Timeline


and

08/07/08:

15:58 Changeset [4301] by curtis
Fix some problems in channel separator and dimension swapper. Still bugs …
15:24 Changeset [4300] by melissa
Fixed various bugs exposed by test suite.
15:17 Changeset [4299] by curtis
Better support for mixed Java versions; more OMEROWriter cleanup.
14:55 Changeset [4298] by curtis
Fix compile errors.
14:27 Changeset [4297] by curtis
Some cleanup. Still need to fix compile problems.
13:51 Changeset [4296] by allison
Fixed bug in id String.
13:47 Changeset [4295] by allison
Working OMEROReader without reflected universe code.
13:45 Changeset [4294] by allison
Progress on main method
13:05 Changeset [4293] by curtis
Update some package descriptions.
10:07 Changeset [4292] by curtis
Update link to Javadocs.
10:05 WikiStart edited by curtis
(diff)

08/06/08:

13:51 Changeset [4291] by curtis
Fix some dimension swapper bugs... but there are still problems.
13:00 Changeset [4290] by curtis
Add Bio-Formats logo at various resolutions (not bundled into any JARs).
12:28 Changeset [4289] by curtis
Add logos for OME and Bio-Formats to About dialog boxes.

08/05/08:

09:02 Changeset [4288] by nor
Fixed edge case curve fitting estimate code.
08:44 Changeset [4287] by melissa
Fixed compile error.
08:31 Changeset [4286] by melissa
Removed debugging statement.
08:10 Changeset [4285] by melissa
Added OME-XML writer.

08/04/08:

14:17 Changeset [4284] by melissa
Slightly modified jmagick.jar to fix class loading problem in ImageJ.
12:02 Changeset [4283] by melissa
ChannelFiller now applies lookup tables if isFalseColor() == true.
11:36 Changeset [4282] by melissa
Don't assume that every plane has the same lookup table.
11:00 Changeset [4281] by melissa
Fixed bug that caused BufferedImages with type TYPE_INT_RGB to be treated …
10:28 Changeset [4280] by melissa
Corrected file index calculation when dimensions have been swapped.

08/01/08:

18:15 Changeset [4279] by melissa
Fixed image count calculation.
16:28 Changeset [4278] by curtis
Update Javadoc links.
12:38 Changeset [4277] by curtis
Fix package statements and tweak formatting.
12:36 Changeset [4276] by curtis
Better recognition of credentials strings.
12:36 Changeset [4275] by curtis
First cut at "Download from OMERO" and "Upload to OMERO" menu options.
12:05 Changeset [4274] by curtis
Fix some jikes warnings and remove some obsolete comments.
09:43 Changeset [4273] by nor
Continued work on estimation for bad curves. Still in progress, still …
02:23 Ticket #315 (Investigate how to handle ROIs and overlays within proprietary file ...) created by melissa
Several supported file formats can contain overlays - notably Zeiss ZVI, …
01:48 Changeset [4272] by melissa
Fix for datasets that don't have .stk files.
00:08 Changeset [4271] by melissa
Added writeLong utility method (fixes TiffTools compile error).

07/31/08:

23:15 Changeset [4270] by melissa
Fixed overwriteIFDValue to handle BigTIFF files.
22:19 Changeset [4269] by melissa
Allow the number of bytes per strip to be > 8192 if the number of bytes …
18:19 Changeset [4268] by melissa
* Fixed various bugs exposed by test suite. * Another patch to …
16:18 Changeset [4267] by ansari
12:33 Changeset [4266] by curtis
Close file at the end of the Bio-Formats MATLAB script.
12:19 Changeset [4265] by curtis
Reorganize some packages: * Move OME/OMERO database connectivity layer …
12:12 Changeset [4264] by curtis
Add hooks for "Download from OME" and "Upload to OME" menu options.

