OMERO version history¶

5.4.8 (September 2018)¶

This release focuses on a number of import performance improvements while including several other fixes as well as an upgrade of Bio-Formats.

Import improvements include:

cli: new experimental –parallel-upload and –parallel-fileset flags to the import command
cli: new fs importtime cli command
cli: add support for –skip, –parallel-upload, –parallel-fileset and –readers options in bulk import configuration files
insight: new options for skipping various import steps to speed up the process (match cli’s –skip option)
insight: supporting imports with thousands of files by providing a lightweight UI
insight: new loading placeholder when browsing data to to show when an image is busy being processed and not ready to generate a thumbnail
insight: added error placeholder when browsing data to indicate a failed import
server: preventing recalculation of checksums for upload
server: providing better performance logging, accessible to users via fs logfile
as well as preservation of Bio-Formats’ knowledge of channel colors where provided.

Other client changes include:

web: better handling of large numbers of channels
web: fixed socket leakage on unclosed web sessions
web: fixed issue with bulk annotation table handling
cli: deprecating admin sessionlist and config list

Sysadmin improvements include:

new %thread% option for omero.fs.repo.path as well as fix a few bugs for dealing with parallel imports
new omero.threads.background_threads property to limit the number of simultaneous imports

This release also upgrades the version of Bio-Formats which OMERO uses to 5.9.2.

5.4.7 (July 2018)¶

This is a security release which also includes a number of bug fixes. It is highly recommended that you upgrade your server.

See the security advisories page for details on 2018-SV1, 2018-SV2 and 2018-SV3.

Impacts of the security vulnerability fixes include:

omero.security.password_required=false no longer applies for administrators: their correct password is always required
administrators can no longer change the password of other administrators who are more privileged in any way
administrators can no longer reset their password and receive the new one by e-mail: they must instead have another administrator who is at least as privileged set a new password manually
cli: the session UUID has been removed from the standard output when logging in but can still be retrieved using bin/omero sessions key

Improvements include:

web: fix loss of privileges when editing full admins
web: fix exceptions on invalid connections
web: fix CSS in group/user search element
web: fix error when public user is disabled
web: gray out user role when editing root user
insight: permit open_with on original files
read-only: reduce error logging for scripts and pixel data
scripts: improve error messages for invalid MATLAB
as well as various documentation improvements

Sysadmin improvements include:

log locale and time zone information on startup

Developer updates include:

cli: clean up “communicator not destroyed” logging
cli: don’t hang when incorrect password passed in a script
java: add a map annotation example
java: throw a clear exception when -1 is used for all groups
web: fix @render_response when extending base templates
matlab: contributions from Kouichi Nakamura for working with annotations

This release also upgrades the version of Bio-Formats which OMERO uses to 5.9.0. Note: this is a significant upgrade and will invalidate the Bio-Formats Memoizer cache. Please see the upgrade guide for further information.

5.4.6 (May 2018)¶

This introduces a significant new subsystem for read-only operation with which servers can be configured not to make changes to the database, the filesystem, or both. The goal is to permit horizontal scaling of OMERO by running multiple servers in parallel to increase the throughput of data and metadata for large-scale analysis or publishing. Additionally, a read-only copy of an existing OMERO can be opened safely to the public for experimentation. For example, this infrastructure supports the public OMERO web and the Jupyter environment of the Image Data Resource. Information on how to configure a read-only server is available at Clustering.

Further improvements include:

enabled big image support in ImageJ/Fiji
reduced the number of threads used by OMERO.web
fixed other bugs in OMERO.web including:
- broken History tab
- handling of script params
- pagination calculations
- public user login
- browsing to user’s data in IE
fixed the chosen login ports for OMERO.cli

Developer updates include:

a new command to set custom physical pixel size using OMERO.cli
deprecated Repository::pixels, TinyImportFixture and OMEROImportFixture
improved test infrastructure
reduced background events in the center panel plugin when not displaying Thumbnails
added extra controls when specifying map and gamma in the rendering engine

This release also upgrades the version of Bio-Formats which OMERO uses to 5.8.2. Note: this is a significant upgrade and will invalidate the Bio-Formats Memoizer cache. Please see the upgrade guide for further information.

