Timeline


and

06/04/08:

17:16 Changeset [4096] by melissa
Use port 1099 by default for OME/OMERO download.
11:09 Changeset [4095] by melissa
* Fixed NPE when calling FluoviewReader.isThisType on a non-TIFF file. * …

06/02/08:

16:58 Changeset [4094] by curtis
Fix initMetadataStore subclass method signatures, and jikes warnings.
16:55 Changeset [4093] by curtis
Fix up date parsing, and other miscellaneous cleanup.
16:28 Changeset [4092] by curtis
Clean up TIFF-based isThisType implementations: * Fixes miscellaneous …
15:51 Changeset [4091] by melissa
Create a blank thumbnail if we weren't able to retrieve one from the …
15:34 Changeset [4090] by curtis
Close only the active reader or writer, rather than all readers and …
14:38 Changeset [4089] by curtis
Rewritten OME-TIFF reader: * Works with the latest OME-TIFF …
13:51 Changeset [4088] by curtis
Fix some CDATA bugs that resulted in certain OME attributes being dropped.
10:36 Changeset [4087] by curtis
Latest OME-Java with correct Correction and Immersion handling.
10:14 Changeset [4086] by melissa
Improved OME-XML population for InCell 1000.

05/30/08:

13:38 Changeset [4085] by curtis
Enable Correction and Immersion for 2008-02 schema.
13:37 Changeset [4084] by curtis
Enable Correction and Immersion for 2008-02 schema.
12:30 Changeset [4083] by melissa
Use JPEG2000Codec instead of manually calling the JAI library. Somehow …
11:35 Changeset [4082] by curtis
Minor tweak.
11:13 Changeset [4081] by curtis
Add documentation for isThisType macro extension function.
11:09 Changeset [4080] by curtis
Update OME plugins URL.
10:40 Changeset [4079] by curtis
Make metadata converter only call property setters for non-null …
08:22 Changeset [4078] by curtis
Use TiffTools.getComment (but leave IFD entry approach commented out).
07:02 Changeset [4077] by curtis
Add isThisType method to macro extensions.

05/29/08:

17:23 Ticket #299 (Parse picture names from Openlab LIFF files) closed by melissa
fixed: r4076
16:56 Changeset [4076] by melissa
* Removed a bunch of duplicate code from PictReader * Fixed OpenlabReader …
15:54 Ticket #298 (SPW changes break Flex reader) closed by curtis
fixed: Fixed in r4075.
15:52 Changeset [4075] by curtis
Fix SPW class node detection; closes ticket #298.
15:19 Ticket #300 (ZVI reader throws ArrayIndexOutOfBoundsException) closed by melissa
fixed: (In [4074]) Fixed C size calculation bug - closes #300.
15:19 Changeset [4074] by melissa
Fixed C size calculation bug - closes #300.
13:42 Ticket #300 (ZVI reader throws ArrayIndexOutOfBoundsException) created by curtis
[…] This problem may be related to the fact that Bio-Formats identifies …

05/28/08:

11:55 Ticket #299 (Parse picture names from Openlab LIFF files) created by curtis
Some Openlab LIFF datasets contain a "picture name" associated with each …
09:46 Changeset [4073] by melissa
Preserve physical dimensions.
08:56 Changeset [4072] by melissa
Place slice names in metadata hashtable.

05/27/08:

10:05 Changeset [4071] by melissa
Reverted pixel size scaling logic - it was correct in the first place.
09:11 Changeset [4070] by melissa
Added ICS writer.
09:09 Changeset [4069] by melissa
Fixed pixel size scaling bug.

05/26/08:

11:58 Changeset [4068] by melissa
Fixed NPEs.
11:45 Changeset [4067] by melissa
Added timestamp parsing logic.

05/24/08:

08:45 Ticket #298 (SPW changes break Flex reader) created by melissa
Attempting to read a Flex file with r4065 produces the following …

05/23/08:

16:50 Changeset [4066] by curtis
Add some "to do" notes.
16:40 Changeset [4065] by curtis
Update MetadataStore to handle SPW data model in ome.xml.r20xxxx.spw …
14:37 Changeset [4064] by curtis
MetadataStore improvements paving the way for a better OME-TIFF reader: …
14:35 Changeset [4063] by curtis
Better error message when plane number is out of bounds.
14:34 Changeset [4062] by curtis
Fix line spacing.
11:25 Changeset [4061] by melissa
Remainder of improvements to openBytes, so that full-size images are read …
10:01 Changeset [4060] by melissa
Slightly improved plane access time.