07/29/08:

15:11 Changeset [4263] by curtis
Set mime type for metadata fields summary doc.
15:10 Changeset [4262] by curtis
Add summary tables for supported metadata fields.
11:44 Changeset [4261] by curtis
Save importer preferences earlier, in case plugin crashes.

07/28/08:

12:25 Changeset [4260] by melissa
Call MetadataTools.populatePixels after core metadata fields have been …
11:34 Changeset [4259] by melissa
Fixed bug in NetcdfTools that prevented Imaris 5.5 files from opening.

07/25/08:

16:49 Ticket #259 (Add support for JPEG2000-compressed SVS files) closed by melissa
fixed: Added JPEG-2000 support for SVS in r4258. JMagick must be installed in …
16:46 Changeset [4258] by melissa
Use JMagick to decompress JPEG-2000 data if JAI fails.
14:26 Changeset [4257] by melissa
Updated all metadata support docs to indicate that …
13:15 Changeset [4256] by melissa
Fixed bug that prevented metadata from being displayed for multi-series …
12:25 Changeset [4255] by melissa
Handle yet another case where there are too many pixels files.
11:24 Changeset [4254] by melissa
Added timestamp support to Metamorph TIFF, courtesy of Thomas Caswell.

07/24/08:

11:51 Ticket #314 (Add support for vector data in PS/EPS files) created by melissa
EPSReader only supports raster data, but should also support vector data. …
11:45 Changeset [4253] by melissa
Throw a more informative exception when vector data is encountered.
11:05 Changeset [4252] by melissa
Fixed NPE.
10:27 Changeset [4251] by melissa
Added metadata support documentation for APLReader, MINCReader and …

07/23/08:

17:15 Changeset [4250] by curtis
Temporary hacks and fixes.
16:47 Changeset [4249] by curtis
Do not start per-pixel lifetime analysis until Start button is pressed.
16:46 Changeset [4248] by nor
More progress bar changes
16:35 Changeset [4247] by nor
Modification to progress bar - when it enters first pass iteration, …
16:30 Changeset [4246] by nor
Disables debugging prints, fixed progress meter
16:22 Changeset [4245] by curtis
* Better per-pixel lifetime progress bar. * Allow specification of …
16:11 Changeset [4244] by nor
Continuing bug fixes to GACurveFitter and BurnInRenderer
15:56 Changeset [4243] by curtis
Encapsulate core raw + derived data into SlimData class.
14:20 Changeset [4242] by melissa
Added support for objective name and physical X, Y, and Z sizes.
14:07 Changeset [4241] by curtis
Initial integration of per-pixel lifetime; miscellaneous bugfixes and …
13:56 Changeset [4240] by nor
unshadowed fields
13:44 Changeset [4239] by nor
Made changes to CurveFitter: it is now an abstract superclass, so children …
12:57 Changeset [4238] by curtis
Fix data offset bug; turn color range text fields red for bad input.
12:35 Changeset [4237] by curtis
Tweak some panel layouts.
12:34 Changeset [4236] by nor
updated (hopefully) for first and last indices
11:48 Changeset [4235] by curtis
Normalize exponential component count methods in various places.
11:36 Changeset [4234] by melissa
Fixed axis size calculations.
11:13 Changeset [4233] by nor
Modified CurveFitters to have first and last indices Moved constants out …
11:04 Changeset [4232] by curtis
Add separate view modes for "spectral projection" and "emission spectrum."
10:51 Ticket #187 (Model some data for testing) closed by curtis
fixed: There is a large quantity of synthetic test data (900 datasets) in the …
10:46 Ticket #85 (Look into other curve fitting algorithms) closed by curtis
fixed: SLIM Plotter now has an infrastructure for including additional curve …
10:43 Changeset [4231] by curtis
Add constructor signature that bins neighboring pixels.
10:42 Changeset [4230] by curtis
Add progress bar to image pane GUI.
10:41 Changeset [4229] by curtis
Remove some obsolete code.

