source: branches/4.2/components/bio-formats/doc/whats-new.txt @ 7334

Revision 7334, 17.5 KB checked in by melissa, 9 years ago (diff)

Updated what's new for today's release.

14.2.2 (2010 December 6):
2* Several bug fixes, notably:
3  - Metadata parsing fixes for Zeiss LSM, Metamorph STK, and FV1000
4  - Prevented leaked file handles when exporting to TIFF/OME-TIFF
5  - Fixed how BufferedImages are converted to byte arrays
6* Proper support for OME-XML XML annotations
7* Added support for SCANCO Medical .aim files
8* Minor improvements to ImageJ plugins
9* Added support for reading JPEG-compressed AVI files
114.2.1 (2010 November 12):
12* Many, many bug fixes
13* Added support for 7 new formats:
14  - CellWorX .pnl
15  - ECAT7
16  - Varian FDF
17  - Perkin Elmer Densitometer
18  - FEI TIFF
19  - Compix/SimplePCI TIFF
20  - Nikon Elements TIFF
21* Updated Zeiss LSM metadata parsing, with generous assistance from Zeiss, FMI, and MPI-CBG
22* Lots of work to ensure that converted OME-XML validates
23* Improved file stitching functionality; non-numerical file patterns and limited regular expression-style patterns are now supported
254.2.0 (2010 July 9):
26* Fixed many, many bugs in all aspects of Bio-Formats
27* Reworked ImageJ plugins to be more user- and developer-friendly
28* Added many new unit tests
29* Added support for approximately 25 new file formats, primarily in the SPM domain
30* Rewrote underlying I/O infrastructure to be thread-safe and based on Java NIO
31* Rewrote OME-XML parsing/generation layer; OME-XML 2010-06 is now supported
32* Improved support for exporting large images
33* Improved support for exporting to multiple files
34* Updated logging infrastructure to use slf4j and log4j
364.1.1 (2009 December 3):
37* Fixed many bugs in popular file format readers
394.1 (2009 October 21):
41* Fixed many bugs in most file format readers
42* Significantly improved confocal and HCS metadata parsing
43* Improved C++ bindings
44* Eliminated references to Java AWT classes in core Bio-Formats packages
45* Added support for reading Flex datasets from multiple servers
46* Improved OME-XML generation; generated OME-XML is now valid
47* Added support for Olympus ScanR data
48* Added OSGi information to JARs
49* Added support for Amira Mesh files
50* Added support for LI-FLIM files
51* Added more informative exceptions
52* Added support for various types of ICS lifetime data
53* Added support for Nikon EZ-C1 TIFFs
54* Added support for Maia Scientific MIAS data
564.0.1 (2009 June 1):
58* Lots of bug fixes in most format readers and writers
59* Added support for Analyze 7.1 files
60* Added support for Nifti files
61* Added support for Cellomics .c01 files
62* Refactored ImageJ plugins
63* Bio-Formats, the common package, and the ImageJ plugins now require Java 1.5
64* Eliminated native library dependency for reading lossless JPEGs
65* Changed license from GPL v3 or later to GPL v2 or later
66* Updated Olympus FV1000, Zeiss LSM, Zeiss ZVI and Nikon ND2 readers to parse
67  ROI data
68* Added option to ImageJ plugin for displaying ROIs parsed from the chosen
69  dataset
70* Fixed BufferedImage construction for signed data and unsigned int data
724.0.0 (2009 March 3):
74* Improved OME data model population for Olympus FV1000, Nikon ND2, Metamorph
75  STK, Leica LEI, Leica LIF, InCell 1000 and MicroManager
76* Added TestNG tests for format writers
77* Added option to ImageJ plugin to specify custom colors when customizing
78  channels
79* Added ability to upgrade the ImageJ plugin from within ImageJ
80* Fixed bugs in Nikon ND2, Leica LIF, BioRad PIC, TIFF, PSD, and OME-TIFF
81* Fixed bugs in Data Browser and Exporter plugins
82* Added support for Axon Raw Format (ARF), courtesy of Johannes Schindelin
83* Added preliminary support for IPLab-Mac file format
