source: branches/4.1/components/bio-formats/doc/whats-new.txt @ 5727

Revision 5727, 16.0 KB checked in by melissa, 10 years ago (diff)

Updated documentation and what's new for today's release.

14.1.1 (2009 December 3):
2* Fixed many bugs in popular file format readers
44.1 (2009 October 21):
6* Fixed many bugs in most file format readers
7* Significantly improved confocal and HCS metadata parsing
8* Improved C++ bindings
9* Eliminated references to Java AWT classes in core Bio-Formats packages
10* Added support for reading Flex datasets from multiple servers
11* Improved OME-XML generation; generated OME-XML is now valid
12* Added support for Olympus ScanR data
13* Added OSGi information to JARs
14* Added support for Amira Mesh files
15* Added support for LI-FLIM files
16* Added more informative exceptions
17* Added support for various types of ICS lifetime data
18* Added support for Nikon EZ-C1 TIFFs
19* Added support for Maia Scientific MIAS data
214.0.1 (2009 June 1):
23* Lots of bug fixes in most format readers and writers
24* Added support for Analyze 7.1 files
25* Added support for Nifti files
26* Added support for Cellomics .c01 files
27* Refactored ImageJ plugins
28* Bio-Formats, the common package, and the ImageJ plugins now require Java 1.5
29* Eliminated native library dependency for reading lossless JPEGs
30* Changed license from GPL v3 or later to GPL v2 or later
31* Updated Olympus FV1000, Zeiss LSM, Zeiss ZVI and Nikon ND2 readers to parse
32  ROI data
33* Added option to ImageJ plugin for displaying ROIs parsed from the chosen
34  dataset
35* Fixed BufferedImage construction for signed data and unsigned int data
374.0.0 (2009 March 3):
39* Improved OME data model population for Olympus FV1000, Nikon ND2, Metamorph
40  STK, Leica LEI, Leica LIF, InCell 1000 and MicroManager
41* Added TestNG tests for format writers
42* Added option to ImageJ plugin to specify custom colors when customizing
43  channels
44* Added ability to upgrade the ImageJ plugin from within ImageJ
45* Fixed bugs in Nikon ND2, Leica LIF, BioRad PIC, TIFF, PSD, and OME-TIFF
46* Fixed bugs in Data Browser and Exporter plugins
47* Added support for Axon Raw Format (ARF), courtesy of Johannes Schindelin
48* Added preliminary support for IPLab-Mac file format
502008 December 29:
51* Improved metadata support for Deltavision, Zeiss LSM, MicroManager, and Leica
52  LEI
53* Restructured code base/build system to be component-driven
54* Added support for JPEG and JPEG-2000 codecs within TIFF, OME-TIFF and OME-XML
55* Added support for 16-bit compressed Flex files
56* Added support for writing JPEG-2000 files
57* Added support for Minolta MRW format
58* Added support for the 2008-09 release of OME-XML
59* Removed dependency on JMagick
60* Re-added caching support to data browser plugin
61* Updated loci.formats.Codec API to be more user-friendly
62* Expanded loci.formats.MetadataStore API to better represent the OME-XML model
63* Improved support for Nikon NEF
64* Improved support for TillVision files
65* Improved ImageJ import options dialog
66* Fixed bugs with Zeiss LSM files larger than 4 GB
67* Fixed minor bugs in most readers
68* Fixed bugs with exporting from an Image5D window
69* Fixed several problems with virtual stacks in ImageJ
712008 August 30:
72* Fixed bugs in many file format readers
73* Fixed several bugs with swapping dimensions
74* Added support for Olympus CellR/APL files
75* Added support for MINC MRI files
76* Added support for Aperio SVS files compressed with JPEG 2000
77* Added support for writing OME-XML files
78* Added support for writing APNG files
79* Added faster LZW codec
80* Added drag and drop support to ImageJ shortcut window
81* Re-integrated caching into the data browser plugin
832008 July 1:
84* Fixed bugs in most file format readers
85* Fixed bugs in OME and OMERO download functionality
86* Fixed bugs in OME server-side import
87* Improved metadata storage/retrieval when uploading to and downloading from
88  the OME Perl server
89* Improved Bio-Formats ImageJ macro extensions
90* Major updates to MetadataStore API
91* Updated OME-XML generation to use 2008-02 schema by default
92* Addressed time and memory performance issues in many readers
93* Changed license from LGPL to GPL
94* Added support for the FEI file format
95* Added support for uncompressed Hamamatsu Aquacosmos NAF files