07/22/08:

22:54 Ticket #313 (Improve Slidebook metadata) created by melissa
We now have several screenshots of the metadata displayed by Slidebook …
22:50 Ticket #312 (Improve TillVision support) created by melissa
TillVisionReader does not currently support workspace files (.vws). The …
21:13 Changeset [4228] by melissa
Fixed NPE.
21:09 Changeset [4227] by melissa
* Moved XML parsing to DataTools utility method. * Fixed Metamorph TIFF …
16:13 Changeset [4226] by curtis
* Split out shared VisAD types into their own class. * Add dummy …
15:08 Changeset [4225] by nor
Continuing modifications to run method of BurnInRenderer. First draft …
14:53 Changeset [4224] by curtis
Initial GUI for toggling view modes, + miscellaneous cleanup.
14:28 Changeset [4223] by curtis
Don't allow 1-component exponential guesses to have negative tau.
14:27 Changeset [4222] by curtis
Width of initial guess should be a percentage of total bins, not …
12:40 Changeset [4221] by curtis
* Split LM curve fitter into separate class. * Add option to switch …
12:31 Changeset [4220] by nor
With 100% reduced println error messages!
12:01 Changeset [4219] by nor
Fixes to curve fitting: - Work around for negative tau issue - Fixed …
10:32 Changeset [4218] by curtis
Fix Slim Plotter bugs when using NOR's fitting code with 2 components.

07/21/08:

16:54 Changeset [4217] by curtis
Add calls to NOR's new curve fitting code (commented out for now).
16:29 Changeset [4216] by nor
Initial commit of BurnInRenderer, modifications to support actual use in …
16:16 Changeset [4215] by curtis
Improve color min/max widgets.
14:34 Changeset [4214] by curtis
Split intensity pane into a separate class.
13:49 Changeset [4213] by nor
base renderer class for SLIM plotter
11:15 Changeset [4212] by nor
Modified data to be passed from double[][] to int[]
10:56 Changeset [4211] by curtis
Initial implementation of subsampling computation.
10:39 Changeset [4210] by curtis
Initial cut at API for curve collection class. Implementation is not …
09:08 Changeset [4209] by melissa
* Check TIFF header starting from offset 0, not the current offset. * …

07/18/08:

10:39 Ticket #233 (Improve time performance of subimage methods) closed by melissa
fixed: There doesn't appear to be an appreciable difference between reading …
10:03 Changeset [4208] by melissa
Reverted to opening planes using TiffTools, rather than using …

07/17/08:

14:35 Changeset [4207] by curtis
Fix problem with command line tools on Unix when directory contains a …
14:25 Changeset [4206] by curtis
Fix problem with command line tools on Windows when directory contains a …
13:58 Ticket #256 (Add new isThisType signature) closed by melissa
fixed: (In [4205]) Added isThisType(RandomAccessStream) to IFormatReader API. …
13:58 Changeset [4205] by melissa
Added isThisType(RandomAccessStream) to IFormatReader API. Closes #256.
10:24 Ticket #290 (Util.openProcessor does not properly handle RGB data) closed by melissa
fixed: (In [4204]) Changed Util.openProcessor methods to Util.openProcessors. …
10:24 Changeset [4204] by melissa
Changed Util.openProcessor methods to Util.openProcessors. These methods …
09:12 Changeset [4203] by melissa
More cleanup. Removed some unused methods from ImageTools, and moved …

07/15/08:

15:47 Changeset [4202] by melissa
More cleanup.
11:24 Changeset [4201] by melissa
Removed debugging statements and fixed Z size parsing.
10:51 Changeset [4200] by melissa
* Minor code cleanup. * Added MinimalTiffReader - this is extended by …

07/14/08:

14:15 Changeset [4199] by curtis
Fix erroneous use of HTML in supported metadata fields docs.
12:29 Changeset [4198] by melissa
* Fixed FV1000 physical size Z calculation (stored in nm, not microns) * …
09:27 Changeset [4197] by melissa
Updated meta-support.txt to reflect current metadata population.
09:25 Changeset [4196] by melissa
Removed commented out min/max setting logic.

