- How do I get support for your software?
- Open source support for the various OME products is provided via either the OME mailing lists or the OME Forums. Commercial support is provided by Glencoe Software, Inc.
- What’s the difference between the OME and the OMERO server?
OMERO server is an enterprise application written in Java that provides integration, visualisation, management, and analysis of biological image data. The OMERO clients allow the scientist to remotely manage, view, annotate and measure multi-dimensional images from anywhere. It is the focus of our current development effort.
The OME server is a Perl-based system which was actively developed until 2005, but is no longer worked on. Questions or comments can directed to the OME mailing lists or the OME Forums. Legacy documentation is still available here.
- Which server platforms do you support?
The OMERO server runs on most Unix-based platforms, including Linux and Mac OS X, and Windows subject to certain prerequisites. See the OMERO Documentation for more details.
- Besides the image data, how do I capture other experimental data?
The OMERO.editor tool can be used to add Protocols and Experimental metadata to Projects, Datasets and Images in OMERO. A movie demonstrating this functionality in the OMERO Beta 4.1 release is here. There is also a user guide available.
It is also possible to annotate projects, datasets and images with a Description, add Comments and Tags, as shown in various movies on the OMERO feature list page.
- High Content data support
Support for High Content Data was first added to the OME-Data model in June 2007.
- Do you have 64-bit support?
Through the usage of a 64-bit Java virtual machine you can use any of the client applications, OMERO API or OMERO.server on a 64-bit platform.
- What license does your software use?
Full licensing information is available on the OME licensing page.
- How do I collaborate with you?
There are lots of ways to work with the OME Consortium. Most people use the OME Forums or the Mailing Lists to communicate their needs, status or problems. If you want to work with our source code, there is now a whole set of documentation to help you to contribute to OME projects. If at all possible, consider coming to the next OME User's Meeting to meet us, tell us what you're doing and discuss how we can both help each other.
- How do I cite OME, OMERO, VisBio, or Bio-Formats?
Details of the best citations to use are available here: Citing OME
- What is the copyright information for OME material?
As OME is a consortium of separate groups, from different institutions, working together on a common product you will find different copyright messages across our code, documentation, products and publications. These messages reflect the origin of that particular part of our material.
Note: the origin is just that, it does not indicate that people from that institution are responsible for that code now. For example, if a file is created by Glencoe, but worked on extensively by team members from Dundee, its copyright will not change.
Agreements exist between the different entities in the consortium to release the material together under a unified license.
- Can I save/convert microscopy files between formats with your software?
Using Bio-Formats, we support conversion from any supported format into a few different "open standard" formats including OME-TIFF. As shown on the supported formats table, you can convert from any format on the list into any format with a green checkmark in the "Export" column.
We have no plans to convert into any vendor's "closed-source" proprietary microscopy formats. Philosophically, we believe that writing to proprietary file formats reinforces the proliferation of proprietary files, and further validates vendors' continued creation of incompatible formats. Instead, we are promoting OME-TIFF as the standard, and believe the community would be best served by petitioning vendors to support OME-TIFF as at least an interchange format. Further, from a practical perspective, we have limited resources, and feel they are better served adding additional readers and fixing bugs rather than creating proprietary format writers. Lastly, the Bio-Formats writer API is open. There is nothing to stop a vendor from creating a writer for their particular format. We would even be happy to include it in Bio-Formats, if they are willing to open source their code.
- How many file formats do you support?
OMERO imports all the formats read by Bio-Formats including microscopy, HCS, tissue scanner and graphics file formats. See the supported formats table for full details.
- What AVI compression formats do you support?
There are a limited number of AVI input compression formats supported by Bio-Formats and thus supported by OMERO.importer:
- MSRLE (Microsoft Run Length Encoding)
More compression formats are supported if you use a MOV container and have QuickTime for Java installed. However, the portability of QTJ is very limited (Mac OS X and Windows only), it has several bugs, and has been deprecated by Apple.