852008 December 29:
86* Improved metadata support for Deltavision, Zeiss LSM, MicroManager, and Leica
87  LEI
88* Restructured code base/build system to be component-driven
89* Added support for JPEG and JPEG-2000 codecs within TIFF, OME-TIFF and OME-XML
90* Added support for 16-bit compressed Flex files
91* Added support for writing JPEG-2000 files
92* Added support for Minolta MRW format
93* Added support for the 2008-09 release of OME-XML
94* Removed dependency on JMagick
95* Re-added caching support to data browser plugin
96* Updated loci.formats.Codec API to be more user-friendly
97* Expanded loci.formats.MetadataStore API to better represent the OME-XML model
98* Improved support for Nikon NEF
99* Improved support for TillVision files
100* Improved ImageJ import options dialog
101* Fixed bugs with Zeiss LSM files larger than 4 GB
102* Fixed minor bugs in most readers
103* Fixed bugs with exporting from an Image5D window
104* Fixed several problems with virtual stacks in ImageJ
1062008 August 30:
107* Fixed bugs in many file format readers
108* Fixed several bugs with swapping dimensions
109* Added support for Olympus CellR/APL files
110* Added support for MINC MRI files
111* Added support for Aperio SVS files compressed with JPEG 2000
112* Added support for writing OME-XML files
113* Added support for writing APNG files
114* Added faster LZW codec
115* Added drag and drop support to ImageJ shortcut window
116* Re-integrated caching into the data browser plugin
1182008 July 1:
119* Fixed bugs in most file format readers
120* Fixed bugs in OME and OMERO download functionality
121* Fixed bugs in OME server-side import
122* Improved metadata storage/retrieval when uploading to and downloading from
123  the OME Perl server
124* Improved Bio-Formats ImageJ macro extensions
125* Major updates to MetadataStore API
126* Updated OME-XML generation to use 2008-02 schema by default
127* Addressed time and memory performance issues in many readers
128* Changed license from LGPL to GPL
129* Added support for the FEI file format
130* Added support for uncompressed Hamamatsu Aquacosmos NAF files
131* Added support for Animated PNG files
132* Added several new options to Bio-Formats ImageJ plugin
133* Added support for writing ICS files
1352008 April 17:
136* Fixed bugs in Slidebook, ND2, FV1000 OIB/OIF, Perkin Elmer, TIFF, Prairie,
137  Openlab, Zeiss LSM, MNG, Molecular Dynamics GEL, and OME-TIFF
138* Fixed bugs in OME and OMERO download functionality
139* Fixed bugs in OME server-side import
140* Fixed bugs in Data Browser
141* Added support for downloading from OMERO 2.3 servers
142* Added configuration plugin
143* Updates to MetadataStore API
144* Updates to OME-XML generation - 2007-06 schema used by default
145* Added support for Li-Cor L2D format
146* Major updates to TestNG testing framework
147* Added support for writing multi-series OME-TIFF files
148* Added support for writing BigTIFF files
1502008 Feb 12:
151* Fixed bugs in QuickTime, SimplePCI and DICOM
152* Fixed a bug in channel splitting logic
1542008 Feb 8:
155* Many critical bugfixes in format readers and ImageJ plugins
156* Newly reborn Data Browser for 5D image visualization
157    + some combinations of import options do not work yet
1592008 Feb 1:
160* Fixed bugs in Zeiss LSM, Metamorph STK, FV1000 OIB/OIF, Leica LEI, TIFF,
161  Zeiss ZVI, ICS, Prairie, Openlab LIFF, Gatan, DICOM, QuickTime
162* Fixed bug in OME-TIFF writer
163* Major changes to MetadataStore API
164* Added support for JPEG-compressed TIFF files
165* Added basic support for Aperio SVS files
166    + JPEG2000 compression is still not supported
167* Improved "crop on import" functionality
168* Improvements to bfconvert and bfview
169* Improved OME-XML population for several formats
170* Added support for JPEG2000-compressed DICOM files
