Note

This documentation is for the new OMERO 5.1. version. See the latest OMERO 5.0.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.

OMERO version history

5.1.1 (April 2015)

A bug-fix release focusing on user-facing issues and cleaning resources for developers. Improvements include:

For OMERO.web:

• significant review of the web share functionality
• correction of thumbnail refreshing
• fixes to the user administration panel
• fix for embedding of the Javascript image viewer

For OMERO.insight:

• improved open actions
• tidying of the menu structure
• correction of the mouse zoom behavior
• fix for the Drag-n-Drop functionality

Other updates include:

• overhaul of the CLI session log-in logic
• cleaning and testing of all code examples
• further removal of the use of deprecated methods

5.1.0 (April 2015)

A full, production-ready release of OMERO 5.1.0; updating the Data Model to the January 2015 schema, including support for units and new more flexible user-added metadata; and introducing new user features, new supported formats and many fixes and performance improvements:

• support for units throughout the Data Model allowing for example, pixel sizes for electron microscopy to be stored in nanometers rather than being set as micrometers
• new, searchable key-value pairs annotations for adding experimental metadata (replacing OMERO.editor, which has been removed)
• improved workflow for rendering settings in the UI and parity between the clients
• import images to OMERO from ImageJ and save ROIs and overlays from ImageJ to OMERO
• importing as another user, previously only available for administrators, is now usable by group owners as well, allowing you to import data that will then be owned by the user you import it for
• improved performance for moving and deleting data
• removed the auto-levels calculation for initial rendering settings to substantially speed up performance, by using the min/max pixel intensities, or defaulting to full pixel range where min/max is unavailable
• import times are much improved for large datasets such as HCS and SPIM data
• improved performance for many file formats and new supported formats via Bio-Formats (now over 140)
• new OMERO.mail feature lets admins configure the server to email users
• support for configuring the server download policy to control access to original file download for public-facing OMERO.web deployments
• many developer updates such as removal of deprecated methods, and updates to OMERO.web and the C++ implementation (see the 5.1.0-m1 to 5.1.0-m5 developer preview release details below and the ‘What’s New’ for developers page)

5.1.0-m5 (March 2015)

Developer preview release - only intended as a developer preview for updating code before the full public release of 5.1.0. Use at your own risk.

Changes include:

• implementation of OMERO.mail for emailing users via the server
• performance improvements for importing large datasets
• support for limiting the download of original files
• various fixes for searching and filtering map annotations and converting between units
• deprecation of IUpdate.deleteObject API method
• versioning of all JavaScript files to fix browser refresh problems
• clarifying usage of OMERO.web views and templates including RequestContext

5.1.0-m4 (February 2015)

Developer preview release - only intended as a developer preview for updating code before the full public release of 5.1.0. Use at your own risk.

Changes include:

• final Database changes - image.series is now exposed in Hibernate
• improved deletion performance
• client bundle clean-up
• other clean-up work including pep8 and removal of deprecated methods and components
• new Map annotations are now included in the UI and search functionality
• ImageJ plugin updates which allow
  • importing of images and saving ROIs to OMERO from within the plugin
  • viewing images stored in OMERO and their ROIs generated within OMERO from within the plugin
  • updating ROIs on OMERO-stored images within the plugin and saving these back to OMERO without needing to re-import the image
• OMERO.matlab updates re: annotations
• OMERO.tables internal HDF5 format has changed

With thanks to Paul Van Schayck and Luca Lianas for their contributions.

5.0.8 (February 2015)

This is a bug-fix release for one specific issue causing OMERO.insight to crash when trying to open the Projection tab for an image with multiple z-stacks.

5.0.7 (February 2015)

This is a bug-fix release covering a number of issues:

• rendering improvements including 32-bit and float support
• vast improvements in Mac launching (separate clients for your Java version)
• faster import of complex plates
• OMERO.dropbox improvements
• ROI and measurement tool fixes
• OMERO.matlab updates

5.1.0-m3 (December 2014)

Developer preview release - 3 of 4 development milestones being released in the lead up to 5.1.0. Only intended as a developer preview for updating code before the full public release of 5.1.0. Use at your own risk.