5.4.5 (March 2018)¶

This is a bug-fix release reactivating the thumbnail cache inadvertently disabled in 5.4.4 while fixing a pyramid issue.

Improvements include:

reactivated thumbnail caching
improved removepyramids help
fixed display of thumbnails when searching for images by ID
increased OMERO.web log size
fixed CLI config list subcommand
fixed leaking services in OMERO.py
improved rendering of non-tile large images using OMERO.py and webgateway

This release does not upgrade the version of Bio-Formats which OMERO uses, which remains at 5.7.3.

5.4.4 (March 2018)¶

This is a bug-fix release which also introduces some new functionality.

It includes a security fix for 2017-SV6. It is highly recommended that you upgrade your server.

Improvements include:

images can now be filtered by Tag in the center panel of OMERO.web
enabled search by “File” and “Tag” annotations separately in OMERO.web, as opposed to only being able to search by All annotations
fixed switching between grid display and thumbnail display in OMERO.web
fixed the image preview and disabled projection in OMERO.insight when trying to project an image with all the channels turned off
fixed parsing of polygons and polyline ROIs so they can be opened in ImageJ
fixed creation of OMERO pyramids for little-endian files
improved error message when login fails for OMERO.insight
improved handling of idle connections in OMERO.insight
improved loading speed of LUT
OMERO.insight and OMERO.importer are now compatible with Java 9

Sysadmin improvements include:

improved installation documentation for OMERO.web, and OMERO.server on Debian 9, Ubuntu 16.04 and CentOS 7
added an admin command and script to allow deletion of corrupted pyramids created by a bug introduced with OMERO 5.2 (new uncorrupted pyramids can then be generated - see OMERO.server upgrade for details)
allowed enforcement of a secure connection when importing data
added commands to the CLI sessions plugin to enable the creation and removal of user sessions

Developer updates include:

improved test infrastructure and coverage
allowed filtering by namespace (ns) in webclient, API and annotations
added support for more rendering parameters to the API
added the option to respect a specific tile size
added a method to load planes using JavaGateway
added an example to the documentation for using “sudo” to create sessions for others with the JavaGateway
documentation is now compatible with Sphinx 1.7

This release does not upgrade the version of Bio-Formats which OMERO uses, which remains at 5.7.3.

5.4.3 (January 2018)¶

This is a bug fix release for a resource leak in omero.gateway.BlitzGateway introduced with 5.4.2 that caused long-running processes to hang. No other changes are included.

5.4.2 (January 2018)¶

This is a bug-fix release.

Improvements include:

added documentation on a complete workflow for publishing data from OMERO.server
added references to the new OMERO pyramid format documentation (within the OME Data Model and File Formats documentation)
faster loading of thumbnails for large Plates after a recent regression
made projecting images belonging to another user only possible for users with the required permissions to save the new images
improved the public user experience for password-less access
updated SwingX library version used by OMERO.insight to stop insight-ij plugin crashing in Fiji
CLI updates:
- import --target into a container without the necessary permissions now fails before file upload starts and more transparently
- admin mail timeout is now configurable via --wait
- added admin log command for inserting statements to the server log

Sysadmin changes include:

added warning about the need to regenerate your NGINX config for every upgrade
fixed documentation bug affecting OMERO-version-specific guidance
improved OMERO.tables startup stability
server performance improvements and reduction in ERROR logging

Developer updates include:

extended Python and Java examples to include Map Annotations and histograms
added methods for updating OMERO.tables
Java Gateway fixes for sessions and rendering
fixed retrieval of Plate thumbnail URLs
improved ‘Editing OMERO.web’ documentation
improved Slice documentation for API deprecations
added instructions to Extensions on how to create CLI plugins that are pip installable
substantial effort to make third-party repositories easily testable; see omero-test-infra for more information

This release also upgrades the version of Bio-Formats that OMERO uses to 5.7.3.