171* EXIF data is now parsed from TIFF files
1732007 Dec 28:
174* Fixed bugs in Leica LEI, Leica TCS, SDT, Leica LIF,
175  Visitech, DICOM, Imaris 5.5 (HDF), and Slidebook readers
176* Better parsing of comments in TIFF files exported from ImageJ
177* Fixed problem with exporting 48-bit RGB data
178* Added logic to read multi-series datasets spread across multiple files
179* Improved channel merging in ImageJ - requires ImageJ 1.39l
180* Support for hyperstacks and virtual stacks in ImageJ - requires ImageJ 1.39l
181* Added API for reading directly from a byte array or InputStream
182* Metadata key/value pairs are now stored in ImageJ's "Info" property
183* Improved OMERO download plugin - it is now much faster
184* Added "open all series" option to ImageJ importer
185* ND2 reader based on Nikon's SDK now uses our own native bindings
186* Fixed metadata saving bug in ImageJ
187* Added sub-channel labels to ImageJ windows
188* Major updates to 4D Data Browser
189* Minor updates to automated testing suite
1912007 Dec 1:
192* Updated OME plugin for ImageJ to support downloading from OMERO
193* Fixed bug with floating point TIFFs
194* Fixed bugs in Visitech, Zeiss LSM, Imaris 5.5 (HDF)
195* Added alternate ND2 reader that uses Nikon's native libraries
196* Fixed calibration and series name settings in importer
197* Added basic support for InCell 1000 datasets
1992007 Nov 21:
200* Fixed bugs in ND2, Leica LIF, DICOM, Zeiss ZVI, Zeiss LSM, FV1000 OIB,
201  FV1000 OIF, BMP, Evotec Flex, BioRad PIC, Slidebook, TIFF
202* Added new ImageJ plugins to slice stacks and do "smart" RGB merging
203* Added "windowless" importer plugin
204    + uses import parameters from IJ_Prefs.txt, without prompting the user
205* Improved stack slicing and colorizing logic in importer plugin
206* Added support for DICOM files compressed with lossless JPEG
207    + requires native libraries
208* Fixed bugs with signed pixel data
209* Added support for Imaris 5.5 (HDF) files
210* Added 4 channel merging to importer plugin
211* Added API methods for reading subimages
212* Major updates to the 4D Data Browser
2142007 Oct 17:
215* Critical OME-TIFF bugfixes
216* Fixed bugs in Leica LIF, Zeiss ZVI, TIFF, DICOM, and AVI readers
217* Added support for JPEG-compressed ZVI images
218* Added support for BigTIFF
219* Added importer plugin option to open each plane in a new window
220* Added MS Video 1 codec for AVI
2222007 Oct 1:
223* Added support for compressed DICOM images
224* Added support for uncompressed LIM files
225* Added support for Adobe Photoshop PSD files
226* Fixed bugs in DICOM, OME-TIFF, Leica LIF, Zeiss ZVI,
227  Visitech, PerkinElmer and Metamorph
228* Improved indexed color support
229* Addressed several efficiency issues
230* Fixed how multiple series are handled in 4D data browser
231* Added option to reorder stacks in importer plugin
232* Added option to turn off autoscaling in importer plugin
233* Additional metadata convenience methods
2352007 Sept 11:
236* Major improvements to ND2 support; lossless compression now supported
237* Support for indexed color images
238* Added support for Simple-PCI .cxd files
239* Command-line OME-XML validation
240* Bugfixes in most readers, especially Zeiss ZVI, Metamorph, PerkinElmer and
241  Leica LEI
242* Initial version of Bio-Formats macro extensions for ImageJ
2442007 Aug 1:
245* Added support for latest version of Leica LIF
246* Fixed several issues with Leica LIF, Zeiss ZVI
247* Better metadata mapping for Zeiss ZVI
248* Added OME-TIFF writer
249* Added MetadataRetrieve API for retrieving data from a MetadataStore
250* Miscellaneous bugfixes
2522007 July 16:
253* Fixed several issues with ImageJ plugins
254* Better support for Improvision and Leica TCS TIFF files
255* Minor improvements to Leica LIF, ICS, QuickTime and Zeiss ZVI readers