All these source formats are at present stored uncompressed in OMERO.server after import, so if your goal is to reduce drive space usage overall, having a compressed source movie is not going to help.
- Are you considering translating Bio-Formats to any other languages?
We are currently actively developing native C++ support for Bio-Formats. Updates on our progress are posted to the mailing lists, please subscribe if you are interested.
In the meantime, documentation is available to help with interfacing from non-Java code. We are committed to exploring and developing these methods further to make Bio-Formats work for as many applications as possible, and welcome community feedback and ideas on this issue.
- We have a lot of data from a home built system. Can you read it?
We can certainly add support for your data. In order to do so, we ask that you send any documentation that you may have regarding the file format in which the data is stored, along with a representative collection of example datasets. Please contact the OME team using our ome-users mailing list for details on how to send data.
- My dataset has multiple files. Which file should I open (or import)?
Please see this table: Bio-Formats Dataset Structure Table
- How do I save a dataset to multiple files?
Examples of how to save a dataset to multiple files are available on the Bio-Formats export page.
- I see an 'OutOfMemory' or 'NegativeArraySize' error message when attempting to open an SVS or JPEG-2000 file. What does this mean?
An 'OutOfMemory' error message indicates that the amount of pixel data in a single image plane exceeds the amount of memory allocated to the JVM. A 'NegativeArraySize' error message indicates that the amount of pixel data in a single image plane exceeds 2 GB.
In the former case, increasing the amount of memory that is allocated to the JVM should solve the problem. In the latter case, you will need to open the image in sections. If you are using Bio-Formats as a library, this means using the 'openBytes(int, int, int, int, int)' method in loci.formats.IFormatReader; if you are using Bio-Formats within ImageJ, this means selecting the 'Crop on import' option.
Note that JPEG-2000 is a very efficient compression algorithm - thus the size of the file on disk will be substantially smaller than the amount of memory required to store the uncompressed pixel data. It is not uncommon for a JPEG-2000 or SVS file to occupy less than 200 MB on disk, and yet have over 2 GB of uncompressed pixel data.
- Why do my Slidebook files take a long time to open?
The Slidebook file format is quite complex, and unfortunately we do not have a lot of information about it. As a result, Bio-Formats must scan through the entire file to find the pixel data, which can be quite slow depending upon the size of the file.
As recent versions of Slidebook support exporting to OME-TIFF, we recommend that you use the Slidebook software to export your .sld and .spl files to OME-TIFF. You can then use Bio-Formats to open the OME-TIFFs directly.
- How can I invoke Bio-Formats from my language of choice?
See the article on interfacing from non-Java code.
- Can you send me the specifications for format XYZ?
- The Bio-Formats website mentions that you have specification documents for format XYZ? Can you please send them to me?
In short, no. Most of the specification documents that we have are covered by non-disclosure agreements; distributing the documents would be a violation of those agreements. The list of specifications that we have for each format is provided merely as an indication of how well the format is supported and how supportive the format's owner has been of Bio-Formats.
If you really need the specification for a particular format, we advise that you contact the format owner directly.
- How do I open compressed Opera FLEX files?
If you see an error message similar to "loci.formats.MissingLibraryException: The LuraWave decoding library, lwf_jsdk2.6.jar, is required to decode this file." when opening PerkinElmer Opera FLEX files, then the files are compressed. The Lurawave codec is then required to decompress your files; unfortunately, we are not able to distribute it.
The best thing to do is to use Macbiophotonics ImageJ to convert your LuraWave .flex files to OME-TIFF, and then import the OME-TIFF files into OMERO. You should be able to open the files in ImageJ by selecting "Plugins > Bio-Formats > Bio-Formats Importer", and save them as OME-TIFF by selecting "Plugins > Bio-Formats > Bio-Formats Exporter".
- Why is bio-formats written in Java?
