22:28 Changeset [3503] by melissa
* Added image name filter. * OMEReader and OMEWriter now use …
17:24 Changeset [3502] by melissa
Uncommented metadata key/value length checking (fixes Metamorph problem). …
17:15 Ticket #230 (Support for sub-channels in ImageJ) closed by melissa
fixed: r3501.
17:14 Ticket #5 (Better channel merging in Bio-Formats Importer) closed by melissa
fixed: Added hooks for spectral projection in r3501. The option to use spectral …
17:14 Changeset [3501] by melissa
Added sub-C labels and hooks for merging using spectral projection.
16:33 Ticket #232 (Fix TIFF performance issues) closed by melissa
invalid: This is/was caused by simultaneously reading 4+ datasets from the Samba …
14:42 Ticket #232 (Fix TIFF performance issues) created by melissa
Some TIFF files take an unacceptably long time to initialize - see …
14:38 Ticket #231 (Improve bfconvert) created by melissa
bfconvert is missing many of the features/command line options that are …
14:34 Ticket #230 (Support for sub-channels in ImageJ) created by melissa
Notes from Curtis: a. Title bar should report sub channel positions (use …
14:32 Ticket #229 (Support multi-series OME-TIFF export) created by melissa
Right now, we only support writing single-series OME-TIFF files. We need …
14:30 Ticket #228 (Add support for writing BigTIFF files) created by melissa
We should somehow allow writing of BigTIFF/BigOME-TIFF files - either add …
09:18 Changeset [3500] by melissa
Check ImageJ version number before calling setOpenAsHyperstack.


17:55 Ticket #227 (Can't save metadata in ImageJ) closed by melissa
fixed: r3499. Still need to clean up SearchableWindow's layout.
17:54 Changeset [3499] by melissa
Can now save metadata.
15:30 Ticket #227 (Can't save metadata in ImageJ) created by melissa
Attempting to save metadata from the metadata window fails; the search …
14:50 Changeset [3498] by melissa
Rewrote LegacyND2Reader to use our own native bindings.
14:44 Changeset [3497] by melissa
Make sure first reader is initialized.
07:55 Changeset [3496] by melissa
Added "open all series" option.


13:52 Changeset [3495] by melissa
Re-added search functionality to OME/OMERO downloader - allows searching …
13:49 Changeset [3494] by melissa
Populate MetadataStore fields for all series; fixed bug with datasets that …
13:46 Changeset [3493] by melissa
Don't allow setOpenAsHyperstack(false) on an instance of CompositeImage.
12:43 Changeset [3492] by melissa
Added notes on multi-series support and ChannelFiller; added OME-TIFF to …
10:23 Changeset [3491] by melissa
Smarter series name parsing.
09:56 Changeset [3490] by curtis
Minor tweak for consistency.
09:49 Changeset [3489] by curtis
Add suggestion from Ville Rantanen to improve performance.


17:33 Changeset [3488] by curtis
Initial version of M function for reading images into MATLAB using …
08:59 Changeset [3487] by melissa
Downloading from OMERO is now much faster. Also, ownership rules are now …


16:05 Changeset [3486] by melissa
* Better parsing of ImageJ TIFF comments. * Detect variation in SizeZ …
16:01 Changeset [3485] by melissa
Call setNormalized(true) so floating point data is handled correctly; take …
15:59 Changeset [3484] by melissa
Differentiate between series in files and series outside of files.
14:08 Ticket #226 ("Use virtual stack" option for Bio-Formats Importer) closed by melissa
fixed: r3482
14:07 Changeset [3483] by curtis
Fix some bugs in Velocity-based autogenerator.
14:06 Changeset [3482] by melissa
Added option to use a virtual stack.


