source: branches/4.2/components/bio-formats/doc/whats-new.txt @ 7183

Revision 7183, 17.0 KB checked in by melissa, 9 years ago (diff)

Fixed a couple of bugs in ImageConverter.

14.2.1 (2010 November 12):
2* Many, many bug fixes
3* Added support for 7 new formats:
4  - CellWorX .pnl
5  - ECAT7
6  - Varian FDF
7  - Perkin Elmer Densitometer
9  - Compix/SimplePCI TIFF
10  - Nikon Elements TIFF
11* Updated Zeiss LSM metadata parsing, with generous assistance from Zeiss, FMI, and MPI-CBG
12* Lots of work to ensure that converted OME-XML validates
13* Improved file stitching functionality; non-numerical file patterns and limited regular expression-style patterns are now supported
154.2.0 (2010 July 9):
16* Fixed many, many bugs in all aspects of Bio-Formats
17* Reworked ImageJ plugins to be more user- and developer-friendly
18* Added many new unit tests
19* Added support for approximately 25 new file formats, primarily in the SPM domain
20* Rewrote underlying I/O infrastructure to be thread-safe and based on Java NIO
21* Rewrote OME-XML parsing/generation layer; OME-XML 2010-06 is now supported
22* Improved support for exporting large images
23* Improved support for exporting to multiple files
24* Updated logging infrastructure to use slf4j and log4j
264.1.1 (2009 December 3):
27* Fixed many bugs in popular file format readers
294.1 (2009 October 21):
31* Fixed many bugs in most file format readers
32* Significantly improved confocal and HCS metadata parsing
33* Improved C++ bindings
34* Eliminated references to Java AWT classes in core Bio-Formats packages
35* Added support for reading Flex datasets from multiple servers
36* Improved OME-XML generation; generated OME-XML is now valid
37* Added support for Olympus ScanR data
38* Added OSGi information to JARs
39* Added support for Amira Mesh files
40* Added support for LI-FLIM files
41* Added more informative exceptions
42* Added support for various types of ICS lifetime data
43* Added support for Nikon EZ-C1 TIFFs
44* Added support for Maia Scientific MIAS data
464.0.1 (2009 June 1):
48* Lots of bug fixes in most format readers and writers
49* Added support for Analyze 7.1 files
50* Added support for Nifti files
51* Added support for Cellomics .c01 files
52* Refactored ImageJ plugins
53* Bio-Formats, the common package, and the ImageJ plugins now require Java 1.5
54* Eliminated native library dependency for reading lossless JPEGs
55* Changed license from GPL v3 or later to GPL v2 or later
56* Updated Olympus FV1000, Zeiss LSM, Zeiss ZVI and Nikon ND2 readers to parse
57  ROI data
58* Added option to ImageJ plugin for displaying ROIs parsed from the chosen
59  dataset
60* Fixed BufferedImage construction for signed data and unsigned int data
624.0.0 (2009 March 3):
64* Improved OME data model population for Olympus FV1000, Nikon ND2, Metamorph
65  STK, Leica LEI, Leica LIF, InCell 1000 and MicroManager
66* Added TestNG tests for format writers
67* Added option to ImageJ plugin to specify custom colors when customizing
68  channels
69* Added ability to upgrade the ImageJ plugin from within ImageJ
70* Fixed bugs in Nikon ND2, Leica LIF, BioRad PIC, TIFF, PSD, and OME-TIFF
71* Fixed bugs in Data Browser and Exporter plugins
72* Added support for Axon Raw Format (ARF), courtesy of Johannes Schindelin
73* Added preliminary support for IPLab-Mac file format
752008 December 29:
76* Improved metadata support for Deltavision, Zeiss LSM, MicroManager, and Leica
77  LEI
78* Restructured code base/build system to be component-driven
79* Added support for JPEG and JPEG-2000 codecs within TIFF, OME-TIFF and OME-XML
80* Added support for 16-bit compressed Flex files
81* Added support for writing JPEG-2000 files
82* Added support for Minolta MRW format