- How do I programatically retrieve metadata from a file?
The GetPhysicalMetadata, PrintTimestamps, and PrintLensNA examples illustrate how to retrieve some commonly used metadata values. All three examples use the loci.formats.meta.MetadataRetrieve class to retrieve metadata, so it's a good idea to read the Javadocs for MetadataRetrieve in order to determine which methods will give you the metadata that you are looking for.
- Isn't Java too slow?
We don't think so - see the discussion on LOCI.
- What happened to the 'openImage' method in IFormatReader?
The 'openImage' method is now in loci.formats.gui.BufferedImageReader. If 'reader' is the IFormatReader object that you are currently using to open images, then all you need to do is add this line of code after declaring 'reader':
BufferedImageReader imageReader = new BufferedImageReader(reader);
You will then need to replace 'reader' with 'imageReader' in subsequent lines of code.
- How do I add support for a file format?
Bio-Formats is an open project, and as such we strongly encourage other developers to contribute file format reader modules. Our time is limited, and we can use all the help we can get. We have created a guide to coding new file format readers that will hopefully be useful to you in your endeavor, and we would be happy to assist you with any questions or problems you encounter—just email us.
- How can I cooperate with the Bio-Formats developers to improve support for a format?
If you are a programmer, you can help by writing and contributing a file format reader module for Bio-Formats—see How do I add support for a file format to Bio-Formats?.
If you are a user, but do not control the format, you can help by letting us know you are interested in the format, and sending us some sample data if possible. Several currently supported formats were added specifically because someone emailed us asking about them. We have an FTP server set up for users to upload large data to us—email us for details.
If you do control the format, you can start by releasing technical details to the community. Publishing a file format specification document, sample data files, and example source code to your web site is extremely useful for external developers to successfully deal with your format. Once you do, we invite you to let us know and we will be glad to work on adding support for the format as our time permits.
If you are a company unwilling to release details publicly, we urge you to reconsider—see Why should my organization open our file format to the community?. If you insist upon keeping your format secret, you could implement your own Bio-Formats file format reader module to enable support in third party applications such as ImageJ, OME and VisBio. Or you could send technical details to the Bio-Formats developers, who will attempt to add support for it, as time permits.
- Why should my organization open our file format to the community?
You may feel that by concealing the details of your format, you can "lock in" your customers to a particular software package, or protect your organization in case of errors, but hiding your format has drawbacks:
You will generate animosity among your users when they cannot easily perform needed operations on their data. As a result, your users may switch to another vendor, or even build their own systems, the next time they upgrade their hardware (or perhaps even immediately).
Your format will almost certainly be reverse engineered anyway, unless you poison your format by hiding behind the DMCA or similar law, in which case your format will be unusable and customers will abandon it completely. Since a reverse-engineered implementation is less likely to completely and correctly reflect the quality and depth of your format, it would be more in your interest to assist the community in an open implementation, or at least provide them with a specification document so that they can create one themselves.
- OME-TIFF is insufficient to my organization's needs, so we provide our own format instead. You'll support it via Bio-Formats anyway, right?
Such an attitude does not serve the best interests of the community, nor is it likely to be advantageous to you, ultimately. Supporting OME-TIFF directly will earn good karma points with your users/customers, while providing yet another impenetrable, incompatible format that makes your users feel trapped and powerless will certainly earn some bad karma.
As OME-TIFF becomes more prevalent, users will increasingly demand direct support for it at acquisition time. It makes more sense to provide this support yourself, rather than rely on a third party such as Bio-Formats to convert the data after the fact.
It may be that OME-XML does not encompass every piece of information you wish to record. However, you can work with the community to extend the specification to accommodate your needs. There are advantages to leveraging the community's efforts:
- Your developers will spend their time more efficiently, and you will produce a more versatile final product. Though interfacing with the community will require some time investment, you will easily regain any time lost by harnessing community code, and your end result will be both more powerful and more maintainable than otherwise.
