were supported, Ice was eventually chosen to be the most appropriate technology:

  • Better cross-language support
  • Faster binary protocol
  • Lower memory overhead

In the end, many of the benefits of a JavaEE application server were not directly applicable to our users, and so the simpler and faster solution was chosen.

Show or hide the answer Do I need a server? / Why?

Why do I have to install OMERO.server to use these tools? Most other image processing applications simply install on my desktop.

OMERO is a client-server application and because of this, OMERO is fundamentally different than most image processing applications that you might have used. OMERO integrates image data from many different different sources, (a range of light microscopy, screening, medical imaging, and soon electron microscopy data formats) into a single resource. A variety of client applications that can all view and analyse data from the same resource. We separate the functions of the server and client applications so that data intensive operations (reading image data from disk, data compression and analysis) are separated from user interaction functionality. This means that users can easily access and share large, multi-terabyte datasets using standard laptops, or even handheld display devices.

So, to make all this happen, you have to install OMERO.server and the OMERO client applications. The client applications are simple, and install just like any other application you use on your desktop or laptop. OMERO.server is a full-blown enterprise data management application, and installing it takes a bit more time. We have provided extensive documentation on server installation.

Currently, we do not provide a running OMERO.server for you to load your data into. If you'd like this facility, please contact Glencoe Software, Inc.

There is however, a demo server you can request an account on to test out OMERO and it is also possible to set up a virtual server on your own machine (detailed How To guide is available here).

Show or hide the answer It failed to start - help?

Begin by reading the rest of the FAQ and the troubleshooting page.

If that doesn't help, please try our forum or email our users list.

Show or hide the answer How do I use MATLAB from OMERO?

See the developer documentation for the Matlab bindings to OMERO.

Show or hide the answer How do I deploy a production version of OMERO.web?

The configuration guide for deploying OMERO.web in a production environment is available at OMERO.web for Windows or OMERO.web for UNIX/Mac.

Show or hide the answer What languages are there API bindings for?

Using the Ice language mapping from http://zeroc.com, OMERO provides access to your data within an OmeroBlitz server from your C++, Java or Python code. More details about OMERO Language Bindings are available:

Show or hide the answer What browsers does OMERO.web support?
  • Firefox 2.0+
  • Internet Explorer 7+
  • Safari 3+
  • Chrome 1+
Show or hide the answer How/Where is my data stored by OMERO?

In our current version, all binary image data, original image files, and annotation data within OMERO are stored in the OMERO Repository (guide for Windows users/guide for UNIX-based users). All other metadata, user info, tags, etc. are stored in the OMERO relational database.

Show or hide the answer What metadata does OMERO read from imported files?

OMERO uses Bio-Formats to read metadata from incoming image files. In general, if Bio-Formats reads the metadata, then OMERO can store it. Please note that supporting ALL metadata in EVERY image file is a huge undertaking, and is a goal, but not a finished task. If you believe we are missing something, please contact us via either the mailing lists or the forums.

Show or hide the answer How do I backup the OMERO server?

Please see the Backup and Restore instructions.

Show or hide the answer OMERO uses PostgreSQL, but we don't. Are you going to support my database or RDMS?

Currently, we are releasing OMERO using PostgreSQL. While support for other RDMS applications is possible, we are just too busy doing other work to also support multiple RDMSs. If you require customization to adapt to another RDMS, contact Glencoe Software, Inc.. They have built an adaptor for OMERO and Oracle 11g.

Show or hide the answer How do I encrypt OMERO communications?

See the SSL section of the OMERO server "Security" page.

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?

Show or hide the answer How do I send log files?

OMERO Server log files are generated under <your omero installation>/var/log, and include the two special files "master.out" and "master.err" as well as several types of rolling files: Blitz-0.log(.1, .2, .3, ...), Processor-0.log(.1, .2, .3, ...)

Client logs files are generated in your home directory under omero/logs. These you can find by going to the "Help" menu and clicking on "Show log file location". In the "log" directory, there are rolling files: importer.log(.1, .2, .3, ...) or omeroinsight.log(.1, .2, .3, ...)

Usually sending us the newest files (those without a numbered ending like ".1") will suffice. If you can then zipping the files first is best.

If your issue relates to OMERO.web, it is worth sending us the Apache, Nginx or IIS logs as well, which can be found usually in the system's /var/log/, e.g. /var/log/apache2, /var/log/httpd, /var/log/nginx or in c:\Windows\System32\LogFiles or c:\inetpub\logs\LogFiles\ by default.

Show or hide the answer Can I edit metadata in OMERO?

This is a long and thorny question. Currently, using the standard OMERO clients (OMERO.insight and OMERO.web) the answer is "No". However, following significant discussion with the community, we intend to provide a facility that stores the original metadata, as first loaded during import, and then the latest version of the metadata, including the latest version of edits from a user.

There is nothing to stop developers writing their own clients (using the OMERO API) to edit metadata on the server.

Show or hide the answer What ports does OMERO use?

The OMERO server can use as few as one port (usually either 4063 or 4064). Enabling OMERO.web requires further ports for HTTP and HTTPS. See the Firewall configuration page for a description of the ports used and how to configure them.

