forked from ome/openmicroscopy
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathhistory.txt
1022 lines (783 loc) · 39.3 KB
/
history.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
OMERO version history
=====================
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 <https://www.openmicroscopy.org/site/support/bio-formats5.1/about/whats-new.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 <https://www.openmicroscopy.org/site/support/bio-formats5.1/about/whats-new.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
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