83* Added support for the 2008-09 release of OME-XML
84* Removed dependency on JMagick
85* Re-added caching support to data browser plugin
86* Updated loci.formats.Codec API to be more user-friendly
87* Expanded loci.formats.MetadataStore API to better represent the OME-XML model
88* Improved support for Nikon NEF
89* Improved support for TillVision files
90* Improved ImageJ import options dialog
91* Fixed bugs with Zeiss LSM files larger than 4 GB
92* Fixed minor bugs in most readers
93* Fixed bugs with exporting from an Image5D window
94* Fixed several problems with virtual stacks in ImageJ
962008 August 30:
97* Fixed bugs in many file format readers
98* Fixed several bugs with swapping dimensions
99* Added support for Olympus CellR/APL files
100* Added support for MINC MRI files
101* Added support for Aperio SVS files compressed with JPEG 2000
102* Added support for writing OME-XML files
103* Added support for writing APNG files
104* Added faster LZW codec
105* Added drag and drop support to ImageJ shortcut window
106* Re-integrated caching into the data browser plugin
1082008 July 1:
109* Fixed bugs in most file format readers
110* Fixed bugs in OME and OMERO download functionality
111* Fixed bugs in OME server-side import
112* Improved metadata storage/retrieval when uploading to and downloading from
113  the OME Perl server
114* Improved Bio-Formats ImageJ macro extensions
115* Major updates to MetadataStore API
116* Updated OME-XML generation to use 2008-02 schema by default
117* Addressed time and memory performance issues in many readers
118* Changed license from LGPL to GPL
119* Added support for the FEI file format
120* Added support for uncompressed Hamamatsu Aquacosmos NAF files
121* Added support for Animated PNG files
122* Added several new options to Bio-Formats ImageJ plugin
123* Added support for writing ICS files
1252008 April 17:
126* Fixed bugs in Slidebook, ND2, FV1000 OIB/OIF, Perkin Elmer, TIFF, Prairie,
127  Openlab, Zeiss LSM, MNG, Molecular Dynamics GEL, and OME-TIFF
128* Fixed bugs in OME and OMERO download functionality
129* Fixed bugs in OME server-side import
130* Fixed bugs in Data Browser
131* Added support for downloading from OMERO 2.3 servers
132* Added configuration plugin
133* Updates to MetadataStore API
134* Updates to OME-XML generation - 2007-06 schema used by default
135* Added support for Li-Cor L2D format
136* Major updates to TestNG testing framework
137* Added support for writing multi-series OME-TIFF files
138* Added support for writing BigTIFF files
1402008 Feb 12:
141* Fixed bugs in QuickTime, SimplePCI and DICOM
142* Fixed a bug in channel splitting logic
1442008 Feb 8:
145* Many critical bugfixes in format readers and ImageJ plugins
146* Newly reborn Data Browser for 5D image visualization
147    + some combinations of import options do not work yet
1492008 Feb 1:
150* Fixed bugs in Zeiss LSM, Metamorph STK, FV1000 OIB/OIF, Leica LEI, TIFF,
151  Zeiss ZVI, ICS, Prairie, Openlab LIFF, Gatan, DICOM, QuickTime
152* Fixed bug in OME-TIFF writer
153* Major changes to MetadataStore API
154* Added support for JPEG-compressed TIFF files
155* Added basic support for Aperio SVS files
156    + JPEG2000 compression is still not supported
157* Improved "crop on import" functionality
158* Improvements to bfconvert and bfview
159* Improved OME-XML population for several formats
160* Added support for JPEG2000-compressed DICOM files
161* EXIF data is now parsed from TIFF files
1632007 Dec 28:
164* Fixed bugs in Leica LEI, Leica TCS, SDT, Leica LIF,
165  Visitech, DICOM, Imaris 5.5 (HDF), and Slidebook readers
166* Better parsing of comments in TIFF files exported from ImageJ
167* Fixed problem with exporting 48-bit RGB data