16:39 Changeset [3481] by curtis
Use Velocity template engine for metadata logic autogenerator.
14:28 Ticket #224 (Display metadata in image info window) closed by melissa
fixed: r3480.
14:28 Changeset [3480] by melissa
Place metadata key/value pairs in the "Info" property.
13:58 Ticket #225 (Hyperstack option for "View stack with") closed by melissa
fixed: r3478 and r3479.
13:58 Changeset [3479] by melissa
Added hyperstack options to Slicer and Colorizer.
13:24 Changeset [3478] by melissa
Added option to view as a HyperStack, if ImageJ version is >= 1.39l.
12:13 Changeset [3477] by melissa
Parse dimensions stored in ImageJ-style comment.
11:45 Changeset [3476] by melissa
Fixed a bunch of miscellaneous bugs and efficiency issues.
11:10 Ticket #226 ("Use virtual stack" option for Bio-Formats Importer) created by curtis
ImageJ's support for virtual stacks has been steadily improving. As of the …


17:05 Ticket #225 (Hyperstack option for "View stack with") created by curtis
The Bio-Formats Importer can currently display image stacks with standard …
16:55 Ticket #224 (Display metadata in image info window) created by curtis
From WSR: > One thing that would be nice would be to have the metadata …
14:21 Changeset [3475] by curtis
List command line script name with usage instead of "java …
14:19 Changeset [3474] by curtis
Move TiffComment utility into command line tools suite as "tiffcomment."
14:09 Changeset [3473] by curtis
Fix bogus earlier fix.
13:34 Changeset [3472] by curtis
Be more forgiving with schemaLocation attribute namespace (or lack …
13:08 Changeset [3471] by curtis
Note that the OMERO JAR files are Bio-Formats dependencies.
13:07 Changeset [3470] by curtis
Change variable names and comments for mapFile-related methods to reflect …
13:03 Changeset [3469] by melissa
Added "-preload" option: reads the given file into a byte array, then uses …
12:44 Changeset [3468] by melissa
Mapped file takes precedence over file on disk.
12:22 Changeset [3467] by melissa
Extended Location's ID mapping logic to allow a String ID to be mapped to …
09:08 Changeset [3466] by melissa
Fixed bug in datasets where the first numeric block has no prefix.


16:34 Changeset [3465] by melissa
FileStitcher's behaviour should no longer be dependent upon which file is …
12:53 Changeset [3464] by melissa
When constructing a CompositeImage, the source stack must be in XYCZT …
11:10 Changeset [3463] by melissa
Check the ImageJ version more thoroughly when attempting to merge >8 bit …
10:04 Changeset [3462] by melissa
Added support for multi-series datasets and fixed a bug with …
09:07 Changeset [3461] by melissa
Read the XML block from the FLEX tag, not ImageDescription.
07:53 Changeset [3460] by melissa
Fixed bug with floating point thumbnails.


15:06 Changeset [3459] by melissa
Updated to take advantage of new features in ImageJ's CompositeImage - can …
14:59 Changeset [3458] by melissa
Updated to v1.39l.
14:47 Ticket #201 (Improve configuration file generator) closed by melissa
fixed: r3457
14:47 Changeset [3457] by melissa
Make sure that only one file from each dataset is placed in the list of …
13:08 Changeset [3456] by melissa
Added convenience method to TiffTools for retrieving the image description …
12:03 Changeset [3455] by curtis
Rearrange order of plugins in the menu and add separators.
09:37 Changeset [3454] by melissa
Retrieve the comment directly from the first IFD - don't use the value of …
09:23 Changeset [3453] by melissa
Call IFormatWriter.setMetadataRetrieve, as appropriate - this fixes a …


11:08 Changeset [3452] by curtis
Fix problem with clean target failing on Windows due to locked files.
10:41 Changeset [3451] by curtis
Since some environments do not install the antcontrib tasks properly from …
08:11 Changeset [3450] by melissa
Fixed NPE when there is only one series.