96* Added support for Animated PNG files
97* Added several new options to Bio-Formats ImageJ plugin
98* Added support for writing ICS files
1002008 April 17:
101* Fixed bugs in Slidebook, ND2, FV1000 OIB/OIF, Perkin Elmer, TIFF, Prairie,
102  Openlab, Zeiss LSM, MNG, Molecular Dynamics GEL, and OME-TIFF
103* Fixed bugs in OME and OMERO download functionality
104* Fixed bugs in OME server-side import
105* Fixed bugs in Data Browser
106* Added support for downloading from OMERO 2.3 servers
107* Added configuration plugin
108* Updates to MetadataStore API
109* Updates to OME-XML generation - 2007-06 schema used by default
110* Added support for Li-Cor L2D format
111* Major updates to TestNG testing framework
112* Added support for writing multi-series OME-TIFF files
113* Added support for writing BigTIFF files
1152008 Feb 12:
116* Fixed bugs in QuickTime, SimplePCI and DICOM
117* Fixed a bug in channel splitting logic
1192008 Feb 8:
120* Many critical bugfixes in format readers and ImageJ plugins
121* Newly reborn Data Browser for 5D image visualization
122    + some combinations of import options do not work yet
1242008 Feb 1:
125* Fixed bugs in Zeiss LSM, Metamorph STK, FV1000 OIB/OIF, Leica LEI, TIFF,
126  Zeiss ZVI, ICS, Prairie, Openlab LIFF, Gatan, DICOM, QuickTime
127* Fixed bug in OME-TIFF writer
128* Major changes to MetadataStore API
129* Added support for JPEG-compressed TIFF files
130* Added basic support for Aperio SVS files
131    + JPEG2000 compression is still not supported
132* Improved "crop on import" functionality
133* Improvements to bfconvert and bfview
134* Improved OME-XML population for several formats
135* Added support for JPEG2000-compressed DICOM files
136* EXIF data is now parsed from TIFF files
1382007 Dec 28:
139* Fixed bugs in Leica LEI, Leica TCS, SDT, Leica LIF,
140  Visitech, DICOM, Imaris 5.5 (HDF), and Slidebook readers
141* Better parsing of comments in TIFF files exported from ImageJ
142* Fixed problem with exporting 48-bit RGB data
143* Added logic to read multi-series datasets spread across multiple files
144* Improved channel merging in ImageJ - requires ImageJ 1.39l
145* Support for hyperstacks and virtual stacks in ImageJ - requires ImageJ 1.39l
146* Added API for reading directly from a byte array or InputStream
147* Metadata key/value pairs are now stored in ImageJ's "Info" property
148* Improved OMERO download plugin - it is now much faster
149* Added "open all series" option to ImageJ importer
150* ND2 reader based on Nikon's SDK now uses our own native bindings
151* Fixed metadata saving bug in ImageJ
152* Added sub-channel labels to ImageJ windows
153* Major updates to 4D Data Browser
154* Minor updates to automated testing suite
1562007 Dec 1:
157* Updated OME plugin for ImageJ to support downloading from OMERO
158* Fixed bug with floating point TIFFs
159* Fixed bugs in Visitech, Zeiss LSM, Imaris 5.5 (HDF)
160* Added alternate ND2 reader that uses Nikon's native libraries
161* Fixed calibration and series name settings in importer
162* Added basic support for InCell 1000 datasets
1642007 Nov 21:
165* Fixed bugs in ND2, Leica LIF, DICOM, Zeiss ZVI, Zeiss LSM, FV1000 OIB,
166  FV1000 OIF, BMP, Evotec Flex, BioRad PIC, Slidebook, TIFF
167* Added new ImageJ plugins to slice stacks and do "smart" RGB merging
168* Added "windowless" importer plugin
169    + uses import parameters from IJ_Prefs.txt, without prompting the user
170* Improved stack slicing and colorizing logic in importer plugin
171* Added support for DICOM files compressed with lossless JPEG
172    + requires native libraries
173* Fixed bugs with signed pixel data
174* Added support for Imaris 5.5 (HDF) files
175* Added 4 channel merging to importer plugin
176* Added API methods for reading subimages
177* Major updates to the 4D Data Browser
1792007 Oct 17:
180* Critical OME-TIFF bugfixes
181* Fixed bugs in Leica LIF, Zeiss ZVI, TIFF, DICOM, and AVI readers
182* Added support for JPEG-compressed ZVI images
183* Added support for BigTIFF
184* Added importer plugin option to open each plane in a new window
185* Added MS Video 1 codec for AVI
1872007 Oct 1:
188* Added support for compressed DICOM images
189* Added support for uncompressed LIM files
190* Added support for Adobe Photoshop PSD files
191* Fixed bugs in DICOM, OME-TIFF, Leica LIF, Zeiss ZVI,
192  Visitech, PerkinElmer and Metamorph
193* Improved indexed color support