168* Added logic to read multi-series datasets spread across multiple files
169* Improved channel merging in ImageJ - requires ImageJ 1.39l
170* Support for hyperstacks and virtual stacks in ImageJ - requires ImageJ 1.39l
171* Added API for reading directly from a byte array or InputStream
172* Metadata key/value pairs are now stored in ImageJ's "Info" property
173* Improved OMERO download plugin - it is now much faster
174* Added "open all series" option to ImageJ importer
175* ND2 reader based on Nikon's SDK now uses our own native bindings
176* Fixed metadata saving bug in ImageJ
177* Added sub-channel labels to ImageJ windows
178* Major updates to 4D Data Browser
179* Minor updates to automated testing suite
1812007 Dec 1:
182* Updated OME plugin for ImageJ to support downloading from OMERO
183* Fixed bug with floating point TIFFs
184* Fixed bugs in Visitech, Zeiss LSM, Imaris 5.5 (HDF)
185* Added alternate ND2 reader that uses Nikon's native libraries
186* Fixed calibration and series name settings in importer
187* Added basic support for InCell 1000 datasets
1892007 Nov 21:
190* Fixed bugs in ND2, Leica LIF, DICOM, Zeiss ZVI, Zeiss LSM, FV1000 OIB,
191  FV1000 OIF, BMP, Evotec Flex, BioRad PIC, Slidebook, TIFF
192* Added new ImageJ plugins to slice stacks and do "smart" RGB merging
193* Added "windowless" importer plugin
194    + uses import parameters from IJ_Prefs.txt, without prompting the user
195* Improved stack slicing and colorizing logic in importer plugin
196* Added support for DICOM files compressed with lossless JPEG
197    + requires native libraries
198* Fixed bugs with signed pixel data
199* Added support for Imaris 5.5 (HDF) files
200* Added 4 channel merging to importer plugin
201* Added API methods for reading subimages
202* Major updates to the 4D Data Browser
2042007 Oct 17:
205* Critical OME-TIFF bugfixes
206* Fixed bugs in Leica LIF, Zeiss ZVI, TIFF, DICOM, and AVI readers
207* Added support for JPEG-compressed ZVI images
208* Added support for BigTIFF
209* Added importer plugin option to open each plane in a new window
210* Added MS Video 1 codec for AVI
2122007 Oct 1:
213* Added support for compressed DICOM images
214* Added support for uncompressed LIM files
215* Added support for Adobe Photoshop PSD files
216* Fixed bugs in DICOM, OME-TIFF, Leica LIF, Zeiss ZVI,
217  Visitech, PerkinElmer and Metamorph
218* Improved indexed color support
219* Addressed several efficiency issues
220* Fixed how multiple series are handled in 4D data browser
221* Added option to reorder stacks in importer plugin
222* Added option to turn off autoscaling in importer plugin
223* Additional metadata convenience methods
2252007 Sept 11:
226* Major improvements to ND2 support; lossless compression now supported
227* Support for indexed color images
228* Added support for Simple-PCI .cxd files
229* Command-line OME-XML validation
230* Bugfixes in most readers, especially Zeiss ZVI, Metamorph, PerkinElmer and
231  Leica LEI
232* Initial version of Bio-Formats macro extensions for ImageJ
2342007 Aug 1:
235* Added support for latest version of Leica LIF
236* Fixed several issues with Leica LIF, Zeiss ZVI
237* Better metadata mapping for Zeiss ZVI
238* Added OME-TIFF writer
239* Added MetadataRetrieve API for retrieving data from a MetadataStore
240* Miscellaneous bugfixes
2422007 July 16:
243* Fixed several issues with ImageJ plugins
244* Better support for Improvision and Leica TCS TIFF files
245* Minor improvements to Leica LIF, ICS, QuickTime and Zeiss ZVI readers
246* Added searchable metadata window to ImageJ importer
2482007 July 2:
249* Fixed issues with ND2, Openlab LIFF and Slidebook
250* Added support for Visitech XYS