5.4.1 (November 2017)¶

This is a bug-fix release.

Improvements include:

labeled zoom slider bars in the UI to differentiate from horizontal scrollbars and make clear thumbnails can be zoomed (including Plate and Well thumbnails)
fixes for installation walkthrough documentation - installation of script dependencies and gunicorn, and clarification of which user account to use for pip install actions
fixed checking of “guest” user
update to fetch third-party artifacts over https to allow OMERO to build even without a local Maven cache already populated
added javax.activation dependency to allow OMERO.insight to work with Java 9
import of files reporting extreme pixel sizes now fail rather than hanging
pyramid-making now aborts when a tile fails
various test fixes
CLI fixes:
- improved help output for graphs commands to make it clearer that --include and --exclude expect class names not object IDs
- allowed setting the OMERO_PASSWORD environment variable instead of using the -w command-line option
- made passwords hidden by default when running omero config get
- fixed the CLI metadata tablestest plugin to not use an empty list of Columns

This release also upgrades the version of Bio-Formats that OMERO uses to 5.7.2.

5.4.0 (October 2017)¶

A full, production-ready release of OMERO 5.4.0; featuring a new configurable user role “Restricted Administrators”; further improvements to OMERO.web; additions to OMERO.cli; and many fixes and performance improvements:

added Administrators with restricted privileges to allow sysadmins to delegate management tasks to facility managers without granting them full system admin privileges, or to allow trusted users such as image analysts to carry out tasks on behalf of all other users
fixed color conversion to RGBA
added support for exporting images in a plate as OME-TIFF
improved creation of rendering settings for images without any stats e.g. 32bit images
improved performance for moving large Plates
fixed projection of images if the range of timepoints specified is not the full range
added support for transfering ownership of all the data of a given user using CLI
renamed “Reverse Intensity” command to “Invert” in image viewers
added support for ImageColumn with Screen and Plate targets in the populate_metadata script
OMERO.web UI fixes:
- improved display of Plates and Wells
- fixed label position for Wells
- added the ability to display Image and Well metadata in the Tables section for the same Plate
- improved copy/paste of rendering settings workflow
- improved layout of left-hand panel including the position of the search panel
- added support for administrators with restricted privileges to create Project/Dataset for other users
- rolled back the display of tables in the viewer
- fixed forgotten password functionality

Sysadmin changes include:

added support for the creation of administrators with restricted privileges in OMERO.web admin panel
added method to create administrators with restricted privileges specifying a password
added specific installation instructions for Debian 9
added configuration to limit queries that public users can do in OMERO.web
created minimal NGINX configuration file that can be included in a fixed file to allow custom NGINX options to be defined only once (e.g. SSL options)
installed django-redis by default
CLI improvements and fixes:
- fixed admin plugin so “cleanse” can handle larger directories
- added to chown plugin ability to target all of given users’ data
- adjusted handling of standard input
- added infrastructure to load external CLI plugins
- dropped support for command admin ports

Developer updates include:

added method to JavaGateway to manipulate admin privileges
fixed issue with JSONP decorator
removed SciPy dependency
adjusted OMERO.blitz API to allow some query results to be cached
added support to the rendering engine to update a series of settings in one call
added method to OMERO.py to manipulate advanced rendering settings
allowed the Maven repository to be overridden
removed unused 3rd party libraries in OMERO.web
added support for PyTables version 3.4+
deprecated Path Object in OMERO Model
updated the documentation for server installation on Mac OS to no longer use the homebrew formulae from https://github.com/ome/homebrew-alt (these are not working and will not be fixed)

Further changes to the Python BlitzGateway are described in What’s new for OMERO 5.4 for developers.

This release also upgrades the version of Bio-Formats which OMERO uses to 5.7.1.

