source: branches/4.1/components/bio-formats/doc/whats-new.txt @ 5625

Revision 5625, 15.9 KB checked in by melissa, 11 years ago (diff)
  • Tweaked ordering of used file list.
  • Updated metadata support docs.
  • Updated what's new for 4.1 release.
  • Updated release number in 4.1 branch.
14.1 (2009 October 21):
3* Fixed many bugs in most file format readers
4* Significantly improved confocal and HCS metadata parsing
5* Improved C++ bindings
6* Eliminated references to Java AWT classes in core Bio-Formats packages
7* Added support for reading Flex datasets from multiple servers
8* Improved OME-XML generation; generated OME-XML is now valid
9* Added support for Olympus ScanR data
10* Added OSGi information to JARs
11* Added support for Amira Mesh files
12* Added support for LI-FLIM files
13* Added more informative exceptions
14* Added support for various types of ICS lifetime data
15* Added support for Nikon EZ-C1 TIFFs
16* Added support for Maia Scientific MIAS data
184.0.1 (2009 June 1):
20* Lots of bug fixes in most format readers and writers
21* Added support for Analyze 7.1 files
22* Added support for Nifti files
23* Added support for Cellomics .c01 files
24* Refactored ImageJ plugins
25* Bio-Formats, the common package, and the ImageJ plugins now require Java 1.5
26* Eliminated native library dependency for reading lossless JPEGs
27* Changed license from GPL v3 or later to GPL v2 or later
28* Updated Olympus FV1000, Zeiss LSM, Zeiss ZVI and Nikon ND2 readers to parse
29  ROI data
30* Added option to ImageJ plugin for displaying ROIs parsed from the chosen
31  dataset
32* Fixed BufferedImage construction for signed data and unsigned int data
344.0.0 (2009 March 3):
36* Improved OME data model population for Olympus FV1000, Nikon ND2, Metamorph
37  STK, Leica LEI, Leica LIF, InCell 1000 and MicroManager
38* Added TestNG tests for format writers
39* Added option to ImageJ plugin to specify custom colors when customizing
40  channels
41* Added ability to upgrade the ImageJ plugin from within ImageJ
42* Fixed bugs in Nikon ND2, Leica LIF, BioRad PIC, TIFF, PSD, and OME-TIFF
43* Fixed bugs in Data Browser and Exporter plugins
44* Added support for Axon Raw Format (ARF), courtesy of Johannes Schindelin
45* Added preliminary support for IPLab-Mac file format
472008 December 29:
48* Improved metadata support for Deltavision, Zeiss LSM, MicroManager, and Leica
49  LEI
50* Restructured code base/build system to be component-driven
51* Added support for JPEG and JPEG-2000 codecs within TIFF, OME-TIFF and OME-XML
52* Added support for 16-bit compressed Flex files
53* Added support for writing JPEG-2000 files
54* Added support for Minolta MRW format
55* Added support for the 2008-09 release of OME-XML
56* Removed dependency on JMagick
57* Re-added caching support to data browser plugin
58* Updated loci.formats.Codec API to be more user-friendly
59* Expanded loci.formats.MetadataStore API to better represent the OME-XML model
60* Improved support for Nikon NEF
61* Improved support for TillVision files
62* Improved ImageJ import options dialog
63* Fixed bugs with Zeiss LSM files larger than 4 GB
64* Fixed minor bugs in most readers
65* Fixed bugs with exporting from an Image5D window
66* Fixed several problems with virtual stacks in ImageJ
682008 August 30:
69* Fixed bugs in many file format readers
70* Fixed several bugs with swapping dimensions
71* Added support for Olympus CellR/APL files
72* Added support for MINC MRI files
73* Added support for Aperio SVS files compressed with JPEG 2000
74* Added support for writing OME-XML files
75* Added support for writing APNG files
76* Added faster LZW codec
77* Added drag and drop support to ImageJ shortcut window