- You will save on support, since many types of support requests will be directed at the community rather than at you specifically. Of course, you will still need to fix bugs in your software. But you will have help from external developers with tasks such as fixing bugs in Bio-Formats and extending the OME-XML specification, whereas if you develop your own proprietary solution, all of these support tasks become your organization's sole responsibility.
- You will be recognized as a progressive, forward-thinking organization dedicated to improving available microscopy tools.
- Why TIFF? What about other container formats?
The one word answer is: compatibility. TIFF files are readable in a large number of existing software tools, and when coupled with OME-XML also flexible enough to accommodate the needs of the microscopy imaging community.
That said, OME-TIFF is merely one example of an alternate pixels container for OME-XML metadata; others are certainly possible. If you do not like TIFF for some reason, you can use the OME-XML format directly, or utilize a different container format. However, we urge you to consider using the OME-XML standard for metadata, rather than creating yet another incompatible metadata representation.
- What file extension should I use when saving OME files?
We would recommend:
OME-XML file: filename.ome.xml
OME-TIFF file: filename.ome.tif
- How can I check the validity of an OME-XML or OME-TIFF file?
Since the online validator is not working just now, we suggest you validate your file on the command line using Bio-Formats.
- What does the online validator check?
The validator does the following steps:
- If OME-TIFF extract the OME-XML from the header.
- Examines the OME-XML block and determines the correct schema.
- Validates the OME-XML against that schema reporting any errors, and then checks with the other older/newer schemas too but just "for info".
- Scans the OME-XML and records all object IDs.
- Scans the OME-XML and checks all Refs and Settings objects point to an ID that is present in the file.
- If OME-TIFF examined the TiffData nodes and calculates the number of TIFF frames needed to make the file complete, then check the TIFF structure to see if there are enough frames present in the file. If not the file is still valid but incomplete (normally part of a multi-file OME-TIFF). Groups of files cannot be checked together yet.
This is just checking the structure of the data. No attempt is made to make sure the data values make sense.
- Why is my LSID being marked as invalid and not accepted?
The LSID specification defines the first three portions as case-insensitive, that is "URN:LSID:(Authority)". The remaining portion is case-sensitive. In OME-XML however we assume lower case for the first two portions "urn:lsid:", for "(Authority)", normally a domain name, any case is acceptable but lower case is recommended for consistency. The remaining portion is case-sensitive.
For full information on our use of LSID in OME-XML see: IDs and LSIDs in OME-XML
- How do I edit the XML in an OME-TIFF?
To edit the XML in an OME-TIFF file you can use
tiffcomment, one of the Bio-Formats tools.
To use the built in editor run:
tiffcomment -edit sample.ome.tif
To extract or view the XML run:
To inject replacement XML into a file run:
tiffcomment -set 'newmetadata.xml' sample.ome.tif
- How do I validate a file on the command line?
This uses the Bio-Formats command line tools.
Download and unzip the tools from our downloads page to produce a collection of command line scripts for Unix/Mac and batch files for Windows. The two commands we will use are
xmlvalid– a command-line XML validation tool
tiffcomment– extracts the OME-XML block in an OME-TIFF file from the comment in the TIFF's first IFD entry.
Note that from version 5.0.0 onwards, the command line tools come bundled with everything you need. For Bio-Formats 4.4.x versions, you will need to download the loci_tools.jar and place it into the same folder as you unzipped bftools.zip into.
Then to validate an OME-XML file
This validates the XML directly.
Then to validate an OME-TIFF file
tiffcomment sample.ome.tif | xmlvalid
This extracts the OME-XML from the TIFF then passed it to the validator.
Typical successful output is:
[~/Work/bftools]$ ./xmlvalid sample.ome Parsing schema path http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd Validating sample.ome No validation errors found. [~/Work/bftools]$
If any errors are found they are reported. When correcting errors it is usually best to work from the top of the file as errors higher up can cause extra errors further down. In this example the output shows 3 errors but there are only 2 mistakes in the file.