256* Added searchable metadata window to ImageJ importer
2582007 July 2:
259* Fixed issues with ND2, Openlab LIFF and Slidebook
260* Added support for Visitech XYS
261* Added composite stack support to ImageJ importer
2632007 June 18:
264* Fixed issues with ICS, ND2, MicroManager, Leica LEI, and FV1000 OIF
265* Added support for large (> 2 GB) ND2 files
266* Added support for new version of ND2
267* Minor enhancements to ImageJ importer
268* Implemented more flexible logging
269* Updated automated testing framework to use TestNG
270* Added package for caching images produced by Bio-Formats
2722007 June 6:
273* Fixed OME upload/download bugs
274* Fixed issues with ND2, EPS, Leica LIF, and OIF
275* Added support for Khoros XV
276* Minor improvements to the importer
2782007 May 24:
279* Better Slidebook support
280* Added support for Quicktime RPZA
281* Better Leica LIF metadata parsing
282* Added support for BioRad PIC companion files
283* Added support for bzip2-compressed files
284* Improved ImageJ plugins
285* Native support for FITS and PGM
2872007 May 2:
288* Added support for NRRD
289* Added support for Evotec Flex (requires LuraWave Java SDK with license code)
290* Added support for gzip-compressed files
291* Added support for compressed QuickTime headers
292* Fixed QuickTime Motion JPEG-B support
293* Fixed some memory issues (repeated small array allocations)
294* Fixed issues reading large (> 2 GB) files
295* Removed "ignore color table" logic, and replaced with Leica-specific solution
296* Added status event reporting to readers
297* Added API to toggle metadata collection
298* Support for multiple dimensions rasterized into channels
299* Deprecated reader and writer methods that accept the 'id' parameter
300* Deprecated in favor of saveImage and saveBytes
301* Moved dimension swapping and min/max calculation logic to delegates
302* Separate GUI logic into isolated loci.formats.gui package
303* Miscellaneous bugfixes and tweaks in most readers and writers
304* Many other bugfixes and improvements
3062007 Mar 16:
307* Fixed calibration bugs in importer plugin
308* Enhanced metadata support for additional formats
309* Fixed LSM bug
3112007 Mar 7:
312* Added support for Micro-Manager file format
313* Fixed several bugs -- Leica LIF, Leica LEI, ICS, ND2, and others
314* Enhanced metadata support for several formats
315* Load series preview thumbnails in the background
316* Better implementation of openBytes(String, int, byte[]) for most readers
317* Expanded unit testing framework
3192007 Feb 28:
320* Better series preview thumbnails
321* Fixed bugs with multi-channel Leica LEI
322* Fixed bugs with "ignore color tables" option in ImageJ plugin
3242007 Feb 26:
325* Many bugfixes: Leica LEI, ICS, FV1000 OIB, OME-XML and others
326* Better metadata parsing for BioRad PIC files
327* Enhanced API for calculating channel minimum and maximum values
328* Expanded MetadataStore API to include more semantic types
329* Added thumbnails to series chooser in ImageJ plugin
330* Fixed plugins that upload and download from an OME server
3322007 Feb 7:
333* Added plugin for downloading images from OME server
334* Improved HTTP import functionality
335* Added metadata filtering -- unreadable metadata is no longer shown
336* Better metadata table for multi-series datasets
337* Added support for calibration information in Gatan DM3
338* Eliminated need to install JAI Image I/O Tools to read ND2 files
339* Fixed ZVI bugs: metadata truncation, and other problems
340* Fixed bugs in Leica LIF: incorrect calibration, first series labeling
341* Fixed memory bug in Zeiss LSM
342* Many bugfixes: PerkinElmer, Deltavision, Leica LEI, LSM, ND2, and others
343* IFormatReader.close(boolean) method to close files temporarily
344* Replaced Compression utility class with extensible Compressor interface