Changes affecting developers include:

• implementation of units in the OMERO clients
• conversions between units
• OMERO.web updates
• server-side Graph work to improve speed for moving and deleting
• OMERO.insight bug-fixes especially for ROIs

5.1.0-m2 (November 2014)

Developer preview release - 2 of 3 development milestones being released in the lead up to 5.1.0. Only intended as a developer preview for updating code before the full public release of 5.1.0. Use at your own risk.

Model changes include:

• units support, meaning units now have real enums
• minor fixes for model changes introduced in m1

The units changes mean that the following fields have changed:

• Plane.PositionX, Y, Z; Plane.DeltaT; Plane.ExposureTime
• Shape.StrokeWidth; Shape.FontSize
• DetectorSettings.Voltage; DetectorSettings.ReadOutRate
• ImagingEnvironment.Temperature; ImagingEnvironment.AirPressure
• LightSourceSettings.Wavelength
• Plate.WellOriginX, Y
• Objective.WorkingDistance
• Pixels.PhysicalSizeX, Y, Z; Pixels.TimeIncrement
• StageLabel.X, Y, Z
• LightSource.Power
• Detector.Voltage
• WellSample.PositionX, Y
• Channel.EmissionWavelength; Channel.PinholeSize; Channel.ExcitationWavelength
• TransmittanceRange.CutOutTolerance; TransmittanceRange.CutInTolerance; TransmittanceRange.CutOut; TransmittanceRange.CutIn
• Laser.RepetitionRate; Laser.Wavelength

Other changes that may affect developers include:

• ongoing C++ implementation improvements
• ongoing work to add unit support in OMERO.insight
• further flake8 work
• removal of webtest app from OMERO.web to a separate repository
• removal of deprecated methods in IContainer and RenderingEngine
• removal of deprecated services IDelete and Gateway
• Blitz gateway fixes
• CLI fixes
• ROI and tables work

5.0.6 (November 2014)

This is a critical security fix for two vulnerabilities:

• 2014-SV3-csrf
• 2014-SV4-poodle

It is strongly suggested that you upgrade your server and follow the steps outlined on the security vulnerability pages.

Additionally, a couple of bug fixes for system administrators are included in this release.

5.1.0-m1 (October 2014)

Developer preview release - 1 of 3 development milestones being released in the lead up to 5.1.0. Only intended as a developer preview for updating code before the full public release of 5.1.0. Use at your own risk.

Model changes include:

• channel value has changed from an int to a float
• acquisitionDate on Image is now optional
• Pixels and WellSample types are no longer annotatable
• the following types are now annotatable: Detector, Dichroic, Filter, Instrument, LightSource, Objective, Shape
• introduction of a “Map” type which permits storing key-value pairs, and a Map annotation type which allows linking a Map on any annotatable object

Other changes that may affect developers include:

• strict flake8’ing of all Python code
• C++ build is now based on CMake and is hopefully much more user-friendly
• new APIs: SendEmail and DiskUsage
• the password table now has a “changed” field

5.0.5 / 4.4.12 (September 2014)

This is a critical security fix for two vulnerabilities:

• 2014-SV1-unicode-passwords
• 2014-SV2-empty-passwords

It is highly suggested that you upgrade your server and follow the steps outlined on the security vulnerability pages.

5.0.4 (September 2014)

This is a bug-fix release for the Java 8 issues. It also features a fix for uploading masks in OMERO.matlab.

You need to upgrade your OMERO server if you want to take advantage of further improvements in Bio-Formats support for ND2 files.

