Timeline


and

01/21/11:

23:19 Changeset [7576] by aivar
Project moved to ImageJ
23:13 Changeset [7575] by aivar
Added utility for dealing with native libraries.
22:27 Changeset [7574] by aivar
New utility class for dealing with native libraries.
21:26 Changeset [7573] by melissa
Backported a bunch of recent ND2 fixes to 4.1.
17:53 Changeset [7572] by curtis
Fix up save dialog behavior.
14:39 Changeset [7571] by melissa
Populate all of the wells, even if no image data is associated with them.
13:17 Changeset [7570] by melissa
Sanitize the XML before we parse it.
13:08 Changeset [7569] by curtis
Working version of Save As J2K plugin. Needed to call …
12:38 Changeset [7568] by melissa
Initial version of Metamorph TIFF HCS support.

01/20/11:

17:53 Changeset [7567] by curtis
Minor tweaks; still broken.
17:33 Changeset [7566] by curtis
Initial version of example JPEG2000 export plugin, courtesy of Albert …
14:51 Changeset [7565] by hinerm
Backport -r7564 to 4.2 branch.
14:49 Changeset [7564] by hinerm
Added a "dist" target to the bf-cpp project. Functionally identical to …
14:16 Changeset [7563] by hinerm
Backport r7562 to 4.2 branch.
14:11 Changeset [7562] by hinerm
Modified the dist target for BF-ITK to no longer copy unnecessary files on …
13:24 Changeset [7561] by melissa
Tweaked MetamorphReader's isThisType to prevent it from picking up files …
13:22 Changeset [7560] by melissa
Tweaked well name detection so that column indexes can only contain at …
13:07 Changeset [7559] by melissa
Clarified CLASSPATH requirements.
12:51 Changeset [7558] by melissa
Added some documentation on file export/conversion.
12:46 Ticket #650 (Update tiffcomment to allow editing on the command line) created by melissa
Right now, the only way to edit TIFF comments is using the GUI displayed …
12:45 Changeset [7557] by hinerm
Forward port from branch 4.2 changes - mistakenly committed to a branch …
12:24 Changeset [7556] by hinerm
Added the java class BioFormatsExtensionPrinter to the svn repository. …
12:22 Changeset [7555] by hinerm
Added a new java class to BF-CPP - BioFormatsExtensionPrinter - to …
12:18 Changeset [7554] by curtis
Add variable for controlling number of channels.

01/19/11:

15:40 Ticket #646 (OME-TIFFs cannot be opened in Fiji with file grouping turned on) closed by melissa
fixed: (In [7553]) Prevent an NPE when attempting to stitch datasets that aren't …
15:40 Changeset [7553] by melissa
Prevent an NPE when attempting to stitch datasets that aren't stitchable. …
14:36 Ticket #627 (Slidebook series grouping is not always correct) closed by melissa
fixed: The series grouping should be correct with r7552, but the pixel data still …
14:35 Changeset [7552] by melissa
Group together separate blocks of pixels that belong to the same stack. …
11:38 Changeset [7551] by melissa
Fixed various metadata population problems when working with multi-file …
11:34 Changeset [7550] by curtis
Migrate workflow project to ImageJ repository. New location is …
11:13 Changeset [7549] by curtis
Remove binary libraries (not needed with Maven).
11:11 Changeset [7548] by curtis
Convert LOCI workflow to Maven.

01/18/11:

13:09 Ticket #649 (Add IFormatWriter.saveBytes signatures that accept a Region) created by melissa
...instead of 4 ints specifying the region.
13:09 Ticket #648 (Add reader wrapper that provides simpler tile access) created by melissa
* void setTileWidth(int width) defaults to optimal width * void …
13:04 Ticket #647 (Add conversion convenience methods to FormatTools) created by melissa
Specifically: * static void convert(IFormatReader, IFormatWriter) * …
12:56 Ticket #646 (OME-TIFFs cannot be opened in Fiji with file grouping turned on) created by melissa
To reproduce: * start Fiji * select Plugins > LOCI > Bio-Formats …
12:35 Ticket #645 (Eliminate log4j warning messages) created by melissa
Several Bio-Formats-related tools still display log4j warning messages; …
12:34 Ticket #644 (Parse additional Andor TIFF tags) created by melissa
In particular: […] See the files in data/andor/benjamin/ for examples …
11:55 Changeset [7547] by aivar
Delete extraneous files
11:54 Changeset [7546] by aivar
Delete extraneous files
11:52 Changeset [7545] by aivar
Delete extraneous files
11:44 Changeset [7544] by melissa
Fixed channel name and wavelength population. See  omero:#3865.