Show or hide the answer What log files does OMERO create and how do configure logging?

See OmeroLogging for more information.

Show or hide the answer How do you download your data using the OMERO.insight client?

It is possible to download data, image or attachments from the OMERO client to your local machine. Please see
OMERO.insight Managing Data for more information about how to do this.

Show or hide the answer What OS permissions do I need to run OMERO?

On all Unix-based systems including Linux and Mac OS X, OMERO clients and server can be installed and run as a regular user. In fact, trying to run the server as root is disallowed.

On Windows, the clients also don't need admin rights, but the server does. Specifically, the user running the server needs rights for starting services.

All ports used by default are above 1024 and also don't require administrator rights.

Whichever user runs the server on any platform will need READ/WRITE permissions to the omero.data.dir.

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

Yes, please look at the OMERO.insight Managing Data page.

Show or hide the answer How do I store my image analysis results in the server?

You can attach analysis results to Projects, Datasets and images on the server, and interact with them via insight.

See: OMERO.insight Managing Data

An example of uploading and attaching a file can be found in the OMERO Python language bindings guide.

You can also use the OMERO.tables service.

Show or hide the answer How do I log in initially to create the users?

Once you have deployed OMERO.web and started the server you can use your browser to access the OMERO.webadmin administration interface on http://your_domain/webadmin/. For more details please see the guide for Windows users or the guide for UNIX-based users.

An administrator panel is also available in OMERO.insight.

Show or hide the answer Can you download entire datasets and/or entire projects?

No, it is currently not possible to download an entire dataset/project from OMERO.

Show or hide the answer How do I setup LDAP support?

Details of how to setup LDAP plug-in are available here.

Show or hide the answer How do I set time zone in OMERO.web

A string representing the time zone is configured in settings.py. Available choices are in the postgres timezone table.

Show or hide the answer Why are my LDAP filters not working?

OMERO uses standard RFC 2254 LDAP filters (http://www.faqs.org/rfcs/rfc2254.html), so they must conform to that syntax and are only able to do what those filters can do. You can test the filters via ldapsearch on your OMERO server (assuming you have the OpenLDAP binaries installed).

Specific filters

memberOf

If using OpenLDAP make sure your directory has the memberOf attribute correctly configured. Some versions of ApacheDS do not support memberOf at all.

Users feedback

LDAP server versions vary. Below, we link to various users experiences on their systems, which may be of use to you:

Show or hide the answer Uploading user photo

'My account' enables you to personalize your user account. To change your avatar click the Browse button and choose one of your favorite pictures from your hard drive. To edit your avatar click 'Crop this picture'. When you are satisfied with the selected rectangular area of an image click the Crop button. For more details please watch the movie.

Show or hide the answer What systems do you support?

Please see the system requirements page.

Show or hide the answer Why is OMERO not starting?

Please have a look on the troubleshooting page for more information or visit one of our communities to ask a specific question.

Show or hide the answer Why can I not login with the LDAP root account?

This is a known limitation. You cannot access OMERO using the LDAP root account. Please login using the local OMERO root account and define another LDAP account as an OMERO administrator.

Show or hide the answer How can OMERO support distributed computing?

OMERO supports distributed computing via the scripting service.

More details about OMERO.grid are available in the sysadmin guide.

Show or hide the answer How do you convert a non-LDAP user to using LDAP?

If you want to take an existing (non-LDAP) user and 'upgrade' them to using LDAP you can do so using the OMERO command line tool:

bin/omero ldap setdn

while logged in as an administrator. The process is also reversible so that the OMERO password for a user rather than the LDAP password will be used. See the caveat in the setdn help output below:

    usage: bin/omero ldap setdn [-h] username dn

    Set DN for user (admins only)

    Once the DN is set for a user, the password set via OMERO is
    ignored, and any attempt to change it will result in an error. When
    you remove the DN, the previous password will be in effect, but if the
    user never had a password, one will need to be set!

    Positional Arguments:
      username            User's OMERO login name
      dn                  User's LDAP distinguished name. If empty, LDAP will be disabled for the user

    Optional Arguments:
      In addition to any higher level options

      -h, --help          show this help message and exit
Show or hide the answer How do I Initialize the Django settings database?

OMERO.web ships with OMERO.server and requires configuration before starting. For more details about how to set up the application, see the server installation guide for your OS - Unix-based/Windows.

Show or hide the answer Why has setup-db failed?

Begin by reading the troubleshooting page. If that doesn't help, please try our forum.

Show or hide the answer I have a crash/exception occurring, how do I send a bug report?

Each of the OMERO clients offers a specific form for reporting bugs. In that form, users can supply their contact details and describe their problem. All of the bugs and comments submitted from the client applications are handled by the OMERO.QA system which provides support services for users of OME's tools and resources. The QA can be used to track and comment on feedback you have submitted to the team as it is dealt with and also manages the import testing of image files which fail to import properly. These files can be submitted by the OMERO.importer or OMERO.insight when an import error is generated and can also be submitted directly to the QA website. More details about OMERO.qa are available here

Show or hide the answer Can OMERO use our existing user accounts?