251* Added composite stack support to ImageJ importer
2532007 June 18:
254* Fixed issues with ICS, ND2, MicroManager, Leica LEI, and FV1000 OIF
255* Added support for large (> 2 GB) ND2 files
256* Added support for new version of ND2
257* Minor enhancements to ImageJ importer
258* Implemented more flexible logging
259* Updated automated testing framework to use TestNG
260* Added package for caching images produced by Bio-Formats
2622007 June 6:
263* Fixed OME upload/download bugs
264* Fixed issues with ND2, EPS, Leica LIF, and OIF
265* Added support for Khoros XV
266* Minor improvements to the importer
2682007 May 24:
269* Better Slidebook support
270* Added support for Quicktime RPZA
271* Better Leica LIF metadata parsing
272* Added support for BioRad PIC companion files
273* Added support for bzip2-compressed files
274* Improved ImageJ plugins
275* Native support for FITS and PGM
2772007 May 2:
278* Added support for NRRD
279* Added support for Evotec Flex (requires LuraWave Java SDK with license code)
280* Added support for gzip-compressed files
281* Added support for compressed QuickTime headers
282* Fixed QuickTime Motion JPEG-B support
283* Fixed some memory issues (repeated small array allocations)
284* Fixed issues reading large (> 2 GB) files
285* Removed "ignore color table" logic, and replaced with Leica-specific solution
286* Added status event reporting to readers
287* Added API to toggle metadata collection
288* Support for multiple dimensions rasterized into channels
289* Deprecated reader and writer methods that accept the 'id' parameter
290* Deprecated in favor of saveImage and saveBytes
291* Moved dimension swapping and min/max calculation logic to delegates
292* Separate GUI logic into isolated loci.formats.gui package
293* Miscellaneous bugfixes and tweaks in most readers and writers
294* Many other bugfixes and improvements
2962007 Mar 16:
297* Fixed calibration bugs in importer plugin
298* Enhanced metadata support for additional formats
299* Fixed LSM bug
3012007 Mar 7:
302* Added support for Micro-Manager file format
303* Fixed several bugs -- Leica LIF, Leica LEI, ICS, ND2, and others
304* Enhanced metadata support for several formats
305* Load series preview thumbnails in the background
306* Better implementation of openBytes(String, int, byte[]) for most readers
307* Expanded unit testing framework
3092007 Feb 28:
310* Better series preview thumbnails
311* Fixed bugs with multi-channel Leica LEI
312* Fixed bugs with "ignore color tables" option in ImageJ plugin
3142007 Feb 26:
315* Many bugfixes: Leica LEI, ICS, FV1000 OIB, OME-XML and others
316* Better metadata parsing for BioRad PIC files
317* Enhanced API for calculating channel minimum and maximum values
318* Expanded MetadataStore API to include more semantic types
319* Added thumbnails to series chooser in ImageJ plugin
320* Fixed plugins that upload and download from an OME server
3222007 Feb 7:
323* Added plugin for downloading images from OME server
324* Improved HTTP import functionality
325* Added metadata filtering -- unreadable metadata is no longer shown
326* Better metadata table for multi-series datasets
327* Added support for calibration information in Gatan DM3
328* Eliminated need to install JAI Image I/O Tools to read ND2 files
329* Fixed ZVI bugs: metadata truncation, and other problems
330* Fixed bugs in Leica LIF: incorrect calibration, first series labeling
331* Fixed memory bug in Zeiss LSM
332* Many bugfixes: PerkinElmer, Deltavision, Leica LEI, LSM, ND2, and others
333* IFormatReader.close(boolean) method to close files temporarily
334* Replaced Compression utility class with extensible Compressor interface
335* Improved testing framework to use .bioformats configuration files