[~/Work/bftools]$ ./xmlvalid broken.ome Parsing schema path http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd Validating broken.ome cvc-complex-type.4: Attribute 'SizeY' must appear on element 'Pixels'. cvc-enumeration-valid: Value 'Non Zero' is not facet-valid with respect to enumeration '[EvenOdd, NonZero]'. It must be a value from the enumeration. cvc-attribute.3: The value 'Non Zero' of attribute 'FillRule' on element 'ROI:Shape' is not valid with respect to its type, 'null'. Error validating document: 3 errors found [~/Work/bftools]$
- How often are new schema versions released?
About once or twice a year for Major releases. It is driven by users' requests for model changes.
The releases are now in sync with releases of OMERO and Bio-Formats.
For more information see Schema version information.
- Some metadata is missing from your schema. What can I do?
This allows others to provide input to ensure the metadata is added in the most appropriate location so it can work in all cases. From there it will progress to a ticket on the Trac and after research to find the most general name for the term it can get rolled into the next schema release.
In the short term it is also possible to use StructuredAnnotations to store the value into the existing schema.
- How can you represent binary image data in XML using plain text?
Binary data is represented in XML using Base64 encoding See RFC 1341 Section 5.2. Binary data is a string of numbers in base 2 represented by a series of bits (binary digits). These same numbers can be represented in base 64 using a series of base 64 digits. The convention for representing base 64 digits is to use the upper and lower case letters (52 digits), the numbers (+10 digits), and two punctuation characters '+' and '/' (total = 64).
Since each byte can represent a value from 0 to 255, we would need two base 64 digits to represent it. If we did that, we would need twice the storage to convert binary into plain text. Instead we can convert 3 bytes at a time into 4-digit base 64 numbers. This makes the plain-text representation of binary data "only" 1/3 larger.
- Where can I get some sample data files?
We have a small collection of sample files available that are designed to demonstrate the format.
General simple samples are available from:
- Which TIFF IFD fields are required in OME-TIFF?
The only requirement is that the ImageDescription directory entry must be present in the first IFD, and populated with a valid OME-XML metadata block.
Otherwise, OME-TIFF files do not need any IFD fields beyond what would be required for a regular TIFF. Please see the TIFF specification for a list of IFD fields required for regular TIFFs.
- Does OMERO Support FLIM files and FLIM analysis?
OMERO supports the uploading and viewing of most FLIM files via Bio-Formats, see the supported formats table for details. Currently, the OME-XML model does not support N-Dimensional Data but our 6D, 7D and 8D solution provides a stop gap, allowing some FLIM data imported with a ModuloAlongT annotation to be correctly displayed in OMERO.insight. We are actively working to add full N-Dimensional Data support to the OME Data Model, OMERO and Bio-Formats.
Our partners at Imperial College London have written FLIMfit, an OMERO client for viewing and analyzing FLIM data.
- What support is there for BigTIFF?
The Bio-Formats library and command line tools can work with BigTIFF files.
OMERO.importer has support for the format as it is using the Bio-Formats library but you should be aware that when working with very large files you may hit other limitations on image size related to the import and rendering support in the OMERO server.
The addition of the 'Big Image' support into OMERO in v4.2 has removed most, but not all, of these restrictions.
- Do you have any support for HDF (Hierarchical Data Format)?
While we have looked at HDF and would be interested to talk to anyone who wants to develop a general HDF solution for storing images and metadata, but we do not at present have an OME format.
Bio-Formats does support some proprietary formats that use HDF and we do make some use of HDF internally in our software.
- 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.
- 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.
- It failed to start - help?
Begin by reading the rest of the FAQ and the troubleshooting page.
- How do I use MATLAB from OMERO?
See the developer documentation for the Matlab bindings to OMERO.