01/17/11:

11:29 Ticket #643 (Slidebook files with maximum projections cannot be read) closed by melissa
fixed: The file mentioned above can now be read, but the pixel data for some …
11:27 Changeset [7543] by melissa
One more adjustment to SizeX/SizeY calculations. See #643.
11:07 Changeset [7542] by rlentz
Added eclipse jar export configuration file
11:01 Ticket #626 (Slidebook valid bits per pixel not parsed) closed by melissa
fixed: (In [7541]) Parse valid bits per pixel from Slidebook files. Closes #626.
11:01 Changeset [7541] by melissa
Parse valid bits per pixel from Slidebook files. Closes #626.
10:17 Changeset [7540] by rlentz
No change

01/14/11:

20:46 Changeset [7539] by aivar
JNI NativeLoader
13:18 Ticket #643 (Slidebook files with maximum projections cannot be read) created by melissa
See data/slidebook/vytas/worms.sld.
13:06 Ticket #642 (Add better isThisType tests) created by melissa
Two new tests should be added: * one in loci.formats.utests that times …
11:50 Ticket #612 (Multi-channel indexed color images treated incorrectly) closed by melissa
fixed: (In [7538]) Set 'falseColor' to true, so that lookup tables are not …
11:50 Changeset [7538] by melissa
Set 'falseColor' to true, so that lookup tables are not improperly …
11:22 Ticket #641 (Add support for Zeiss FCS files) created by melissa
See data in data/zeiss-fcs/chris/ and description in …
10:48 Changeset [7537] by rlentz
changed the implementation to floating point
09:15 Changeset [7536] by rlentz
Test from Michael Bien
08:53 Ticket #637 (Plane numbers in status bar are sometimes incorrect) closed by melissa
fixed: (In [7535]) Fixed plane index in status bar. Closes #637.
08:53 Changeset [7535] by melissa
Fixed plane index in status bar. Closes #637.

01/13/11:

21:44 Changeset [7534] by aivar
Multiple changes to get discovery and workflow save/restore to Preferences …
16:28 Changeset [7533] by rlentz
Configured for 64 bit linux.
16:15 Changeset [7532] by rlentz
16:13 Changeset [7531] by rlentz
14:40 Changeset [7530] by hinerm
Update bf-cpp proxy list to match latest Java source files.
14:32 Changeset [7529] by hinerm
Backport latest bf-itk to 4.2 branch.
13:56 Changeset [7528] by melissa
Corrected pixel type for 32-bit images, as Andor/Fluoview assumes that all …
13:46 Changeset [7527] by rlentz
13:29 Ticket #640 (Add a few more options to bfconvert) created by melissa
In particular: * '-range', similar to showinf's '-range' * '-channel', …
12:18 Changeset [7526] by aivar
Copied over workflow stuff from DeepZoom plugin.
12:17 Changeset [7525] by rlentz
10:58 Changeset [7524] by rlentz
Tested SobelFilter Sample under OSX with latest CUDA and jogamp libraries. …
09:47 Changeset [7523] by rlentz
Restructured libs and code to reflect CUDA 3.2 and Jogamp's signed build …

01/12/11:

20:05 Ticket #639 (Make sure that static fields are being used properly) created by melissa
There are several static (non-final) HashMaps/Hashtables throughout the …
20:05 Changeset [7522] by melissa
Make primitive type static variables volatile.
15:34 Changeset [7521] by rlentz
update
15:20 Changeset [7520] by rlentz
update
15:19 Changeset [7519] by rlentz
update
15:19 Changeset [7518] by rlentz
update
15:17 Changeset [7517] by rlentz
update 7
14:40 Changeset [7516] by aivar
You can now create a workflow, save to XML, create another workflow from …
13:20 Changeset [7515] by rlentz
update
12:17 Ticket #638 (Add support for Zeiss LSM files that have differing bits per sample) created by melissa
See the file in data/zeiss-lsm/aaron-o*/. Each non-thumbnail IFD has a …
11:35 Ticket #637 (Plane numbers in status bar are sometimes incorrect) created by melissa
See attached screenshot. Specifying a range of planes to open can cause …
10:39 Ticket #633 (FV1000 LUTs are not displayed correctly in ImageJ) closed by melissa
fixed: (In [7514]) Fixed indexed flag and LUT parsing. Closes #633.
10:39 Changeset [7514] by melissa
Fixed indexed flag and LUT parsing. Closes #633.
10:09 Changeset [7513] by hinerm
Enhanced ant dist script to copy BioFormatsIO.dll to the dist directory.

01/11/11:

21:29 Changeset [7512] by aivar
Made the test plugin input and output names more meaningful.
21:13 Changeset [7511] by aivar
Workflow updates, works with new PluginModule, hooks up to …
21:11 Changeset [7510] by aivar
Added new tests during test-driven development.
21:11 Changeset [7509] by aivar
This package is basically a copy of loci.multiinstanceplugin. Also …
15:07 Ticket #636 (Allow ImageReader to call isThisType(..., false)) created by melissa
There are three pieces to this ticket: 1) Add a setter to ImageReader …
14:28 Changeset [7508] by melissa
Fixed NPE.
14:27 Changeset [7507] by melissa
Backported changes to Openlab reader for importing HCS data.
13:53 Changeset [7506] by rlentz
Updated the Readme text to the following: ( Please ensure installation of …
13:45 Changeset [7505] by rlentz
No change here.
13:44 Changeset [7504] by rlentz
Several updates to clarify the examples provided to enable OpenCL …
13:20 Changeset [7503] by curtis
Backport r7494,r7496 bugfixes to 4.2 branch.
12:56 Changeset [7502] by melissa
Don't overwrite existing image names.
12:40 Changeset [7501] by rlentz
Added a readme This code was developed to show how to use JOCL to …
12:39 Changeset [7500] by melissa
Search more thoroughly for image descriptions. Image descriptions are no …
09:14 Changeset [7499] by melissa
Fixed compile error in r7498.
09:03 Changeset [7498] by melissa
Backported ScreenReader to 4.2.

01/10/11:

20:11 Changeset [7497] by aivar
Fleshed out WorkFlow.finalize. ModuleFactory now has a register method …
16:18 Changeset [7496] by curtis
Fix signedness averaging problem with convertTo8Bit method.
16:14 Changeset [7495] by aivar
Added proper ComponentFactory. Renamed chain -> wire, component -> …
15:56 Changeset [7494] by curtis
Fix problem where custom LUTs override grayscale mode. This happened …
14:22 Changeset [7493] by melissa
Slightly more robust well name checking.
10:25 Changeset [7492] by melissa
Fixed import that caused compile failure in r7491.
10:15 Changeset [7491] by melissa
Merged file grouping and channel name parsing fixes from trunk.

01/07/11:

17:22 Changeset [7490] by aivar
Added method call for Rick's project.
13:38 Changeset [7489] by melissa
Prevent potential NPE if the "Info" property is not set on the ImagePlus …
12:43 Changeset [7488] by melissa
Sanitize OME-XML before attempting to create a MetadataStore.

01/06/11:

10:56 Changeset [7487] by melissa
Use a ConcurrentHashMap instead of a HashMap.