3372007 Jan 5:
338* Added support for Prairie TIFF
339* Fixed bugs in Zeiss LSM, OIB, OIF, and ND2
340* Improved API for writing files
341* Added feature to read files over HTTP
342* Fixed bugs in automated testing framework
343* Miscellaneous bugfixes
3452006 Dec 22:
346* Expanded ImageJ plugin to optionally use Image5D or View5D
347* Improved support for ND2 and JPEG-2000 files
348* Added automated testing framework
349* Fixed bugs in Zeiss ZVI reader
350* Miscellaneous bugfixes
3522006 Nov 30:
353* Added support for ND2/JPEG-2000
354* Added support for MRC
355* Added support for MNG
356* Improved support for floating-point images
357* Fixed problem with 2-channel Leica LIF data
358* Minor tweaks and bugfixes in many readers
359* Improved file stitching logic
360* Allow ImageJ plugin to be called from a macro
3622006 Nov 2:
363* Bugfixes and improvements for Leica LIF, Zeiss LSM, OIF and OIB
364* Colorize channels when they are split into separate windows
365* Fixed a bug with 4-channel datasets
3672006 Oct 31:
368* Added support for Imaris 5 files
369* Added support for RGB ICS images
3712006 Oct 30:
372* Added support for tiled TIFFs
373* Fixed bugs in ICS reader
374* Fixed importer plugin deadlock on some systems
3762006 Oct 27:
377* Multi-series support for Slidebook
378* Added support for Alicona AL3D
379* Fixed plane ordering issue with FV1000 OIB
380* Enhanced dimension detection in FV1000 OIF
381* Added preliminary support for reading NEF images
382* Added option to ignore color tables
383* Fixed ImageJ GUI problems
384* Fixed spatial calibration problem in ImageJ
385* Fixed some lingering bugs in Zeiss ZVI support
386* Fixed bugs in OME-XML reader
387* Tweaked ICS floating-point logic
388* Fixed memory leaks in all readers
389* Better file stitching logic
3912006 Oct 6:
392* Support for 3i SlideBook format (single series only for now)
393* Support for 16-bit RGB palette TIFF
394* Fixed bug preventing import of certain Metamorph STK files
395* Fixed some bugs in PerkinElmer UltraView support
396* Fixed some bugs in Leica LEI support
397* Fixed a bug in Zeiss ZVI support
398* Fixed bugs in Zeiss LSM support
399* Fixed a bug causing slow identification of Leica datasets
400* Fixed bugs in the channel merging logic
401* Fixed memory leak for OIB format
402* Better scaling of 48-bit RGB data to 24-bit RGB
403* Fixed duplicate channels bug in "open each channel in a separate window"
404* Fixed a bug preventing PICT import into ImageJ
405* Better integration with HandleExtraFileTypes
406* Better virtual stack support in Data Browser plugin
407* Fixed bug in native QuickTime random access
408* Keep aspect ratio for computed thumbnails
409* Much faster file stitching logic
4112006 Sep 27:
412* PerkinElmer: support for PE UltraView
413* Openlab LIFF: support for Openlab v5
414* Leica LEI: bugfixes, and support for multiple series
415* ZVI, OIB, IPW: more robust handling of these formats (eliminated
416  custom OLE parsing logic in favor of Apache POI)
417* OIB: better metadata parsing (but maybe still not perfect?)
418* LSM: fixed a bug preventing import of certain LSMs
419* Metamorph STK: fixed a bug resulting in duplicate image planes
420* User interface: use of system look & feel for file chooser dialog
421  when available
422* Better notification when JAR libraries are missing
4242006 Sep 6:
425* Leica LIF: multiple distinct image series within a single file
426* Zeiss ZVI: fixes and improvements contributed by Michel Boudinot
427* Zeiss LSM: fixed bugs preventing the import of certain LSM files
428* TIFF: fixed a bug preventing import of TIFFs created with Bio-Rad software
4302006 Mar 31:
431* First release
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