5.3.5 (October 2017)¶

This is a security release - see the security advisory for further details.

It is highly recommended that you upgrade your server.

5.3.4 (September 2017)¶

This is a security release - see the security advisory for further details.

This release also upgrades the version of Bio-Formats which OMERO uses to 5.5.3.

It is highly recommended that you upgrade your server.

5.3.3 (June 2017)¶

This is a bug-fix release.

Improvements include:

support for two new lookup tables from Janelia
fixed loading of Well in right-panel when browsing Well under Tag tree or from search results
fixed rotation of labels in figure scripts

Sysadmin changes include:

clarified the upgrade of the “Open With” option
allowed installation of OMERO.web with ice 3.5
fixed recursive loading of feedback in OMERO.web
provided patch for OMERO.server installation on OS using OpenSSL 1.1.0 e.g. Debian 9 see Troubleshooting OMERO

Developer updates include:

added an example of how to retrieve shapes from a ROI using batch querying for scalability
improved logging of errors during deletion
added new methods to Java Gateway
improved login options in Java Gateway
specified an image’s dataset in its URL to give more context to OMERO.web apps

This release also upgrades the version of Bio-Formats which OMERO uses to 5.5.2.

5.3.2 (May 2017)¶

This is a bug-fix release.

Improvements include:

improved populate_metadata plugin
fixed deletion of a range of objects from CLI
textual annotations without a namespace can now be added at import using the CLI
improved thumbnails retrieval in OMERO.web
added “Open With” option to the right-hand panel in OMERO.web
private group owners are now not offered the ability to annotate other people’s data in OMERO.web UI, an action which was not permitted by the server anyway
preview of wells now available in the right-hand panel

Sysadmin changes include:

made the Django middleware classes configurable using a new property
added property to allow connections from specified origins (CORS)
administrators can now use the CLI to move data between groups without belonging to those groups
for OMERO.web apps to be available via “Open With” option, administrators need to use the “omero.web.open_with” configuration option

Developer updates include:

exposed more enumerations from ome-model
added ROIs support to the Web API

This release also upgrades the version of Bio-Formats which OMERO uses to 5.5.0.

5.3.1 (April 2017)¶

This is a bug-fix release focusing on shares.

Improvements include:

enabled viewing images in share
enabled importing hidden image files (Windows client issue)
clarified installation of OMERO.web
saved polygon and polyline as defined in the OME model
fixed viewing of images without pixels size
added support for large image export as jpeg/png from OMERO.insight

This release also upgrades the version of Bio-Formats which OMERO uses to 5.4.1.

5.3.0 (March 2017)¶

A full, production-ready release of OMERO 5.3.0; featuring a major reworking of OMERO.web and web apps; dropping support for Windows for the server and for deploying OMERO.web using Apache; and introducing new user features and many fixes and performance improvements:

improved support for many file formats via Bio-Formats 5.4.0
introduced ROI Folders
new UI for displaying Screen Plate Well data in OMERO.web and OMERO.insight
support for lookup tables and reverse intensity rendering
color mapping for multiple channels without set colors has been improved to use RGBRGB rather than RGBBB (i.e. to loop through red, green, blue rather than setting all later channels to blue)
support for histograms in the clients and server
ability to filter by ratings in OMERO.web
added ‘Open With…’ functionality to OMERO.web
color of shapes is now handled according to the data model, using RGBA rather than ARGB format (an sql script is available to upgrade existing shapes; this will not happen automatically as part of the OMERO upgrade)
improved performance for moving and deleting data
Wells can now be annotated and searched by annotations
enabled downloading/exporting of plate data
improved reading of tables data
script improvements including ability to create tiled images from big ROIs, fixes for creating standard images from ROIs, and to stop the Combine_Images script from ignoring pixel sizes set on the target images
names for plates and images set in the metadata read by Bio-Formats are now imported into OMERO and the filename (which was previously used) is only used where an alternative has not been set
many bug fixes