07/11/08:

15:19 Changeset [4195] by curtis
Invert manual caching flag.
15:18 Changeset [4194] by curtis
Minor tweaks.
14:26 Changeset [4193] by curtis
Add "Bio-Formats Mass Importer" example plugin.
12:10 Changeset [4192] by curtis
Update list of libraries.
12:00 Ticket #277 (Bio-Formats drag and drop window) closed by curtis
fixed: (In [4191]) Add drag and drop support to shortcut window; closes #277.
12:00 Changeset [4191] by curtis
Add drag and drop support to shortcut window; closes #277.
11:17 Changeset [4190] by melissa
A couple of fixes to SPW population.

07/10/08:

15:38 Changeset [4189] by curtis
Move window placement utility method into common utility class.
15:38 Changeset [4188] by curtis
Tweak import statements.
15:37 Changeset [4187] by curtis
Remove unneeded files.
15:36 Changeset [4186] by curtis
First cut at Bio-Formats configuration window. No drag and drop support …
14:56 Changeset [4185] by allison
Update Eclipse build path; fix loci.apps.flow build errors.
14:52 Changeset [4184] by allison
Update OMERO libraries to 3.0 Beta 3.
13:37 Changeset [4183] by melissa
Fixed the WellSampleIndex values.
11:48 Ticket #311 (Split build into multiple components) created by curtis
The current dependency tree has a few wrinkles, especially with respect to …
09:25 Changeset [4182] by curtis
Reorder method declarations.
09:24 Changeset [4181] by melissa
Recognize .tf2, .tf8, and .btf extensions as TIFF/BigTIFF.
09:01 Changeset [4180] by melissa
Added support for TillVision data.

07/09/08:

15:51 Changeset [4179] by melissa
Added logic to reorder channels based on metadata values.
14:09 Ticket #307 (Split IndexedColorModel into Index16ColorModel and Index32ColorModel) closed by melissa
fixed: (In [4178]) Moved 16-bit lookup table support from IndexedColorModel to …
14:09 Changeset [4178] by melissa
Moved 16-bit lookup table support from IndexedColorModel to …
13:44 Ticket #221 (Add support for Olympus APL file format) closed by melissa
fixed: (In [4177]) * Tweaked MDBParser API to be more usable. * Added Olympus APL …
13:44 Changeset [4177] by melissa
* Tweaked MDBParser API to be more usable. * Added Olympus APL reader - …
13:34 Ticket #310 (Overhaul Bio-Formats Importer) created by curtis
The Bio-Formats Importer plugin has become quite complex. The logic is …
13:29 Ticket #309 (Document supported metadata fields in each format) created by curtis
The Bio-Formats web site has a handy table showing all the supported file …
13:20 Ticket #308 (Sort data repository into different categories) created by curtis
Our repository of test files contains a large quantity of data: over 140 …
13:00 Ticket #307 (Split IndexedColorModel into Index16ColorModel and Index32ColorModel) created by curtis
Core Java has an IndexColorModel class for 24-bit RGB look-up tables keyed …
10:41 Changeset [4176] by melissa
Fixed a couple of offset bugs in mdbtools - the constituent MDB files in …

07/08/08:

15:12 Changeset [4175] by curtis
Fix some bugs and add more constructor options, including null linked …
15:07 Changeset [4174] by curtis
Remove "image processor" from list of source types.
15:06 Changeset [4173] by curtis
Fix thread title.
14:37 Changeset [4172] by ansari
14:36 Changeset [4171] by ansari
14:30 Changeset [4170] by ansari
Updating ij.jar to nightly build (1.41f)
14:28 Changeset [4169] by ansari
Updating flow app files
13:18 Changeset [4168] by melissa
Set a default creation date, if one is not present in the file.
07:53 Changeset [4167] by melissa
Fixed Windows path name bug.
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