- How do I deploy a production version of OMERO.web?
- 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:
- What browsers does OMERO.web support?
- Firefox 2.0+
- Internet Explorer 7+
- Safari 3+
- Chrome 1+
- 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.
- 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.
- How do I backup the OMERO server?
Please see the Backup and Restore instructions.
- 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.
- How do I encrypt OMERO communications?
See the SSL section of the OMERO server "Security" page.
- 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?
- 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
- 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.
- 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.
- What log files does OMERO create and how do configure logging?
See OmeroLogging for more information.
- 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.
- 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.
- Can you upload non image related files in to projects?
Yes, please look at the OMERO.insight Managing Data page.
- 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.
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.
- 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.
- Can you download entire datasets and/or entire projects?
No, it is currently not possible to download an entire dataset/project from OMERO.
- How do I setup LDAP support?
Details of how to setup LDAP plug-in are available here.
- 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.
- 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).
If using OpenLDAP make sure your directory has the
memberOfattribute correctly configured. Some versions of ApacheDS do not support memberOf at all.
LDAP server versions vary. Below, we link to various users experiences on their systems, which may be of use to you:
- 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.
- What systems do you support?
Please see the system requirements page.
- Why is OMERO not starting?
- Why can I not login with the LDAP root account?
This is a known limitation. You cannot access OMERO using the LDAP
rootaccount. Please login using the local OMERO
rootaccount and define another LDAP account as an OMERO administrator.
- 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.
- 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
- How do I Initialize the Django settings database?
- Why has setup-db failed?
- 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
- 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
- How do I use OMERO.web through Apache?
- Does time machine adequately backup OMERO?
No. Though with regular database dumps as outlined on the backup and restore page, this can be achieved.
- 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.
- How should I migrate between OMERO versions?
You can see detailed upgrade documentation for each OMERO version on the OMERO upgrade page.
- 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.
- How do server quotas work?
Currently it is not possible to set up quotas for OMERO accounts.
- 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?
The launch of OMERO 5 featured the introduction of OMERO.fs, a new repository infrastructure which allows multiple drives. See the FS configuration documentation for further details.
- Why can I connect locally to OMERO but not remotely?
- Does OMERO store data in OME-TIFF/OME-XML format?
Metadata is stored in a relational database (PostgreSQL) and binary data in the OMERO binary repository, in an optimized proprietary format if you are using OMERO 4, or in its original file format if you are using OMERO 5. Export to OME-TIFF is supported.
- 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.
- 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.
- 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.
- 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.
- 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.
- Can I open an image stored in OMERO in ImageJ?
Yes, an OMERO ImageJ plugin is available. Visit our Downloads page.
- 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
The connection is always secured. You can also choose to transfer all data in a secure manner.
- 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.
- 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
- 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.
- Can I modify the Acquisition metadata?
No, not yet. The acquisition metadata e.g. Objective, Detector are READ-ONLY.
- 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.
- Can I combine multiple files into channels?
- We have a script that lets you do this. Look under "Combine Images" in the using utility scripts guide.
- 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 user guide for export scripts.
- 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.
- 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.
- 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:
- How do I add my own agent to OMERO.insight?
See How to Build an Agent in the developer documentation.
- 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.
- My file failed to import. What should I do?
When a file import fails, it should provide you with an error message. You can view it by selecting "Failed". You can also submit the error for correction. Most errors are usually corrected by the next major release. Finally - you can try reimporting the image.
To help fix the error, we recommend that you send us your original 'failed' file during this process (by selecting "Mark to Send"), 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.
If your file fails to import due to losing network connection after being left running for a long period unattended, you should check your sleep settings (System preferences > Energy Saver on Mac OSX, or Control panel > Hardware and Sound > Power options on Windows 7) and change them so your computer never goes to sleep when you intend to leave a large import running.
- What protocols do the OMERO java client use?
The OMERO java clients use TCP/IP.
- 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.