Sysadmin changes include:

added support for Ice 3.6.3
official OMERO.web apps are now all installable from PyPI
OMERO.web has been decoupled from the server and can now be deployed separately
dropped support for Windows for OMERO.server
OMERO.web deployment via Apache is no longer supported
OMERO.web also now requires Python 2.7
CLI improvements including updates to the import output to make it more usable by scripts etc.
options added for customizing the tree in OMERO.web
introduced hide-password option in CLI
new options added to omero config
removed deprecated client menu properties

Developer updates include:

performed major code cleanup
major Web API rework
adjustment to support the upcoming Java 1.9
made python testing package public so it can be used by external clients
improved build system integration with local Maven
made Scripts repository and official OMERO.web apps pep8 and flake8 compatible
removed restriction on name length
added support for enumeration changes
utils script classes deprecated
deprecated shares
deprecated search bridges
disabled jquery cache

Further details on breaking changes are available on What’s new for OMERO 5.3 for developers. Work on the Web API is ongoing and will include moving away from the use of JSONP and introducing Django CORS.

5.2.8 (March 2017)¶

This is a security release including three security vulnerability fixes.

2017-SV1-filename prevents users from accessing and manipulating other people’s data by creating an original file and changing its path to point to another user’s file on the underlying filesystem.

2017-SV2-edit-rw prevents users in read-write groups from editing official scripts.

2017-SV3-delete-script prevents the deletion of official scripts by users without the correct permissions to do so.

It is highly recommended that you upgrade your server.

5.2.7 (December 2016)¶

This is a release aimed at system administrators or developers wanting to build OMERO with Ice 3.6.3.

This release also upgrades the version of Bio-Formats which OMERO uses to 5.1.10.

All scripts handling Regions of Interest (ROIs) now support ROI not linked to any plane as defined by the OME Model.

5.2.6 (October 2016)¶

This is a bug-fix release focusing on services closure and a DB upgrade fix. Improvements include:

fixed closure of session in Java when using Ice 3.5
fixed memory leak where services were not correctly closed
added a DB upgrade patch to fix errors only affecting DBs that have been upgraded from OMERO 4.4
fixed a MATLAB regression introduced in 5.2.2, casting error.
fixed error in logs on getProjectedThumbnail

Support for OMERO.web deployment using Apache has also been deprecated and is likely to be removed during the 5.3.x line.

5.2.5 (August 2016)¶

This is a security release to fix the access privileges of the share function, which were potentially allowing users to access private data belonging to other users via the API.

See 2016-SV2-share for details. Shares will now respect user privileges as set by the group permission level. Note that Shares now only support images even when used via the API.

It is highly recommended that you upgrade your server. For those not in a position to do so as a matter of urgency, a workaround is provided which deletes all shares and disables their creation.

5.2.4 (May 2016)¶

This is a security release to fix the cleanse.py script used by the “bin/omero admin cleanse” command, which was not properly respecting user permissions and may lead to data loss.

See 2016-SV1-cleanse for details. The script and command have now been made admin-only.

It is highly suggested that you upgrade your server or apply the patch available from the security page.

5.2.3 (May 2016)¶

A bug-fix release. Improvements include:

fixed problem with float images
all scripts currently exposed to users via our website have been reviewed and fixed where necessary so they are all now 5.2.x compatible, and a new omero-install workflow has been developed to ensure these are reviewed regularly going forward
better support for metadata annotations in clients including tag/tagset support and performance issues
fixes in OMERO.web for deleting MIFs
improvements to the navigation of large datasets and display of plates in OMERO.web
other OMERO.web bug fixes
OMERO.insight and CLI import improvements
other OMERO.insight bug fixes, including for downloading data

Developer updates include:

Java gateway improvements

System administrator updates include:

Ice 3.6.2 support for UNIX-like systems, including specific installation walkthroughs
redis support for websessions caching
a fix to allow OMERO.web to be run in a Docker container
improved OMERO.web configuration
warnings added regarding the end of Windows support in the 5.3.0 release (note that we will be preparing a guide for migrating from Windows for existing servers and adding it to the documentation as soon as we can)

This release also upgrades the version of Bio-Formats which OMERO uses to 5.1.9.