78* Re-integrated caching into the data browser plugin
802008 July 1:
81* Fixed bugs in most file format readers
82* Fixed bugs in OME and OMERO download functionality
83* Fixed bugs in OME server-side import
84* Improved metadata storage/retrieval when uploading to and downloading from
85  the OME Perl server
86* Improved Bio-Formats ImageJ macro extensions
87* Major updates to MetadataStore API
88* Updated OME-XML generation to use 2008-02 schema by default
89* Addressed time and memory performance issues in many readers
90* Changed license from LGPL to GPL
91* Added support for the FEI file format
92* Added support for uncompressed Hamamatsu Aquacosmos NAF files
93* Added support for Animated PNG files
94* Added several new options to Bio-Formats ImageJ plugin
95* Added support for writing ICS files
972008 April 17:
98* Fixed bugs in Slidebook, ND2, FV1000 OIB/OIF, Perkin Elmer, TIFF, Prairie,
99  Openlab, Zeiss LSM, MNG, Molecular Dynamics GEL, and OME-TIFF
100* Fixed bugs in OME and OMERO download functionality
101* Fixed bugs in OME server-side import
102* Fixed bugs in Data Browser
103* Added support for downloading from OMERO 2.3 servers
104* Added configuration plugin
105* Updates to MetadataStore API
106* Updates to OME-XML generation - 2007-06 schema used by default
107* Added support for Li-Cor L2D format
108* Major updates to TestNG testing framework
109* Added support for writing multi-series OME-TIFF files
110* Added support for writing BigTIFF files
1122008 Feb 12:
113* Fixed bugs in QuickTime, SimplePCI and DICOM
114* Fixed a bug in channel splitting logic
1162008 Feb 8:
117* Many critical bugfixes in format readers and ImageJ plugins
118* Newly reborn Data Browser for 5D image visualization
119    + some combinations of import options do not work yet
1212008 Feb 1:
122* Fixed bugs in Zeiss LSM, Metamorph STK, FV1000 OIB/OIF, Leica LEI, TIFF,
123  Zeiss ZVI, ICS, Prairie, Openlab LIFF, Gatan, DICOM, QuickTime
124* Fixed bug in OME-TIFF writer
125* Major changes to MetadataStore API
126* Added support for JPEG-compressed TIFF files
127* Added basic support for Aperio SVS files
128    + JPEG2000 compression is still not supported
129* Improved "crop on import" functionality
130* Improvements to bfconvert and bfview
131* Improved OME-XML population for several formats
132* Added support for JPEG2000-compressed DICOM files
133* EXIF data is now parsed from TIFF files
1352007 Dec 28:
136* Fixed bugs in Leica LEI, Leica TCS, SDT, Leica LIF,
137  Visitech, DICOM, Imaris 5.5 (HDF), and Slidebook readers
138* Better parsing of comments in TIFF files exported from ImageJ
139* Fixed problem with exporting 48-bit RGB data
140* Added logic to read multi-series datasets spread across multiple files
141* Improved channel merging in ImageJ - requires ImageJ 1.39l
142* Support for hyperstacks and virtual stacks in ImageJ - requires ImageJ 1.39l
143* Added API for reading directly from a byte array or InputStream
144* Metadata key/value pairs are now stored in ImageJ's "Info" property
145* Improved OMERO download plugin - it is now much faster
146* Added "open all series" option to ImageJ importer
147* ND2 reader based on Nikon's SDK now uses our own native bindings
148* Fixed metadata saving bug in ImageJ
149* Added sub-channel labels to ImageJ windows
150* Major updates to 4D Data Browser
151* Minor updates to automated testing suite
1532007 Dec 1:
154* Updated OME plugin for ImageJ to support downloading from OMERO
155* Fixed bug with floating point TIFFs
156* Fixed bugs in Visitech, Zeiss LSM, Imaris 5.5 (HDF)
157* Added alternate ND2 reader that uses Nikon's native libraries
