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.. Content for this page should be opened as a PR against
.. https://github.com/openmicroscopy/openmicroscopy/blob/develop/history.txt
.. initially and transferred to this page via the autogen job
OMERO version history
=====================
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 :secvuln:`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 <https://idr.openmicroscopy.org/>`_.
Information on how to configure a read-only server
is available at :doc:`/developers/Server/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 :secvuln:`2017-SV6 <2017-SV6-job-file-link>`. **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 :doc:`/sysadmins/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 :doc:`/developers/cli/extending` on how to
create CLI plugins that are ``pip`` installable
- substantial effort to make third-party repositories easily testable;
see `omero-test-infra <https://github.com/openmicroscopy/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 :doc:`/sysadmins/restricted-admins` 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
:doc:`/developers/whatsnew`.
This release also upgrades the version of Bio-Formats which OMERO uses to `5.7.1 <http://www.openmicroscopy.org/2017/09/20/bio-formats-5-7-1.html>`_.
5.3.5 (October 2017)
--------------------
This is a security release - see the
:secvuln:`security advisory <2017-SV4-guest-user>` for further details.
It is highly recommended that you upgrade your server.
5.3.4 (September 2017)
----------------------
This is a security release - see the
:secvuln:`security advisory <2017-SV5-filename-2>` for further details.
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>`_.
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 <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 <https://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 <https://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
`What's new for OMERO 5.3 for developers <http://docs.openmicroscopy.org/omero/5.3.0/developers/whatsnew.html>`_. 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 <https://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 <https://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 <https://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 <https://www.openmicroscopy.org/2015/12/07/bio-formats-5-1-7.html>`_.
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