15:18 Changeset [3449] by melissa
Updated MetadataStore population logic to handle multiple series.
13:33 Changeset [3448] by melissa
Scale thumbnails in series chooser if "Autoscale images" is checked.
12:46 Changeset [3447] by melissa
Dimension order is not dependent upon Z and T sizes.
10:10 Changeset [3446] by melissa
Make sure absolute file paths are used.
09:43 Changeset [3445] by melissa
More robust support for stitching multi-series datasets - now supports an …


12:39 Changeset [3444] by melissa
Added logic to handle multiple series in a group of files; patterns such …
12:30 Ticket #222 (SDT reader should fully parse SETUP metadata block) closed by melissa
fixed: r3443
12:27 Changeset [3443] by melissa
* Fully parse SDT file info and setup blocks. * Significantly improved SDT …
11:34 Ticket #223 (Make Exporter work with 48-bit RGB data) closed by melissa
fixed: r3442
11:33 Changeset [3442] by melissa
Exporter now handles 48-bit RGB stacks correctly; doesn't display "Pixel …
08:56 Changeset [3441] by melissa
Fixed NPE.


15:50 Changeset [3440] by melissa
2007 Dec 01 release of LOCI Tools
15:50 Changeset [3439] by melissa
2007 Dec 01 release of LOCI Tools
15:50 Changeset [3438] by melissa
2007 Dec 01 release of LOCI Tools
15:50 Changeset [3437] by melissa
2007 Dec 01 release of LOCI Tools
15:50 Changeset [3436] by melissa
2007 Dec 01 release of LOCI Tools
15:50 Changeset [3435] by melissa
2007 Dec 01 release of LOCI Tools
15:50 Changeset [3434] by melissa
2007 Dec 01 release of LOCI Tools
15:50 Changeset [3433] by melissa
2007 Dec 01 release of LOCI Tools
15:34 Changeset [3432] by melissa
* Added OMERO JARs; updated build scripts appropriately. * Updated what's …
15:18 Changeset [3431] by melissa
Updated all OME download logic to support downloading from OMERO.
15:15 Changeset [3430] by melissa
Moving OMEUtils to loci.formats.ome.


13:05 Ticket #223 (Make Exporter work with 48-bit RGB data) created by melissa
If the Exporter plugin is called on a 48-bit RGB stack, the resulting file …
09:51 Changeset [3429] by melissa
Added reader to download images from an OMERO database.


17:12 Changeset [3428] by melissa
Fixed floating point issues.
14:51 Changeset [3427] by melissa
Fixed C and T size detection.
12:57 Changeset [3426] by melissa
Only check once to see if the native library exists.
10:37 Changeset [3425] by melissa
Allow for array of strings in image description.
10:21 Ticket #217 (Write alternate ND2 reader using Nikon SDK) closed by melissa
fixed: Reader added in r3424. A couple of super important notes about the native …
10:13 Changeset [3424] by melissa
Added alternate ND2 reader that uses the Nikon ND2 SDK.
08:59 Changeset [3423] by melissa
Save pixel sizes directly, instead of retrieving them from the metadata …


18:28 Changeset [3422] by curtis
Both 2007-06 and 2003 (FC) metadata implementations now compile, though …
14:00 Changeset [3421] by curtis
Fix javadoc warning.
13:57 Changeset [3420] by curtis
Update package statements to reflect their status as "major" components.
13:41 Ticket #222 (SDT reader should fully parse SETUP metadata block) created by curtis
Currently the SDT reader parses the SETUP string from the header into an …
13:10 Changeset [3419] by melissa
Corrected pixel type detection.


13:51 Changeset [3418] by curtis
Add support for optional bioformats.sdt.intensity system property and …
12:56 Changeset [3417] by curtis
Do not reset intensity flag on close.
12:15 Changeset [3416] by melissa
Slicer and Colorizer now preserve calibration information.
12:06 Changeset [3415] by melissa
Use correct series name when calling MetadataStore.setImage.
10:23 Ticket #221 (Add support for Olympus APL file format) created by melissa
We have one Olympus APL dataset, which contains the following files: * 3 …
10:00 Ticket #214 (Add support for InCell1000 HCS format) closed by melissa
fixed: Very basic support added in r3414.
09:59 Changeset [3414] by melissa
Added basic reader for InCell 1000 datasets.
09:01 Changeset [3413] by melissa
Populate MetadataStore.
08:05 Changeset [3412] by melissa
Save/load windowless option in ImageJ preferences file.
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