5.0.3 (August 2014)

This is a bug-fix release addressing a number of issues including:

• improved metadata saving in MATLAB
• many bug fixes for ND2 files
• several other bug fixes to formats including LZW, CZI, ScanR, DICOM, InCell 6000
• support for NDPI and Zeiss LSM files larger than 4GB
• export of RGB images in ImageJ
• search improvements
• group owner enhancements
• Webclient updates including multi-file download

To take advantage of improvements in Bio-Formats support for ND2 files, you need to upgrade your OMERO.server as well as your clients.

5.0.2 (May 2014)

This is a bug-fix release addressing a number of issues across all components, including:

• import improvements for large image datasets
• shared rendering settings
• better tagging workflows
• disk space usage reporting for OMERO.web admins
• OMERO.matlab annotation handling
• custom Web Start intro page templates
• searching by image ID

To take advantage of improvements in Bio-Formats support for .czi files, you need to upgrade your OMERO.server as well as your clients.

4.4.11 (April 2014)

This is a bug-fix release for the Java Web Start issue. You only need to upgrade if this is a blocker for you and you cannot upgrade to 5.0.x as yet. Also note that the OMERO.insight-ij plugin version 4.4.x no longer works for Fiji, we are working on a fix for this. Plugin version 5.0.x is unaffected.

5.0.1 (April 2014)

This is a bug-fix release addressing a number of issues across all components, including:

• code signing to fix the Java Web Start issues
• stability improvements to search
• MATLAB fixes
• improvements to groups, user menus, file name settings etc
• new import scenario documentation covering ‘in-place’ importing.

5.0.0 (February 2014)

This represents a major change in how the OMERO server handles files at import compared with all previous versions of OMERO. Referred to as ‘OMERO.fs’, this change means that OMERO uses Bio-Formats to read your files directly from the filesystem in their original format, rather than converting them and duplicating the pixel data for storage. In addition, it continues our effort to support new multidimensional images. The changes are especially important for sites working with large multi-GB datasets, e.g. long time lapse, HCS and digital pathology data.

4.4.10 (January 2014)

This is a bug-fix release addressing a number of issues across all components, including:

• improved tile-loading
• better network-disconnect handling
• more flexible
• webapp deployment
• Ice 3.5.1 support (except Windows)
• improved modification of metadata, users and groups

4.4.9 (October 2013)

This is a bug-fix release addressing a number of issues across all components, also including:

• Ice compatibility issues
• new scripting sharing service
• new user help website
• new partner project pages.

The minimum system requirement is Java 1.6 (Java 1.5 is no longer supported).

A security vulnerability was identified and resolved, meaning that we strongly recommend all users upgrade their OMERO clients and servers.

4.4.8p1 (July 2013)

This is a patch release addressing a network connection problem in the clients introduced by a new version of Java.

4.4.8 (May 2013)

This is bug-fix release addressing two specific issues: a problem with the OMERO.insight client for Linux, and image thumbnails not loading for Screens/Plates in Private/Read-Only groups in OMERO.web. You only need to upgrade if you are an OMERO.insight user on Linux or you are using OMERO.web to view HCS data in Private or Read-Only groups.

4.4.7 (April 2013)

This is a point release including several new features and fixes across all components. This includes improvements in viewing of ‘Big’ tiled images, new permission features, new OMERO.web features, and several utility functions in OMERO.matlab.

4.4.6 (February 2013)

This is bug-fix release addressing a number of issues across all components. This includes a major fix to repair the C++ binding support for Ice 3.4. There has also been a potentially breaking update to the CLI.

4.4.5 (November 2012)

This is bug-fix release focusing on improvements to the OMERO clients. OMERO.web now supports “batch de-annotation”, filtering of images by name and improved export to OME-TIFF and JPEG. OMERO.insight has fixes to thumbnail selection and image importing and exporting.

4.4.4 (September 2012)

This is a bug-fix release addressing a number of issues across all components.

