Timeline


and

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.

05/04/08:

10:42 Ticket #291 (Some DICOM files throw ArrayIndexOutOfBounds) created by melissa
See dicom/hansen/8bitrle.dcm and dicom/hansen/16bitrle.dcm

05/02/08:

17:00 Ticket #282 (Slidebook image names are truncated) closed by curtis
fixed: Never mind, it seems to be working for me now (using the latest code is …
16:42 Ticket #282 (Slidebook image names are truncated) reopened by curtis
Sorry to do this, but on my system all the files in slidebook/alex are …
16:08 WikiStart edited by curtis
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15:15 Ticket #282 (Slidebook image names are truncated) closed by melissa
fixed: r3996.
15:15 Changeset [3996] by melissa
Fixed image names, hopefully for the last time.
11:25 Ticket #288 (Animated GIF reader sometimes leaves "trails") closed by melissa
fixed: r3995.
11:25 Changeset [3995] by melissa
Don't assume that images are transparent.
09:40 Ticket #287 (SimplePCI reader fails to parse dimensional parameters for some CXDs) closed by melissa
fixed: r3994.
09:40 Changeset [3994] by melissa
Fixed bug where sizeC was set to 0.

05/01/08:

15:12 WikiStart edited by curtis
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14:05 Ticket #156 (Investigate LOCI Java software development in Eclipse) closed by curtis
fixed: I added some Eclipse project files to the repository, so it is now …

04/29/08:

15:58 Ticket #290 (Util.openProcessor does not properly handle RGB data) created by curtis
We currently use ChannelSeparator to ensure that image planes are split …
15:51 Ticket #289 (Review and adjust ImageJ color-related options) created by curtis
The options available in the Bio-Formats Importer plugin for handling …
15:14 Ticket #288 (Animated GIF reader sometimes leaves "trails") created by curtis
Image frames do not always get cleared from the previous frame when they …
14:59 Ticket #287 (SimplePCI reader fails to parse dimensional parameters for some CXDs) created by curtis
Bio-Formats reports zero channels, which wreaks general havoc elsewhere. …
13:04 Changeset [3993] by curtis
Fix Windows file path bug.
12:54 Changeset [3992] by curtis
Fix jikes warnings, and ignore .class files.
12:03 Changeset [3991] by curtis
Utility for extracting raw values from SDT files.
11:38 Changeset [3990] by nor
Remove obsolete implementation.
11:32 Changeset [3989] by nor
Initial checkin of slim plotter curve fitting utilities, and associated …

04/28/08:

16:21 Changeset [3988] by curtis
Add TiffData entity and properties to MetadataStore.

04/25/08:

19:26 Ticket #286 (Investigate improving AVI support based on new AVI_Reader) created by curtis
Michael Schmid created an updated AVI_Reader for ImageJ that fixes a …
18:59 Changeset [3987] by curtis
Remove unnecessary variable.
18:59 Changeset [3986] by curtis
Fix threading problem with POI formats.
16:42 Changeset [3985] by curtis
Update OME uploader to work with new Dataset implementation.
16:07 Changeset [3984] by curtis
Update Dataset logic to harness Bio-Formats more effectively.
16:06 Changeset [3983] by curtis
Tweak documentation.
08:48 Ticket #282 (Slidebook image names are truncated) reopened by melissa

04/24/08:

22:29 Ticket #285 (LSM timestamps not reliably parsed) created by melissa
See zeiss-lsm/anuradha/test2.lsm, which has 75 timepoints.
16:42 Changeset [3982] by curtis
Fixed multi-schema OME-XML support, and added 2008-02 schema version.
16:42 Changeset [3981] by curtis
Tweaks for 2008-02 schema version.
16:41 Changeset [3980] by curtis
Fix node creation logic.
15:05 Changeset [3979] by melissa
Fixed bug in metadata block detection logic.
14:30 Changeset [3978] by curtis
Tweak some autogenerator output.
14:19 Changeset [3977] by curtis
New autogenerator is done and produces compilable code! Time for testing.
14:14 Changeset [3976] by curtis
Remove unnecessary reflection logic.
11:57 Changeset [3975] by allison
Revised saving options.
10:41 Changeset [3974] by melissa
Removed calls to DataTools.sanitizeXML - for some reason, this breaks ND2.
10:15 Ticket #282 (Slidebook image names are truncated) closed by melissa
fixed: r3973
10:15 Changeset [3973] by melissa
Parse channel names.
08:00 Changeset [3972] by melissa
Set physical X and Y sizes.

04/23/08:

11:09 Changeset [3971] by melissa
Commented out application of 16 bit LUTs, since ImageJ doesn't really …
10:19 Changeset [3970] by melissa
Cast to ReaderWrapper instead of ImageReader.
09:56 Ticket #261 (omeul should upload OME-XML metadata) closed by melissa
fixed: As of r3969, original metadata is uploaded.
09:55 Changeset [3969] by melissa
OMEWriter now uploads original metadata (if available). Also added a …
08:01 Changeset [3968] by melissa
Fixed ArrayIndexOutOfBounds.