345* Improved testing framework to use .bioformats configuration files
3472007 Jan 5:
348* Added support for Prairie TIFF
349* Fixed bugs in Zeiss LSM, OIB, OIF, and ND2
350* Improved API for writing files
351* Added feature to read files over HTTP
352* Fixed bugs in automated testing framework
353* Miscellaneous bugfixes
3552006 Dec 22:
356* Expanded ImageJ plugin to optionally use Image5D or View5D
357* Improved support for ND2 and JPEG-2000 files
358* Added automated testing framework
359* Fixed bugs in Zeiss ZVI reader
360* Miscellaneous bugfixes
3622006 Nov 30:
363* Added support for ND2/JPEG-2000
364* Added support for MRC
365* Added support for MNG
366* Improved support for floating-point images
367* Fixed problem with 2-channel Leica LIF data
368* Minor tweaks and bugfixes in many readers
369* Improved file stitching logic
370* Allow ImageJ plugin to be called from a macro
3722006 Nov 2:
373* Bugfixes and improvements for Leica LIF, Zeiss LSM, OIF and OIB
374* Colorize channels when they are split into separate windows
375* Fixed a bug with 4-channel datasets
3772006 Oct 31:
378* Added support for Imaris 5 files
379* Added support for RGB ICS images
3812006 Oct 30:
382* Added support for tiled TIFFs
383* Fixed bugs in ICS reader
384* Fixed importer plugin deadlock on some systems
3862006 Oct 27:
387* Multi-series support for Slidebook
388* Added support for Alicona AL3D
389* Fixed plane ordering issue with FV1000 OIB
390* Enhanced dimension detection in FV1000 OIF
391* Added preliminary support for reading NEF images
392* Added option to ignore color tables
393* Fixed ImageJ GUI problems
394* Fixed spatial calibration problem in ImageJ
395* Fixed some lingering bugs in Zeiss ZVI support
396* Fixed bugs in OME-XML reader
397* Tweaked ICS floating-point logic
398* Fixed memory leaks in all readers
399* Better file stitching logic
4012006 Oct 6:
402* Support for 3i SlideBook format (single series only for now)
403* Support for 16-bit RGB palette TIFF
404* Fixed bug preventing import of certain Metamorph STK files
405* Fixed some bugs in PerkinElmer UltraView support
406* Fixed some bugs in Leica LEI support
407* Fixed a bug in Zeiss ZVI support
408* Fixed bugs in Zeiss LSM support
409* Fixed a bug causing slow identification of Leica datasets
410* Fixed bugs in the channel merging logic
411* Fixed memory leak for OIB format
412* Better scaling of 48-bit RGB data to 24-bit RGB
413* Fixed duplicate channels bug in "open each channel in a separate window"
414* Fixed a bug preventing PICT import into ImageJ
415* Better integration with HandleExtraFileTypes
416* Better virtual stack support in Data Browser plugin
417* Fixed bug in native QuickTime random access
418* Keep aspect ratio for computed thumbnails
419* Much faster file stitching logic
4212006 Sep 27:
422* PerkinElmer: support for PE UltraView
423* Openlab LIFF: support for Openlab v5
424* Leica LEI: bugfixes, and support for multiple series
425* ZVI, OIB, IPW: more robust handling of these formats (eliminated
426  custom OLE parsing logic in favor of Apache POI)
427* OIB: better metadata parsing (but maybe still not perfect?)
428* LSM: fixed a bug preventing import of certain LSMs
429* Metamorph STK: fixed a bug resulting in duplicate image planes
430* User interface: use of system look & feel for file chooser dialog
431  when available
432* Better notification when JAR libraries are missing
4342006 Sep 6:
435* Leica LIF: multiple distinct image series within a single file
436* Zeiss ZVI: fixes and improvements contributed by Michel Boudinot
437* Zeiss LSM: fixed bugs preventing the import of certain LSM files
438* TIFF: fixed a bug preventing import of TIFFs created with Bio-Rad software
4402006 Mar 31:
441* First release
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