5.2.2 (February 2016)¶

A bug-fix release which also introduces some new client features. Improvements include:

display of ROI masks in OMERO.web image viewer
display of OMERO.tables data for Wells in the OMERO.web right hand panel
‘Populate Metadata’ script to enable generation of OMERO.tables for Wells is now usable from both OMERO.web and OMERO.insight (note this is still in development and has some limitations)
measurement tool fixes
fixed pixel size metadata and scalebar in OMERO.web image viewer for images with pixel size units other than micrometer
fixed OMERO.web handling of turning off interpolation of pixels
previous and next buttons fixed in OMERO.web image viewer
delete and change group performance improvements
better handling of dates in search
client support for map annotations in OME-TIFF
disabled orphaned container feature
OMERO.web clean-up to remove obsolete volume viewer

Developer updates include:

Python API examples for creating Polygon and Mask shapes
Python API example for “Populate Metadata” to create OMERO.tables for Wells
OMERO.tables documentation extended
updated ‘What’s New for developers’ to clarify that pojos has been renamed as omero.gateway.model
dynamic scripts functionality documented
dynamic loading of omero.client server settings into HTTP sessions

System administrator updates include:

clarification of OMERO.web documentation for nginx deployment, including an experimental solution to resolve download issues
documentation of hard-linking issues for in-place import on linux systems

Note that the OMERO Virtual Appliance has been discontinued and will not be updated for version 5.2.2 or any later releases.

This release also upgrades the version of Bio-Formats which OMERO uses to 5.1.8.

5.2.1 (December 2015)¶

A bug-fix release focusing on improving installation documentation and workflows. Other improvements include:

bug fix for missing hierarchy when viewing High Content Screening data
improvements to the right-hand panel in OMERO.insight
measurement tool fixes
OMERO.web fix for displaying size units

System administrator updates include:

improved installation documentation, including detailed walkthroughs for specific OS
OMERO.web deployment fixes

Developer updates include:

OMERO Javadocs now link to the relevant version of Bio-Formats Javadocs for inherited methods
clean-up of server dependencies
jstree clean-up
CLI graph operation improvements for deleting
minimal-omero-client and pom-omero-client clean-up

This release also upgrades the version of Bio-Formats which OMERO uses to 5.1.7.

5.2.0 (November 2015)¶

A full, production-ready release of OMERO 5.2.0; dropping support for Java 1.6; featuring major upgrading of OMERO.web; re-working of the Java Gateway; and introducing new user features and many fixes and performance improvements:

improved support for many file formats via Bio-Formats 5.1.5
faster import for images with a large number of ROIs
performance improvements for OMERO.web including faster data tree loading
Java Web Start has been dropped, it is no longer possible to launch the desktop clients from the web
reworked display of metadata and annotations in both UI clients
many bugs fixed

Developer and system administrator updates include:

the OMERO web framework no longer bundles a copy of the Django package, this dependency must be installed manually
updated jstree to 3.08 and now using json for all tree loading to substantially improve performance
removed FastCGI support, OMERO.web can be deployed using WSGI
configuration property omero.graphs.wrap which allowed switching back to the old server code for moving and deleting data has now been removed. You should migrate to using the new graph request operations before 5.3 when the old request operations will be removed
introduced new Java Gateway to facilitate the development of Java applications
aligned OMERO Rect with OME-XML schema for ROI. Clients using the OMERO.blitz server API to work with ROIs will need to be updated