194* Addressed several efficiency issues
195* Fixed how multiple series are handled in 4D data browser
196* Added option to reorder stacks in importer plugin
197* Added option to turn off autoscaling in importer plugin
198* Additional metadata convenience methods
2002007 Sept 11:
201* Major improvements to ND2 support; lossless compression now supported
202* Support for indexed color images
203* Added support for Simple-PCI .cxd files
204* Command-line OME-XML validation
205* Bugfixes in most readers, especially Zeiss ZVI, Metamorph, PerkinElmer and
206  Leica LEI
207* Initial version of Bio-Formats macro extensions for ImageJ
2092007 Aug 1:
210* Added support for latest version of Leica LIF
211* Fixed several issues with Leica LIF, Zeiss ZVI
212* Better metadata mapping for Zeiss ZVI
213* Added OME-TIFF writer
214* Added MetadataRetrieve API for retrieving data from a MetadataStore
215* Miscellaneous bugfixes
2172007 July 16:
218* Fixed several issues with ImageJ plugins
219* Better support for Improvision and Leica TCS TIFF files
220* Minor improvements to Leica LIF, ICS, QuickTime and Zeiss ZVI readers
221* Added searchable metadata window to ImageJ importer
2232007 July 2:
224* Fixed issues with ND2, Openlab LIFF and Slidebook
225* Added support for Visitech XYS
226* Added composite stack support to ImageJ importer
2282007 June 18:
229* Fixed issues with ICS, ND2, MicroManager, Leica LEI, and FV1000 OIF
230* Added support for large (> 2 GB) ND2 files
231* Added support for new version of ND2
232* Minor enhancements to ImageJ importer
233* Implemented more flexible logging
234* Updated automated testing framework to use TestNG
235* Added package for caching images produced by Bio-Formats
2372007 June 6:
238* Fixed OME upload/download bugs
239* Fixed issues with ND2, EPS, Leica LIF, and OIF
240* Added support for Khoros XV
241* Minor improvements to the importer
2432007 May 24:
244* Better Slidebook support
245* Added support for Quicktime RPZA
246* Better Leica LIF metadata parsing
247* Added support for BioRad PIC companion files
248* Added support for bzip2-compressed files
249* Improved ImageJ plugins
250* Native support for FITS and PGM
2522007 May 2:
253* Added support for NRRD
254* Added support for Evotec Flex (requires LuraWave Java SDK with license code)
255* Added support for gzip-compressed files
256* Added support for compressed QuickTime headers
257* Fixed QuickTime Motion JPEG-B support
258* Fixed some memory issues (repeated small array allocations)
259* Fixed issues reading large (> 2 GB) files
260* Removed "ignore color table" logic, and replaced with Leica-specific solution
261* Added status event reporting to readers
262* Added API to toggle metadata collection
263* Support for multiple dimensions rasterized into channels
264* Deprecated reader and writer methods that accept the 'id' parameter
265* Deprecated in favor of saveImage and saveBytes
266* Moved dimension swapping and min/max calculation logic to delegates
267* Separate GUI logic into isolated loci.formats.gui package
268* Miscellaneous bugfixes and tweaks in most readers and writers
269* Many other bugfixes and improvements
2712007 Mar 16:
272* Fixed calibration bugs in importer plugin
273* Enhanced metadata support for additional formats
274* Fixed LSM bug
2762007 Mar 7:
277* Added support for Micro-Manager file format
278* Fixed several bugs -- Leica LIF, Leica LEI, ICS, ND2, and others
279* Enhanced metadata support for several formats
280* Load series preview thumbnails in the background
281* Better implementation of openBytes(String, int, byte[]) for most readers
282* Expanded unit testing framework
2842007 Feb 28:
285* Better series preview thumbnails
286* Fixed bugs with multi-channel Leica LEI
287* Fixed bugs with "ignore color tables" option in ImageJ plugin
2892007 Feb 26:
290* Many bugfixes: Leica LEI, ICS, FV1000 OIB, OME-XML and others
291* Better metadata parsing for BioRad PIC files
292* Enhanced API for calculating channel minimum and maximum values
293* Expanded MetadataStore API to include more semantic types
294* Added thumbnails to series chooser in ImageJ plugin
295* Fixed plugins that upload and download from an OME server
2972007 Feb 7:
298* Added plugin for downloading images from OME server
299* Improved HTTP import functionality
300* Added metadata filtering -- unreadable metadata is no longer shown