05/21/08:

13:56 Changeset [4059] by melissa
Added reader for Aquacosmos files and switched FEIReader's license.
08:59 Changeset [4058] by melissa
Initial version of ScreenPlateWell support. FlexReader is currently the …

05/20/08:

13:40 Ticket #279 (Add support for FEI SEM format) closed by melissa
fixed: (In [4057]) Preliminary support for FEI format - closes ticket 279.
13:40 Changeset [4057] by melissa
Preliminary support for FEI format - closes ticket 279.

05/19/08:

13:48 Changeset [4056] by melissa
Fixed absolute path bug, and a couple problems with RGB files.
08:47 Changeset [4055] by curtis
Switch OME Notes and LOCI Plugins to GPL, for consistency.
08:29 Changeset [4054] by melissa
Fixed offset calculation.

05/16/08:

16:30 Changeset [4053] by curtis
Miscellaneous cleanup.
09:38 Changeset [4052] by melissa
Support for < 8 bit BMP images; minor LSM bug fix.

05/15/08:

15:31 Changeset [4051] by curtis
Update the license in a few more places.
15:28 Changeset [4050] by curtis
Update license in OME metadata source code templates.
13:45 Changeset [4049] by curtis
Update license document to GPL.
13:26 Changeset [4048] by curtis
Licensing and packaging changes. * Change Bio-Formats and SLIM Plotter …
13:22 Changeset [4047] by curtis
Add some implementation notes for tasks left to do in the OME-TIFF writer.
13:20 Changeset [4046] by curtis
Simplify TIFF comment surgery utility to use latest API.
11:34 Changeset [4045] by curtis
Remove standalone OutputFilter class in favor of anonymous inner class.

05/14/08:

17:21 Changeset [4044] by melissa
Fixed NPE when creating a window title for a multi-file dataset with no …
12:52 Changeset [4043] by melissa
Improved init time for JP2K ND2 files - files that previously took 10+ …
11:13 Changeset [4042] by melissa
Fixed bug when trying to read an OME-TIFF file in the same directory as a …
09:52 Changeset [4041] by melissa
Fixed bug in parsing UUID filenames. UUIDs are still not fully supported, …

05/13/08:

20:01 Changeset [4040] by melissa
Make sure C is before Z and T in dimension order string if the stack is …
19:43 Changeset [4039] by melissa
Some speed improvements.
16:14 Changeset [4038] by curtis
No more need for this utility.
11:39 Changeset [4037] by melissa
Fixed lingering Zeiss LSM bugs, and a bug in RandomAccessStream's …

05/12/08:

12:54 Changeset [4036] by curtis
Update to version-agnostic OME-XML metadata store logic.
12:15 Changeset [4035] by melissa
Fix for Zeiss LSM files with incorrect bits per sample and strip byte …
08:06 Changeset [4034] by melissa
Corrected event count calculation.

05/11/08:

13:47 Changeset [4033] by melissa
Added logic to handle BGR images.

05/10/08:

16:16 Ticket #297 (Add support for Patch-Master electrophysiology files) created by melissa
We have one sample of an electrophysiology file generated by HEKA …
13:00 Changeset [4032] by melissa
Fixed off-by-1 in DeltaT population; adjusted DeltaT values to start with …

05/09/08:

14:51 Changeset [4031] by melissa
* Removed some obsolete logic from LSM reader. * Improved …
13:43 Changeset [4030] by curtis
Document preferred entity traversal order for property population.
11:37 Changeset [4029] by melissa
Fixed bug in how double images are handled.
10:49 Changeset [4028] by curtis
Macro from Wayne Rasband that uses the BF macro extensions to open files.
08:25 Changeset [4027] by melissa
Bug fixes.

05/08/08:

16:14 Changeset [4026] by allison
Progress on main method.
10:30 Changeset [4025] by melissa
Fixed dimension order and swapped Z/T sizes.