04/22/08:

15:18 Changeset [3967] by melissa
* Fixed NPE * FileStitcher now swaps dimensions if a Z (or T) axis is …
12:35 Changeset [3966] by curtis
Must use Double rather than Integer.
12:05 Changeset [3965] by melissa
Moved image count correction logic for line scan images.
11:49 Changeset [3964] by allison
saveBytes method still does not work correctly.
10:44 Changeset [3963] by melissa
Cleaned up image name parsing.
10:38 Ticket #284 (ZVI reader ignores xy positions beyond the first) created by curtis
See data/zeiss-zvi/vladan/vladan.zvi for an example.

04/21/08:

20:32 Ticket #283 (OMERO download has strange CLASSPATH requirements) created by melissa
To successfully download from OMERO in ImageJ, one must have either …
10:34 Ticket #282 (Slidebook image names are truncated) created by melissa
See for instance slidebook/john/1.sld and slidebook/john/60x.sld. For …
07:56 Ticket #281 (Attempting to colorize single channel data throws an exception) closed by melissa
fixed: r3962
07:55 Changeset [3962] by melissa
Don't use CompositeImage to colorize single-channel stacks.

04/20/08:

19:40 Changeset [3961] by curtis
Remove legacy case logic.
14:17 Ticket #267 (Write ImageJ plugin to swap dimension labels) closed by melissa
fixed: r3960. Decided not to implement this as a separate plugin, since it's …
14:15 Changeset [3960] by melissa
Added option to swap dimension labels.

04/18/08:

18:00 Ticket #281 (Attempting to colorize single channel data throws an exception) created by curtis
For example, try the following macro command: […]
17:44 Changeset [3959] by curtis
Progress on metadata store autogenerator. MetadataStore/MetadataRetrieve …
17:42 Changeset [3958] by curtis
Initial version of direct 2003-FC schema hierarchy.
15:44 Changeset [3957] by curtis
Add missing getImageCount function.
15:22 Changeset [3956] by curtis
Align documentation text better.
15:14 Changeset [3955] by curtis
Fix some problems with Bio-Formats macro extensions, add a few missing …
14:55 Changeset [3954] by melissa
Treat XZ and XT scans like regular XY images.
14:45 Changeset [3953] by melissa
Adjust effective channel count if RGB planes were written.
13:46 Changeset [3952] by melissa
Updated plane width/height calculation based on new files.
12:59 Ticket #280 (Move ImageJ-specific logic out of OMEUtils) created by melissa
loci.formats.ome.OMEUtils contains a fair amount of code that is specific …
12:50 Changeset [3951] by melissa
Added utility methods for packing and swapping floats/doubles. Fixed how …
12:49 Changeset [3950] by melissa
Fixed ArrayIndexOutOfBounds; one more getUsedFiles fix.
12:47 Changeset [3949] by melissa
Fixed getUsedFiles to return all of the files in the dataset.
07:57 Ticket #279 (Add support for FEI SEM format) created by melissa
We have several files in the FEI SEM format (data/fei/, .img extension). …

04/17/08:

14:13 Ticket #278 (Move OME/OMERO plugins out of loci_tools.jar) created by melissa
To reduce complaints about the size of loci_tools.jar (currently > 16 MB), …
12:39 Changeset [3948] by melissa
When applying scaling factors, don't assume that the source image is …
10:16 Ticket #269 (OMEReader does not read all metadata) closed by melissa
fixed: Original metadata is retrieved as of r3947.
10:15 Changeset [3947] by melissa
OMEReader now extracts appropriate OriginalMetadata elements from the OME …
09:01 Changeset [3946] by allison
Login works now
07:34 Changeset [3945] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3944] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3943] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3942] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3941] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3940] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3939] by melissa
2008 Apr 17 release of LOCI Tools
07:34 Changeset [3938] by melissa
2008 Apr 17 release of LOCI Tools
07:30 Changeset [3937] by melissa
Added what's new for today's release.
07:29 Changeset [3936] by melissa
Fixed ArrayIndexOutOfBounds.

04/16/08:

21:48 Changeset [3935] by melissa
If an XML TIFF comment is found, do not place it in the metadata …
18:22 Changeset [3934] by curtis
Progress on metadata store autogenerator. Not ready yet.
17:37 Changeset [3933] by curtis
Temporarily comment out offending lines of metadata conversion logic.
17:37 Changeset [3932] by curtis
Fix NullPointerException.
17:34 Changeset [3931] by curtis
Allow construction of legacy OME-XML documents using OMEXMLFactory.
17:28 Changeset [3930] by melissa
Added bytesToDouble.
17:08 Changeset [3929] by melissa
Minor tweaks to timestamp parsing logic; place timestamps in OME-XML.
16:23 Ticket #277 (Bio-Formats drag and drop window) created by curtis
Wayne Rasband suggests: What I would like to see is a "Bio-Formats" …
15:37 Changeset [3928] by curtis
Code from Tom Caswell to parse timestamp for each image plane.
15:02 Changeset [3927] by melissa
Colorize channels by default.
14:48 Changeset [3926] by melissa
Moved CompositeImage coloring logic to the colorizer plugin; as a result, …
10:34 Changeset [3925] by melissa
Remainder of ND2 bug fixes.
08:49 Ticket #276 (Make ND2 reader faster) created by melissa
Initializing ND2 files is painfully slow, especially if the file is larger …
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