158* Fixed calibration and series name settings in importer
159* Added basic support for InCell 1000 datasets
1612007 Nov 21:
162* Fixed bugs in ND2, Leica LIF, DICOM, Zeiss ZVI, Zeiss LSM, FV1000 OIB,
163  FV1000 OIF, BMP, Evotec Flex, BioRad PIC, Slidebook, TIFF
164* Added new ImageJ plugins to slice stacks and do "smart" RGB merging
165* Added "windowless" importer plugin
166    + uses import parameters from IJ_Prefs.txt, without prompting the user
167* Improved stack slicing and colorizing logic in importer plugin
168* Added support for DICOM files compressed with lossless JPEG
169    + requires native libraries
170* Fixed bugs with signed pixel data
171* Added support for Imaris 5.5 (HDF) files
172* Added 4 channel merging to importer plugin
173* Added API methods for reading subimages
174* Major updates to the 4D Data Browser
1762007 Oct 17:
177* Critical OME-TIFF bugfixes
178* Fixed bugs in Leica LIF, Zeiss ZVI, TIFF, DICOM, and AVI readers
179* Added support for JPEG-compressed ZVI images
180* Added support for BigTIFF
181* Added importer plugin option to open each plane in a new window
182* Added MS Video 1 codec for AVI
1842007 Oct 1:
185* Added support for compressed DICOM images
186* Added support for uncompressed LIM files
187* Added support for Adobe Photoshop PSD files
188* Fixed bugs in DICOM, OME-TIFF, Leica LIF, Zeiss ZVI,
189  Visitech, PerkinElmer and Metamorph
190* Improved indexed color support
191* Addressed several efficiency issues
192* Fixed how multiple series are handled in 4D data browser
193* Added option to reorder stacks in importer plugin
194* Added option to turn off autoscaling in importer plugin
195* Additional metadata convenience methods
1972007 Sept 11:
198* Major improvements to ND2 support; lossless compression now supported
199* Support for indexed color images
200* Added support for Simple-PCI .cxd files
201* Command-line OME-XML validation
202* Bugfixes in most readers, especially Zeiss ZVI, Metamorph, PerkinElmer and
203  Leica LEI
204* Initial version of Bio-Formats macro extensions for ImageJ
2062007 Aug 1:
207* Added support for latest version of Leica LIF
208* Fixed several issues with Leica LIF, Zeiss ZVI
209* Better metadata mapping for Zeiss ZVI
210* Added OME-TIFF writer
211* Added MetadataRetrieve API for retrieving data from a MetadataStore
212* Miscellaneous bugfixes
2142007 July 16:
215* Fixed several issues with ImageJ plugins
216* Better support for Improvision and Leica TCS TIFF files
217* Minor improvements to Leica LIF, ICS, QuickTime and Zeiss ZVI readers
218* Added searchable metadata window to ImageJ importer
2202007 July 2:
221* Fixed issues with ND2, Openlab LIFF and Slidebook
222* Added support for Visitech XYS
223* Added composite stack support to ImageJ importer
2252007 June 18:
226* Fixed issues with ICS, ND2, MicroManager, Leica LEI, and FV1000 OIF
227* Added support for large (> 2 GB) ND2 files
228* Added support for new version of ND2
229* Minor enhancements to ImageJ importer
230* Implemented more flexible logging
231* Updated automated testing framework to use TestNG
232* Added package for caching images produced by Bio-Formats
2342007 June 6:
235* Fixed OME upload/download bugs
236* Fixed issues with ND2, EPS, Leica LIF, and OIF
237* Added support for Khoros XV
238* Minor improvements to the importer
2402007 May 24:
241* Better Slidebook support
242* Added support for Quicktime RPZA
243* Better Leica LIF metadata parsing
244* Added support for BioRad PIC companion files
245* Added support for bzip2-compressed files
246* Improved ImageJ plugins
247* Native support for FITS and PGM
2492007 May 2:
250* Added support for NRRD
251* Added support for Evotec Flex (requires LuraWave Java SDK with license code)