• OMERO.insight fixes include connection and configuration options and tagging on import.
• OMERO.web improvements include big image and ROI viewer fixes, improved admin and group functionality and rendering/zooming fixes.
• OMERO.server now has improved LDAP support and VM and homebrew deployments as well as fixes for file downloads above 2GB, permissions, memory leaks and JDK5.

4.4.3 (August 2012)

This is a critical security fix for:

• 2012-SV1-ldap-authentication

Anyone using OMERO 4.4.2 or earlier with LDAP authentication should immediately upgrade to 4.4.3.

4.4.2 (August 2012)

This release is a major bug fix for archiving files larger than 2 GB. If you do not archive files larger than 2 GB, you do not need to upgrade your clients or your server. There is also a minor fix for an OMERO.imagej plugin security issue, but it is only necessary to update the version of Bio-Formats that is installed in ImageJ.

4.4.1 (July 2012)

This is a minor release which fixes two import issues. See #9372 and #9377. If you are not using BigTIFF or PerkinElmer .flex files, then you do not need to upgrade.

4.4.0 (July 2012)

This is a major release, which focuses on providing new functionality for controlling access to data, as well as significant improvements in our client applications.

The major theme of 4.4.0 is what we refer to as “Permissions”, the system by which users control access to their data. It is now possible to move data between groups, and much, much more.

We also added a few more things for users in 4.4.0, like:

• OMERO.insight webstart
• Importing from OMERO.insight is now complete
• Better integration of OMERO.insight with ImageJ
• A bottom-to-top reworking of the OMERO.web design

For developers and sysadmins, there are a few things as well:

• Support for Ice 3.4
• Removed support for PostgreSQL 8.3

Beta 4.3.4 (January 2012)

This is a point release is a security update to address an LDAP vulnerability.

Beta 4.3.3 (October 2011)

This point release is a short follow on to 4.3.2 to handle various issues found by users.

Beta 4.3.2 (September 2011)

This is a point release, focusing on fixes for OMERO.web, export, and documentation. A couple of LDAP fixes were also added, following requests from the community. We also included something many of you have asked for some time, OMERO on virtual machines.

Beta 4.3.1 (July 2011)

This point release focuses on fixes for Big Images, OMERO.web and others.

Beta 4.3.0 (June 2011)

This is a major release, focusing on new functionality for large, tiled images, and significant improvements in our client applications.

The major theme of 4.3.0 is what we refer to as “Big Images”, namely images with X,Y images larger that 4k x 4k. With this release, OMERO’s server and Java and web clients support tiling and image pyramids. This means we have the functionality you have probably seen in online map tools, ready for use in any image file format supported by OMERO (and obviously Bio-Formats). This is especially important for digital pathology, and other uses of stitched imaging.

While the major focus of 4.3.0 was Big Images, there are a number of other new updates. For users, we have worked hard to synchronise functionality and appearance across the OMERO clients. This includes viewing of ROIs in OMERO.web. We are not done, but we have made a lot of progress. Moreover, data import is now MUCH faster and available from within OMERO.insight.

Beta 4.2.2 (December 2010)

Fixes blocker reported using 4.2.1. Starting with this milestone, all tickets for the insight client are managed on Trac.

Beta 4.2.1 (November 2010)

This is a point release, focusing on fixes for delete functionality, and significant improvements in the way OMERO.web production server is deployed.

Beta 4.2.0 (July 2010)

This release is a major step for OMERO, enabling a number of critical features for a fully functional data management system:

• User and Group Permissions and data visibility between users
• updates to the OME SPW Model and improvements in HCS data visualisation
• SSL connection between OMERO clients and server;
• full scripting system, accessible from command line and within OMERO.insight, including Figure Export and FLIM Analysis
• ROIs generated in OMERO.insight stored on server
• extended use of OMERO.Tables for analysis results
• performance improvements for import and server-side import histories
• revamped, fully functional OMERO.web web browser interface
• upgrade of Backend libraries in OMERO.server

Beta 4.1.1 (December 2009)

This release fixes a series of small bugs in our previous Beta 4.1 release.

