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OMERO version history
=====================
5.4.0-m3 (August 2017)
----------------------
Developer preview release. Intended *only as a developer preview* for updating
code before the full public release of 5.4.0. **Use at your own risk.**
Changes include:
- improved display of plate in OMERO.web
- various improvements in integration tests
- fixed import related bugs in OMERO.insight
- fixed synchronization of controls enabling copy/paste of
rendering settings in OMERO.web
- fixed projection of images
- removed Scipy dependency
This release also upgrades the version of Bio-Formats which OMERO uses to 5.6.0-m1
5.4.0-m2 (July 2017)
--------------------
Developer preview release. Intended *only as a developer preview* for updating
code before the full public release of 5.4.0. **Use at your own risk.**
Changes include:
- fixed OMERO.server permissions bug with restricted administrators
- adjusted OMERO.blitz API to allow some query results to be cached
- improve OMERO.web experience and fixed bugs for restricted administrators
- improve OMERO.cli:
- fixed admin plugin so "cleanse" can handle larger directories
- have chgrp plugin check administrator Chgrp restriction
- added to chown plugin ability to target all of given users' data
- adjusted handling of standard input
- various improvements in integration tests
5.4.0-m1 (July 2017)
--------------------
Developer preview release. Intended *only as a developer preview* for updating
code before the full public release of 5.4.0. **Use at your own risk.**
Changes include:
- added support for new security privileges to allow users to perform some
admin tasks without having admin privileges e.g. import for others
- added specific installation instructions for Debian 9
This release also upgrades the version of Bio-Formats which OMERO uses to
`5.5.3 <https://www.openmicroscopy.org/2017/07/05/bio-formats-5-5-3.html>`_.
5.3.3 (June 2017)
-----------------
This is a bug-fix release.
Improvements include:
- support for two new lookup tables from `Janelia <https://www.janelia.org/>`_
- 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 :doc:`/sysadmins/troubleshooting`
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 <https://www.openmicroscopy.org/2017/06/15/bio-formats-5-5-2.html>`_.
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 <http://www.openmicroscopy.org/2017/05/08/bio-formats-5-5-0.html>`_.
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 <http://www.openmicroscopy.org/2017/04/13/bio-formats-5-4-1.html>`_.
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
:doc:`/developers/whatsnew`. 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.
:secvuln:`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.
:secvuln:`2017-SV2-edit-rw` prevents users in read-write groups from
editing official scripts.
:secvuln:`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 <http://www.openmicroscopy.org/2016/05/09/bio-formats-5-1-10.html>`_.
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 :secvuln:`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 :secvuln:`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 <http://blog.openmicroscopy.org/tech-issues/future-plans/deployment/2016/03/22/windows-support/>`_
(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. `See whats-new for more information <http://www.openmicroscopy.org/2016/04/18/bio-formats-5-1-9.html>`_.
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. `See whats-new for more information <http://www.openmicroscopy.org/2016/02/15/bio-formats-5-1-8.html>`_.
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 :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 <http://blog.openmicroscopy.org/tech-issues/future-plans/2015/09/23/java-web-start/>`_.
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 <http://blog.openmicroscopy.org/tech-issues/2015/07/21/java-issue/>`_. 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:
- :secvuln:`2014-SV3-csrf`
- :secvuln:`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:
- :secvuln:`2014-SV1-unicode-passwords`
- :secvuln:`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:
- :secvuln:`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 :ticket:`9372`
and :ticket:`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