5.1.4 (September 2015)¶

A bug-fix release covering all components. Improvements include:

channel buttons fixed in OMERO.web
improved UI experience when moving annotated data between groups in OMERO.web
improved performance for loading annotations in the right-hand panel of OMERO.web
much better handling of ROIs covering large planes in OMERO.insight
rendering setting fixes for copy and paste actions in OMERO.insight
rendering fixes for floating point data
Admins can now configure whether the clients interpolate images by default
better formatting of Delta-T and exposure times in the clients
directories are now preserved when downloading multiple original files
various improvements to the OMERO-ImageJ handling of ROIs and measurements, including the ability to name measurement tables
current session key can now be returned via the CLI
other CLI improvements including usability of ‘chmod’ for downgrading group permissions, and listing empty tagsets
added support for groups in OMERO.matlab methods

Developer updates include:

improvements to web logging to log full request and status code
fixed joda-time version mismatch
cleanup of old insight code to remove remaining references to OMERO.editor

Support for deployment of OMERO.web using FastCGI has also been deprecated in this release and is scheduled to be removed in 5.2.0. Sysadmins should move to using WSGI instead. We are also intending to stop distributing Java Webstart for launching OMERO.insight from your browser, as security concerns mean browsers are increasingly moving away from supporting this type of application. You can read further information regarding this decision on our Web Start blog post.

5.1.3 (July 2015)¶

A bug-fix release which also introduces some new functionality. Improvements include:

tagging actions extended; you can now use tag sets to tag images on import
tagging ome-tiff images at import has also been fixed
greatly improved workflow and bug fixes for the Share functionality in OMERO.web which enables you to share images with users outside of your group (including removal of part of the UI)
group admins and owners can now change ownership of data via the CLI
better reporting for the ‘delete’ and ‘chgrp’ functionality in the CLI
fixed display of images in plates with multiple acquisitions
fixed export of results as .xls files from OMERO.insight
improved workflow for ImageJ and OMERO interactions
support for WSGI OMERO.web deployment
fixed OMERO.mail service for web errors
fixes for ROI display in OMERO.web (thanks to Luca Lianas of CRS4)
fixes and workflow improvements for running scripts and script dialogs

Developer updates include:

OMERO.web clean-up (removal of ‘-locked’)
reorganization of the server bundle to move various licenses and dependencies under a new ‘share’ folder
refactoring of ‘Chown2’, ‘Chmod2’, ‘Chgrp2’ and ‘Delete2’
addition of dynamic scripts
the ‘rstring’ implementation is now more lenient and should better handle unicode
Bio-Formats submodule removed from OMERO; decoupling effort means OMERO now consumes the Bio-Formats release build from the artifactory

This release also includes the fix for the Java security issue, as discussed in the recent blog post. Testing suggests this fix should not have any performance implications. You should upgrade your Java version to take advantage of the security fix.

5.1.2 (May 2015)¶

A bug-fix release which also introduces some new functionality. Improvements include:

support for Read-Write groups
the LDAP plugin can now set users as group owners whether on creation or via the improved sync_on_login option
users logged into the webclient can now automatically log in via webstart
results tables from ImageJ/Fiji can be attached to images in OMERO and the ImageJ/Fiji workflow has been improved
better delete functionality and warnings in the UI
improved graph operations like ‘delete’ and ‘chgrp’, as well as the new ‘chmod’ operation (for changing group permissions), are now used across the clients including the CLI
an API for setting and querying session timeouts is now available via the CLI
magnification now reflects microscopy values (e.g. 40x) rather than a percentage in both clients
more readable truncation of file names in the OMERO.insight data tree
OMERO.web fixes and improvements including:
- interpolation
- optimization of plate grid and right-hand panel
- option to download single original files
- significant speed-up in loading large datasets
deployment fixes include:
- new default permissions on the var/ directory
- better checks of the DropBox directory permissions
- new and some deprecated environment variables
- a startup check for lock files on NFS
- use /var/run for omero.fcgi

Critical bugs which were fixed include:

the in-place import file handle leak (which was a regression in 5.1.1)
various unicode and unit failures were corrected

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:

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:

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 from Dundee University Computing department. 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.