Beta 4.1 (October 2009)

Improved support for metadata, especially for confocal microscopy; OMERO supports all of the file formats enabled by Bio-Formats. Export to OME-TIFF and QuickTime/AVI/MPEG from OMERO. Various improvements to OMERO clients to improve workflow and use.

This release introduces OMERO.qa - a feedback mechanism, to allow us to communicate more effectively with our community. OMERO.qa supports uploading of problematic files, and tracking of responses to any user queries. Moreover, OMERO.qa includes a demo feature: in collaboration with Urban Liebel at Karlsruhe Institute of Technology, we are providing demo accounts for OMERO. Use the Demo link at qa to contact us if you are interested in this.

For users who have had problems with memory-based crashes in OMERO.insight, the new OpenGL-based ImageViewer may be of interest. Also, we are now taking advantage of our modeling of HCS data, and releasing our first clients that support Flex, MIAS, and InCell 1000 file formats. OMERO.dropbox has been substantially extended, and now supports all the file formats supported by OMERO.

Beta 4.0.1 (April 2009)

A quick patch release that fixes some bugs and adds some new functionality:

• Fixed Windows installation and updated docs.
• Bug fixes (scriptingEngine, importer).
• Fix .lif import, add Li-Cor 2D (OMERO does gels!).
• API .dv and OME .ome.tiff now supported by OMERO.fs.
• Support negative pixel values in Rendering Engine.
• Archived images are now fully supported in OMERO.
• OMERO.web merged with OmeroPy in distribution.

Beta 4.0 (March 2009)

This release consists of a major change in the remoting infrastructure, complete migration of existing OMERO clients to the ICE framework, two new OMERO clients, and integration of OMERO.editor into OMERO.insight.

OMERO.server updates:

• remove JBOSS, and switch all remoting to ICE
• improve session management, supporting creation of many thousands of session
• addition of an import service for server-side importing
• DB upgrades to support the metadata completion facilities
• substantial improvement to the interaction between the indexing engine and the rest of server.

OMERO.importer updates:

• migration to Blitz interface, giving much faster performance
• more efficient importing, complete metadata support for Zeiss LSM510, Leica LIF, Zeiss ZVI, Applied Precision DV, and MetaMorph STK
• addition of command line importer for batch import

OMERO.insight updates:

• migration to Blitz interface, giving much faster performance
• updates to metadata display, include complete support for OME Data Model
• much expanded integration of protocol management via OMERO.editor, within OMERO.insight
• support for image delete
• refinement of Projection Interface

OMERO.web: all new browser-based client for OMERO. Enables sharing of images with colleagues with an account on server.

OMERO.editor: a management tool for experimental protocols, now fully integrated with OMERO.insight, so that protocols and experimental descriptions can be saved along with images and datasets. Includes a new parameters function, so that protocols in traditional documents can be easily imported into OMERO. Supports, tables and .xls files. Also runs as a standalone application.

OMERO.fs: a new OMERO client, that monitors a specific directory and enables automatic imports. In its first incarnation, has quite limited functionality, supporting automatic import of LSM510 files only.

Beta 3.2 (November 2008)

The final update in the Beta3.x series. A number of fixes:

• faster thumbnailing and better support for large numbers of thumbnails
• improved handling of Leica .lei and Zeiss .zvi files
• extended support for reading OMERO.editor files in OMERO.insight
• measurement tool fixes in OMERO.insight
• fixed memory problem in OMERO.insight on Windows
• fixed thumbnailing and session bugs on OMERO.server
• fixed DB upgrades for older PostgreSQL versions

Beta 3.0 (June 2008)

This release of OMERO is a major update of functionality. In OMERO.server, we have added support for StructuredAnnotations a flexible data management facility that allows essentially any kind of accessory data to be linked to images and experiments stored in OMERO. Alongside this, we provide an indexing engine, that provides a flexible searching facility for essentially any text stored in an installation of OMERO.server. Finally, we are releasing our first examples of clients that use the OMERO.blitz server, a flexible, distributed interface that supports a range of client environments. One very exciting addition is OMERO matlab, a gateway that can be used to access OMERO from Matlab®.

