history.txt

OMERO version history
=====================

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

5.0.6 (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.

5.0.5 / 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
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 :about_plone:`Usable Image <project-history/catriona>`.
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.