OMERO.server supports the use of an LDAP server to query information for the purposes of automatic user creation. Details of how to setup the LDAP plug-in are available here

Show or hide the answer How do I use OMERO.web through Apache?

Configuration guides for accessing OMERO.web through Apache are available for Windows users and UNIX-based OS users.

Show or hide the answer Does time machine adequately backup OMERO?

No. Though with regular database dumps as outlined on the backup and restore page, this can be achieved.

Show or hide the answer How should I backup OMERO?

You can see detailed backup advice and information about what should be backed up on the backup and restore page.

Show or hide the answer How should I migrate between OMERO versions?

You can see detailed upgrade documentation for each OMERO version on the OMERO upgrade page.

Show or hide the answer Can I store my binary repository on a share?

You can store your OMERO binary repository on a share as long as you are aware of the consequences of that share disappearing and the permissions that are required on that share. The user that is running the OMERO server must be able to read, write and create directories on this share.

If the share disappears or is inaccessible you will see degraded performance, potential problems with search, object indexing, thumbnails and raw data access. It is recommended that you do so with caution and perhaps keep your thumbnail and full text directories on local and/or highly available disk.

Show or hide the answer How do server quotas work?

Currently it is not possible to set up quotas for OMERO accounts.

Show or hide the answer Why can I connect locally to OMERO but not remotely?

A number of things may be the problem. Good places to start looking for answers are the security (for firewall problems), LDAP (if you are using LDAP authentication) or troubleshooting pages.

Show or hide the answer Does OMERO store data in OME-TIFF/OME-XML format?

No.

Metadata is stored in a relational database (PostgreSQL) and binary data in an optimized proprietary format in the OMERO binary repository. Export to OME-TIFF is supported.

Show or hide the answer How do I get an original image back from the server?
If you are using OMERO 4.4 and chose to archive the original image when importing, you can download it in OMERO.insight or OMERO.web from the download archived files button in the metadata browser. If you are using OMERO 5, your original file will be stored on the server and the saving options menu will give you the option to download it in that format.
Show or hide the answer How can I scale OMERO using load-balancing or clustering?

The exact answer to this depends on

  • what type of usage you are expecting (number of simultaneous users, number of images per day, average size of images, etc.)
  • if you have already run into performance issues
  • what your network and hardware configurations are

Depending on all these and more factors, there are various methods of scaling OMERO and if you contact the list we will do our best to make sensible suggestions.

If you would like to look into the existing load-balancing infrastructure, take a look at: Server/Clustering

There are also classes and interfaces that can be used on a sites to providing session-based balancing and failover, but inevitably these need to be tailored to the specific environment. Technical information on these is available here.

Before going down this road, optimizing your PostgreSQL installation, your filesystem, and your available RAM may be more productive.

Show or hide the answer What anonymous data do the OMERO applications collect?

During the start up of any of our software (bio-formats in ImageJ, importer, insight, webclient, or server) an upgrade check is performed by sending us the following information:

  • Java virtual machine version
  • operating system details (architecture, version and name)
  • current server or client version
  • your (external) IP address and HTTP header information (this is standard with every web request your browser makes) .

This information is used to determine if an upgrade is required. We also use this information to determine usage statistics, primarily to support grant applications for our work.

Additionally, when you use the comment or error-feedback feature in our clients you can also send us an optional email address and comment. These feedback messages may also contain the full pathname of any file you were having trouble with (such as the path to your image file or client application).

In all cases, our goal is to collect this data for the purpose of aiding you with your use of OMERO or for the research and development of our products. Other then this, we collect no personally identifiable information.

Further information about our data collection processes can be found on the Upgrade check guide.

Show or hide the answer Do I use Ice 3.3 or Ice 3.4?

OMERO versions 4.3 and earlier support only Ice 3.3. You will need to download these from ZeroC's previous versions section.

OMERO 4.4 adds support for Ice 3.4 while keeping support for Ice 3.3. For OMERO.server and OMERO.web, you will need to pick the appropriate downloads for the version of Ice you've installed locally. The downloads for Ice 3.4 have "ice34" in the zip name.

OMERO 4.4.9 adds support for Ice 3.5. You can also now download versions of the clients for all three supported Ice versions.

Show or hide the answer Can I store the repository on multiple drives?

If we need to expand the space for the binary repository can it spread across multiple drives? Can we have multiple repositories? What is the best way to do this?

One of our next major features will include a re-examination of the repository infrastructure to hopefully allow more than one. At the moment, however, you can only access one repository.

If you would like to access additional disk space of a new drive from the same OMERO instance, you can symlink some directories from /OMERO off to the new location. /OMERO/Pixels tends to be the largest directory, and it will contain up to 1000 files and 1000 directories. You can move any number of those on the other disk, replacing them with symlinks.

Show or hide the answer Why am I getting read/write errors after reinitialising OMERO?

If you decide to wipe clean you OMERO installation you have to clean both the database and the binary repository. If you clean and reinitialising only the database or only the binary repository your system will be left in an unknown state and will produce either read or write errors.

Full instructions for backing up, cleaning, or restoring you OMERO server are available in the documentation.

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