01/05/11:

16:15 Changeset [7486] by melissa
Added optional cacheing of directory listings, courtesy of Lee Kamentsky.
14:19 Ticket #635 (Add support for Image-Pro .ips metadata files) created by melissa
See files in data/imagepro/alex/. The .ips file is some sort of metadata …

01/04/11:

13:09 Ticket #634 (File grouping does not work in ImageJ on Windows) closed by melissa
fixed: (In [7485]) Escape backslashes when finding a pattern. Closes #634.
13:09 Changeset [7485] by melissa
Escape backslashes when finding a pattern. Closes #634.
12:05 Changeset [7484] by melissa
Various fixes to allow retrieval of pixel data from truncated TIFFs.

12/31/10:

14:16 Ticket #272 (Ability to explicitly disable file stitching for certain files) closed by melissa
fixed: This was added in r6349; adding "no_stitch=true" to a .bioformats file …
13:39 Changeset [7483] by melissa
Fixed a handful of bugs introduced in r7481.
11:07 Changeset [7482] by melissa
Moved 'void setWriteSequentially(boolean)' from TiffWriter to …
11:04 Changeset [7481] by melissa
Expanded special strip unpacking case to allow multiple strips.
10:56 Changeset [7480] by melissa
Set a more reasonable timeout when checking for updates.

12/30/10:

13:26 Ticket #634 (File grouping does not work in ImageJ on Windows) created by melissa
The file separator ('\') causes the file pattern to be incorrectly …

12/29/10:

20:35 Changeset [7479] by aivar
Added comments.
17:41 Ticket #619 (Add tests for ScreenReader) closed by melissa
fixed: (In [7478]) Added tests for screen detection. Closes #619.
17:41 Changeset [7478] by melissa
Added tests for screen detection. Closes #619.
17:40 Changeset [7477] by melissa
Allow sparse plates.
17:39 Changeset [7476] by melissa
Prevent a NPE when calling isThisType on a file with no parent directory.
15:45 Changeset [7475] by melissa
Attach non-well files as companion metadata files.
14:05 Ticket #624 (Allow FileStitcher to stitch files with multiple series) closed by melissa
fixed: (In [7474]) Allow multi-series files to be stitched if the file pattern …
14:05 Changeset [7474] by melissa
Allow multi-series files to be stitched if the file pattern contains only …
13:06 Changeset [7473] by melissa
Make type detection slightly more restrictive; this should allow the tests …
12:47 Ticket #628 (Update ScreenReader to handle InCell 3000 data) closed by melissa
fixed: (In [7472]) Added more flexible plate/well detection, so that InCell 3000 …
12:47 Changeset [7472] by melissa
Added more flexible plate/well detection, so that InCell 3000 datasets are …
09:11 Ticket #613 (Investigate consolidating 'showinf' and 'bfview') closed by melissa
fixed: (In [7471]) 'bfview' now has the same behavior as 'showinf', except that a …
09:11 Changeset [7471] by melissa
'bfview' now has the same behavior as 'showinf', except that a deprecation …

12/28/10:

12:05 Ticket #580 (Virtual stack with split channels, timepoints and/or planes) closed by melissa
fixed: (In [7470]) Allow virtual stacks to be sliced. Closes #580.
12:05 Changeset [7470] by melissa
Allow virtual stacks to be sliced. Closes #580.

12/27/10:

17:24 Changeset [7469] by melissa
Removed duplicate variable declaration, which prevented 2008-09 and …
16:39 Changeset [7468] by aivar
Grayscale image wasn't showing up.
15:29 Ticket #601 (Investigate using MediaUtil for block-based JPEG decoding) closed by melissa
fixed: After some investigation, I have yet to find a way to retrieve the …
14:40 Changeset [7467] by melissa
Fixed NPE introduced in r7433.
14:37 Changeset [7466] by melissa
Fixed one more IFD caching bug.
13:34 Ticket #631 (EPS coloring is often incorrect) closed by melissa
fixed: (In [7465]) Fixed how EPS images with two channels are handled. Closes …
13:34 Changeset [7465] by melissa
Fixed how EPS images with two channels are handled. Closes #631.
10:47 Ticket #603 (Move get/setMetadataOptions methods to IFormatReader) closed by melissa
invalid: The [get,set]MetadataOptions methods are actually declared in the …
10:41 Ticket #630 (Bio-Rad LUTs do not look correct) closed by melissa
fixed: (In [7464]) Reset ColorModel after setting the display range; this …
10:41 Changeset [7464] by melissa
Reset ColorModel after setting the display range; this prevents LUTs from …
09:49 Ticket #632 (Some metadata is not populated for Zeiss LSM files) closed by melissa
fixed: (In [7463]) Preserve user name and emission wavelengths. Closes #632.
09:49 Changeset [7463] by melissa
Preserve user name and emission wavelengths. Closes #632.