OMERO Beta3.0 includes a substantial reworking of our clients as well. OMERO.insight has been substantially updated, with an updated interface to provide a more natural workflow and support for many different types of annotations, through the StructuredAnnotations facility. The new search facilities are supported with smart user interfaces, with auto-complete, etc. New file formats have been added to OMERO.importer, including support for OME-XML, and an improved import history facility is now available. Finally, Beta3.0 includes the first release of our experimental electronic notebook tool, OMERO.editor. This represents our recent efforts to capture as much metadata around an experiment as possible.

Beta 2.3.3 insight (April 2008)

A new Beta 2.3.3 OMERO.insight has been released, this adds rotation to ellipse figure, and new format for saving intensity values.

Note: this version saves the ROIs in a format which is incompatible with previous saved ROIs.

Beta 2.3.1 importer (February 2008)

A new Beta 2.3.1 OMERO.importer has been released which includes a number of new formats: Zeiss AxioVision ZVI (Zeiss Vision Image), Nikon NIS-Elements .ND2 , Olympus FluoView FV1000, ICS (Image Cytometry Standard), PerkinElmer UltraView, and Jpeg2000.

The OMERO downloads for Beta 2.3 include a number of new options: a new import history feature, a Windows server installation, and a new tagging feature for OMERO.insight.

Note: milestone:3.0-Beta2.3 and prior Mac OS X installers for OMERO.server do not work on Mac OS X Leopard (10.5). Please follow the UNIX-based platform manual install instructions. Mac OS X installers for OMERO.insight and OMERO.importer work just fine under Leopard and can be used.

Beta 2.3 (December 2007)

This is a patch release for OMERO.server to fix a memory problem. In OMERO.insight, updating of the tagging facility, viewing of others’ rendering settings and support for server-side compression of images before transport to client.

Beta 2.2 (November 2007)

In this release we have updated OMERO.server to run a newer version of JBOSS and provided support for copying display settings across a range of images. More new file formats. OMERO.insight has been updated to support copying display settings across many images. Image Viewer has been substantially updated.

Beta 2.1 (August 2007)

This is a client-only release. OMERO.insight now supports basic ROI measurements and a series of new file formats have been added. The OMERO downloads for Beta 2.0 have been simplified. OMERO.insight and OMERO.importer have been combined into a single download file called ‘OMERO.clients’ and the user documentation is now included inside of the server and client downloads.

Beta 2.0 (June 2007)

Note: this version will still work with the Beta 1 server release.

This major update provided our first support for multiple platforms via OMERO.Blitz. OMERO.insight now supports viewing work of multiple users. Beta 2 is our first release of the Web2.0-like ‘tag’ system developed in collaboration with Usable Image. This version addresses issues with using our tools under Java 1.6

Beta 1.1 (March 2007)

Patch release to fix time-out issues.

Beta 1 (January 2007)

The first public OMERO release, providing simple data management. Limited file format support (DV, STK, TIFF). Simple data visualization and management.

Milestone M3 (November 2006)

Rendering and compression API and client-side import. Access control and permissions system. Importer based on Bio-Formats.

Milestone M2 (July 2006)

The stateful rendering service is functional and all rendering code moved from Shoola Java client to the server. Also, the stateless services (IQuery,IUpdate,IPojos) are frozen and testing and documentation is checked and solidified.

Milestone M1 (April 2006)

Contains minimal functionality needed to run Shoola Java client without Perl server to demonstrate acceleration of metadata access. Application deployed on JBoss (http://www.jboss.org). No ACLs or permissions.