- 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.
- Can you upload non image related files?
Yes, you can upload 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. A managing data user guide is available here.
- 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.
- What are the supported Permissions in an OMERO Group?
- 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 Read-only or Read-Annotate permissions, these cannot be severed. However, it is possible to 'promote' a Private group to use Read-Only or Read-Annotate permissions.
- What operations are allowed and restricted with a Collaborative Group?
Please see the Permissions page for full details.
- 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
- Can I move data between groups?
Yes - this functionality was introduced in the 4.4.0 release. Previously, it is NOT possible to move data between groups.
See the user guide for sharing data.
- 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.
- Can I use Java Web Start under OS X 10.8?
The new security features in Mac OS X 10.8 (Mountain Lion) prevent users from launching OMERO.insight via Java Web Start using the standard system security settings. The system wide setting needs to be changed in preferences, and this has security implications.
If you must use Java Web Start to launch OMERO.insight on you machine you must make the following changes:
- Go to the System Preferences
- Select Security & Privacy
- Click the lock to make changes and authorise as an admin (if necessary)
- Select "Allow applications downloaded from: Anywhere"
You should now be able to launch OMERO.insight via Java Web Start. You should be extra vigilant about the source of any downloaded applications while your computer is in this state.
If you stop needing to use OMERO.insight via Java Web Start we recommend you reset your settings:
- Select "Allow applications downloaded from: Mac App Store and identified developers"
See OMERO.insight webstart security and code-signing for more information.
- 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)
- 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/sessions. If your home(
$HOMEis 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/logfolders 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_TEMPDIRenvironment variable pointing to a temporary directory located on the local file system (e.g.
- What are Runs and Fields?
Run corresponds to PlateAcquisition and Fields to WellSamples in the Screen/Plate/Well OME model for HCS.
- Why is my Java Web Start shortcut broken under OS X 10.8?
There seems to be a general problem with the shortcuts created by Java Web Start on Mac OS X 10.8 (Mountain Lion). The shortcuts give an error on launch and do not start OMERO.insight. There does not seem to be a work around for this. You have to either install the standard stand-alone version of the OMERO.insight client, or launch it each time form the Web Start location on your server.
- Why is OS X 10.8 directing me to download Java?
As of Mac OS X 10.8 (Mountain Lion) new installs of the system and new laptops do not come with Java pre-installed by Apple. When you run a java application like the OMERO.insight client you are prompted to install Java directly from java.com
- Does OMERO.web work with Internet Explorer 8?
Yes, but if you're using Internet Explorer 8 you must have "Compatibility Mode" turned off.
- What is Ivy?
- Ivy is dependency manager which OMERO uses to organize the various jar depends of the server and client components. Similar to Maven, Ivy uses description files -- ivy.xml -- to define the various transitive dependencies for each artifact.
- Sample code?
Sample code is provided on the developer sites for each product.
- Where can I get the source code for your applications?
The source is maintained in git and can be browsed via gitweb.
See the checking out the source code page in the developer documentation for further information.
- How do I build on Windows?
For building everything except for the C++ bindings, the installing OMERO from source documentation provides details for checking out and building. Omero C++ language bindings has info for compiling the C++ code with Visual Studio.
- How do I build OMERO from Eclipse?
After checking out the source, you will need to run:
to have the Eclipse paths properly setup. This should be done minimally after a successful invocation of just "./build.py" or optimally after running "./build.py test-compile".
After that you can either import the top-level OMERO_HOME/.project or any of the individual projects under components. For more information, see the build system Developer documentation.
- How do I run OMERO.importer from Eclipse?
After checking out the source, you will need to run:
to have the Eclipse paths properly setup. After that you can import either the top-level OMERO_HOME/.project or the individual importer project under components/tools. For more information, see the OmeroDevelopement page on the OMERO server trac.
- Where can I track issues and daily builds?