05/07/08:

17:38 Ticket #296 (Stitching multiple series needs improvement) created by curtis
The FileStitcher and AxisGuesser classes currently have logic for …
17:03 Ticket #295 (Better support for renamed Leica files) closed by melissa
fixed: (In [4024]) Rewrote support for renamed/missing files - closes #295. …
17:03 Changeset [4024] by melissa
Rewrote support for renamed/missing files - closes #295. There are still …
16:58 Changeset [4023] by curtis
Fix some file stitching bugs, and remove some obsolete logic.
16:57 Changeset [4022] by curtis
Fix setId bug introduced in r4018.
15:51 Changeset [4021] by curtis
Tweak usage.
15:41 Changeset [4020] by curtis
Remove unnecessary import.
15:41 Changeset [4019] by curtis
Some cleanup to file stitcher. Still has problems.
14:27 Changeset [4018] by melissa
Removed setId(String, boolean).
14:05 Changeset [4017] by curtis
Clean up close methods.
13:47 Changeset [4016] by curtis
Fix up animation thread.
13:32 Ticket #274 (Add animate key to ImageViewer) closed by curtis
fixed
13:31 Changeset [4015] by curtis
Some improvements to the image viewer: * Display "no image plane" …
13:06 Changeset [4014] by curtis
Reverse order of channel separator and file stitcher.
12:01 Changeset [4013] by curtis
Add another example Bio-Formats macro from Sebastien Huart.
11:47 Changeset [4012] by curtis
Fix ZVI bug on Windows caused by previous OIB fix.

05/06/08:

16:06 Changeset [4011] by curtis
Use ChannelSeparator for now to avoid problems with Util.openProcessor.
16:03 Changeset [4010] by curtis
Add some ImageJ macros that demonstrate how to call Bio-Formats.
15:15 Changeset [4009] by curtis
Fix some problems that Wayne Rasband pointed out: * Use ChannelSeparator …
14:52 Changeset [4008] by curtis
Add certainty flag to main's test output.
14:50 Changeset [4007] by curtis
Script for generating test lifetime data.
14:20 Ticket #295 (Better support for renamed Leica files) created by melissa
See the "CFP-DsRed YFP neg", GFP-YFPcaax, "RNA FISH", and fish datasets in …
13:33 Changeset [4006] by melissa
Removed unnecessary import statements.
13:27 Ticket #280 (Move ImageJ-specific logic out of OMEUtils) closed by melissa
fixed: r4005.
13:24 Changeset [4005] by melissa
Moved ImageJ-specific stuff from OMEUtils to OMEPlugin. Also updated …
11:44 Ticket #294 (Add support for Aquacosmos .naf format) created by melissa
.naf files are generated by Hamamatsu Aquacosmos software.
11:29 Changeset [4004] by curtis
Fix bug that caused erroneous stitching by resetting the patternIds flag.

05/05/08:

14:59 Changeset [4003] by melissa
Fixed compile error.
14:21 Ticket #285 (LSM timestamps not reliably parsed) closed by melissa
fixed: r4002. There were two problems - the offset to the timestamps was not …
14:18 Changeset [4002] by melissa
Fixed timestamp parsing bug.
14:15 Ticket #293 (SDT file possibly has wrong channel count) closed by melissa
fixed: r4000 and r4001 include a bunch of speed improvements for SDT/channel …
14:12 Changeset [4001] by melissa
Speed improvements to channel splitting.
12:41 Changeset [4000] by curtis
Speed up SDT reading.
12:05 Ticket #291 (Some DICOM files throw ArrayIndexOutOfBounds) closed by melissa
fixed: r3999.
12:05 Changeset [3999] by melissa
Fixed ArrayIndexOutOfBounds exceptions and applied patch from John Hansen.
09:24 Ticket #292 (SDT file possibly has wrong channel count) closed by melissa
duplicate: Apparently I clicked "create ticket" twice - this is a duplicate of #293.
09:21 Ticket #293 (SDT file possibly has wrong channel count) created by melissa
The channel count and pixel values for sdt/brian/clone7_atp1.sdt appear to …
09:21 Ticket #292 (SDT file possibly has wrong channel count) created by melissa
The channel count and pixel values for sdt/brian/clone7_atp1.sdt appear to …
09:14 Ticket #174 (Investigate usage of Sanselan image library) closed by melissa
fixed: We already support everything that Sanselan supports, so I see no value …
08:41 Changeset [3998] by melissa
Added hack to correct for the fact that SVI writes ICS files upside-down.
08:28 Changeset [3997] by melissa
Make sure the corresponding NetcdfFile gets closed.
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