301* Better metadata table for multi-series datasets
302* Added support for calibration information in Gatan DM3
303* Eliminated need to install JAI Image I/O Tools to read ND2 files
304* Fixed ZVI bugs: metadata truncation, and other problems
305* Fixed bugs in Leica LIF: incorrect calibration, first series labeling
306* Fixed memory bug in Zeiss LSM
307* Many bugfixes: PerkinElmer, Deltavision, Leica LEI, LSM, ND2, and others
308* IFormatReader.close(boolean) method to close files temporarily
309* Replaced Compression utility class with extensible Compressor interface
310* Improved testing framework to use .bioformats configuration files
3122007 Jan 5:
313* Added support for Prairie TIFF
314* Fixed bugs in Zeiss LSM, OIB, OIF, and ND2
315* Improved API for writing files
316* Added feature to read files over HTTP
317* Fixed bugs in automated testing framework
318* Miscellaneous bugfixes
3202006 Dec 22:
321* Expanded ImageJ plugin to optionally use Image5D or View5D
322* Improved support for ND2 and JPEG-2000 files
323* Added automated testing framework
324* Fixed bugs in Zeiss ZVI reader
325* Miscellaneous bugfixes
3272006 Nov 30:
328* Added support for ND2/JPEG-2000
329* Added support for MRC
330* Added support for MNG
331* Improved support for floating-point images
332* Fixed problem with 2-channel Leica LIF data
333* Minor tweaks and bugfixes in many readers
334* Improved file stitching logic
335* Allow ImageJ plugin to be called from a macro
3372006 Nov 2:
338* Bugfixes and improvements for Leica LIF, Zeiss LSM, OIF and OIB
339* Colorize channels when they are split into separate windows
340* Fixed a bug with 4-channel datasets
3422006 Oct 31:
343* Added support for Imaris 5 files
344* Added support for RGB ICS images
3462006 Oct 30:
347* Added support for tiled TIFFs
348* Fixed bugs in ICS reader
349* Fixed importer plugin deadlock on some systems
3512006 Oct 27:
352* Multi-series support for Slidebook
353* Added support for Alicona AL3D
354* Fixed plane ordering issue with FV1000 OIB
355* Enhanced dimension detection in FV1000 OIF
356* Added preliminary support for reading NEF images
357* Added option to ignore color tables
358* Fixed ImageJ GUI problems
359* Fixed spatial calibration problem in ImageJ
360* Fixed some lingering bugs in Zeiss ZVI support
361* Fixed bugs in OME-XML reader
362* Tweaked ICS floating-point logic
363* Fixed memory leaks in all readers
364* Better file stitching logic
3662006 Oct 6:
367* Support for 3i SlideBook format (single series only for now)
368* Support for 16-bit RGB palette TIFF
369* Fixed bug preventing import of certain Metamorph STK files
370* Fixed some bugs in PerkinElmer UltraView support
371* Fixed some bugs in Leica LEI support
372* Fixed a bug in Zeiss ZVI support
373* Fixed bugs in Zeiss LSM support
374* Fixed a bug causing slow identification of Leica datasets
375* Fixed bugs in the channel merging logic
376* Fixed memory leak for OIB format
377* Better scaling of 48-bit RGB data to 24-bit RGB
378* Fixed duplicate channels bug in "open each channel in a separate window"
379* Fixed a bug preventing PICT import into ImageJ
380* Better integration with HandleExtraFileTypes
381* Better virtual stack support in Data Browser plugin
382* Fixed bug in native QuickTime random access
383* Keep aspect ratio for computed thumbnails
384* Much faster file stitching logic
3862006 Sep 27:
387* PerkinElmer: support for PE UltraView
388* Openlab LIFF: support for Openlab v5
389* Leica LEI: bugfixes, and support for multiple series
390* ZVI, OIB, IPW: more robust handling of these formats (eliminated
391  custom OLE parsing logic in favor of Apache POI)
392* OIB: better metadata parsing (but maybe still not perfect?)
393* LSM: fixed a bug preventing import of certain LSMs
394* Metamorph STK: fixed a bug resulting in duplicate image planes
395* User interface: use of system look & feel for file chooser dialog
396  when available
397* Better notification when JAR libraries are missing
3992006 Sep 6:
400* Leica LIF: multiple distinct image series within a single file
401* Zeiss ZVI: fixes and improvements contributed by Michel Boudinot
402* Zeiss LSM: fixed bugs preventing the import of certain LSM files
403* TIFF: fixed a bug preventing import of TIFFs created with Bio-Rad software
4052006 Mar 31:
406* First release
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