Most of the projects are built per commit, and builds along with unit tests, and javadocs (or similar) can be found at http//hudson.openmicroscopy.org.uk
Issues for server, clients and the model are all tracked on a single trac site http://trac.openmicroscopy.org.uk/omero
- How do I add Structured Annotations to an object(image/project/dataset...)?
Structured annotations permit the attachment of data and metadata outside the OMERO data model to certain types within the model. More details about structure of annotations is available here.
- How do I login to OMERO?
If you wish to log in by OMERO.insight please follow the instruction on: OMERO.insight getting started guide.
If you wish to log in by OMERO.web please go to one of the following urls:
- What frame of reference does OME uses to map ROI to a picture?
In OMERO, ROIs are defined by one or more Shapes (e.g. Rectangle, Ellipse), allowing an ROI to span multiple Z and T sections.
The position of a Shape on an image plane is given by x and y coordinates from the top left of the image.
Different shapes, listed here are measured differently:
- Rectangle has x and y to define the location of the top, left of a rectangle,
Ellipse has cx and cy to denote the x, y coordinates of the ellipse center.
- How do I use closeOnDestroy & detachOnDestroy?
closeOnDestroy and detachOnDestroy are used to decide whether or not a session will persist after your current client disconnects. If a session is left alive (detached and not closed), then other processes can attach to it and continue processing where the first client left off. If multiple clients connect to a session at the same time, only the setting (closeOnDestroy or detachOnDestroy) of the last session to disconnect will be taken into account. Before that, the session is kept alive.
By default, the setting is "closeOnDestroy". Therefore, if you plan on re-using a session, use detachOnDestroy before calling client.closeSession(). Otherwise, you don't need to worry about either of these methods.
- Rules configuration in OMERO model?
At one point in time, it was suggested that rule based validation of OMERO model objects would be beneficial. While this is still true, the implementation and usage overhead of such a feature was deemed too high at this point. Right now these rules are unimplemented and unused even though some may still appear in OMERO model DSL files.
- Is there a database diagram?
The OMERO database schema is reasonably large and complex so a diagram is not the greatest way to represent it. As it has been requested a few times we generated one for version 4.1. We would not recommend trying to work from it.
It is available here but is a very large pdf:
Database Diagram for OMERO 4.1 generated March 2010
The PDF has two layers so in an application that supports layers the lines can be turned off to see the tables easier.
If anyone can recommend a good application for generating a diagram from either a Postgres database or direct from the SQL please get in touch.
- In OMERO what are atime/ctime/mtime, and how are they used?
These stand for:
- access time
- creation time
- modification time
They are to allow clients to write as much information as is available on the linux file system into the database. These values are left in the user space, i.e. the server doesn't try to control them, for example when you access a file the
atimeis NOT incremented.
These are defined in "file system" terms as opposed to "biologist" frame of reference, where creation could be the "acquisition" timestamp. This acquisition information is stored in the OME data model.
- Can OMERO store images as doubles?
Can you store images back to OMERO from Matlab as doubles? They seem to be rounded to integers.
If you access the pixel values through the API, you can write images back to OMERO as doubles. The values will be stored correctly and if retrieved using the API the values will be correct.
The OMERO rendering engine does not yet support this data type. We have a ticket for that: see #1303. Therefore the OMERO clients cannot display this data correctly at present.
The values are stored correctly and will be viewable through the clients when the rendering engine has been update to full 32 bit data.
- How do I access shared data from the API?
If you are using the API to access/analyse and store data, you do you access shared data?
Shared data is stored in a different Experimenter Group to your own data.
You have a few options:
- In your ice.config file you can set omero.group to the shared group id that you want to be logged into.
- You can pass in the group ID when you are logging into the server from the API.
- You can change the Security Context of you Session after you have logged in.
Once you are logged into a group context that is collaborative, service methods will begin returning shared data as well as your own, unless the JavaDocs specifically state that it's a method which returns only your own data.