12/24/10:

16:15 Ticket #479 (Add support for Trestle slide data) closed by melissa
fixed: (In [7462]) * Fixed various TIFF-parsing related problems introduced in …
16:15 Changeset [7462] by melissa
* Fixed various TIFF-parsing related problems introduced in r7459. * …
15:15 Changeset [7461] by melissa
Fixed a bug in ZipHandle.isZipFile(String) that was introduced in r7460.
14:50 Ticket #608 (Zip file URLs are not supported) closed by melissa
fixed: (In [7460]) Updated ZipHandle and ZipReader to use a ZipInputStream …
14:50 Changeset [7460] by melissa
Updated ZipHandle and ZipReader to use a ZipInputStream instead of a …
14:49 Changeset [7459] by melissa
Fill in IFD values after the IFDs have been parsed, thus reducing the …
11:54 Changeset [7458] by melissa
A few small speed improvements for reading Openlab files.

12/23/10:

18:53 Changeset [7457] by aivar
Resources directory.
18:40 Changeset [7456] by aivar
More documentation.
13:02 Changeset [7455] by melissa
Added initial version of Trestle reader, see #479.
11:50 Changeset [7454] by melissa
Made PGM parsing more flexible, as required for #479.
10:48 Ticket #599 (Add optimal tile size methods) closed by melissa
fixed: (In [7453]) Added methods for retrieving the optimal size of a sub-image. …
10:48 Changeset [7453] by melissa
Added methods for retrieving the optimal size of a sub-image. Closes …
09:21 Ticket #568 (Review results of testing project) closed by melissa
fixed: Many of the issues reported here were invalid or have since been fixed. …
09:20 Ticket #633 (FV1000 LUTs are not displayed correctly in ImageJ) created by melissa
See data/fv1000/jean-claude/villositerat0heurea.oib. The first channel …
09:19 Ticket #632 (Some metadata is not populated for Zeiss LSM files) created by melissa
See data/zeiss-lsm/gaetan/blastocyste.lsm: - the user name "adenot" is …
09:17 Ticket #631 (EPS coloring is often incorrect) created by melissa
See data/eps/frank/075095##_F_3C.eps. The main part of the image should …
09:15 Ticket #630 (Bio-Rad LUTs do not look correct) created by melissa
See biorad/chris/4C_tweek12;nSyb_PLC-PH-GFP_HRPstain.pic. With the LUT …

12/22/10:

17:09 Ticket #629 (Add support for Leica Stereo Microscope data) created by melissa
See files in data/leica-sm/grant/. It looks to be one or more plain TIFFs …
17:01 Changeset [7452] by melissa
Fixed .nd/.stk file searching, to prevent problems with multiple …
14:20 Changeset [7451] by melissa
Append 'Z' to the dimension order string when appropriate. See …
12:45 Ticket #622 (.aim to TIFF conversion is not quite right) closed by melissa
invalid: This is actually a set of problems in ImageJ's native TIFF reader. I can …
12:35 Changeset [7450] by curtis
Update legacy auto-display plugin package name.
12:13 Ticket #628 (Update ScreenReader to handle InCell 3000 data) created by melissa
InCell 3000 files have names like this: 20041103 1049_01_REF-1049-03 - …
12:11 Ticket #443 (Add support for IN Cell 3000 datasets) closed by melissa
fixed: (In [7449]) Added reader for InCell 3000 files. Closes #443.
12:11 Changeset [7449] by melissa
Added reader for InCell 3000 files. Closes #443.
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