252* Added support for gzip-compressed files
253* Added support for compressed QuickTime headers
254* Fixed QuickTime Motion JPEG-B support
255* Fixed some memory issues (repeated small array allocations)
256* Fixed issues reading large (> 2 GB) files
257* Removed "ignore color table" logic, and replaced with Leica-specific solution
258* Added status event reporting to readers
259* Added API to toggle metadata collection
260* Support for multiple dimensions rasterized into channels
261* Deprecated reader and writer methods that accept the 'id' parameter
262* Deprecated in favor of saveImage and saveBytes
263* Moved dimension swapping and min/max calculation logic to delegates
264* Separate GUI logic into isolated loci.formats.gui package
265* Miscellaneous bugfixes and tweaks in most readers and writers
266* Many other bugfixes and improvements
2682007 Mar 16:
269* Fixed calibration bugs in importer plugin
270* Enhanced metadata support for additional formats
271* Fixed LSM bug
2732007 Mar 7:
274* Added support for Micro-Manager file format
275* Fixed several bugs -- Leica LIF, Leica LEI, ICS, ND2, and others
276* Enhanced metadata support for several formats
277* Load series preview thumbnails in the background
278* Better implementation of openBytes(String, int, byte[]) for most readers
279* Expanded unit testing framework
2812007 Feb 28:
282* Better series preview thumbnails
283* Fixed bugs with multi-channel Leica LEI
284* Fixed bugs with "ignore color tables" option in ImageJ plugin
2862007 Feb 26:
287* Many bugfixes: Leica LEI, ICS, FV1000 OIB, OME-XML and others
288* Better metadata parsing for BioRad PIC files
289* Enhanced API for calculating channel minimum and maximum values
290* Expanded MetadataStore API to include more semantic types
291* Added thumbnails to series chooser in ImageJ plugin
292* Fixed plugins that upload and download from an OME server
2942007 Feb 7:
295* Added plugin for downloading images from OME server
296* Improved HTTP import functionality
297* Added metadata filtering -- unreadable metadata is no longer shown
298* Better metadata table for multi-series datasets
299* Added support for calibration information in Gatan DM3
300* Eliminated need to install JAI Image I/O Tools to read ND2 files
301* Fixed ZVI bugs: metadata truncation, and other problems
302* Fixed bugs in Leica LIF: incorrect calibration, first series labeling
303* Fixed memory bug in Zeiss LSM
304* Many bugfixes: PerkinElmer, Deltavision, Leica LEI, LSM, ND2, and others
305* IFormatReader.close(boolean) method to close files temporarily
306* Replaced Compression utility class with extensible Compressor interface
307* Improved testing framework to use .bioformats configuration files
3092007 Jan 5:
310* Added support for Prairie TIFF
311* Fixed bugs in Zeiss LSM, OIB, OIF, and ND2
312* Improved API for writing files
313* Added feature to read files over HTTP
314* Fixed bugs in automated testing framework
315* Miscellaneous bugfixes
3172006 Dec 22:
318* Expanded ImageJ plugin to optionally use Image5D or View5D
319* Improved support for ND2 and JPEG-2000 files
320* Added automated testing framework
321* Fixed bugs in Zeiss ZVI reader
322* Miscellaneous bugfixes
3242006 Nov 30:
325* Added support for ND2/JPEG-2000
326* Added support for MRC
327* Added support for MNG
328* Improved support for floating-point images
329* Fixed problem with 2-channel Leica LIF data
330* Minor tweaks and bugfixes in many readers
331* Improved file stitching logic
332* Allow ImageJ plugin to be called from a macro
3342006 Nov 2:
335* Bugfixes and improvements for Leica LIF, Zeiss LSM, OIF and OIB
336* Colorize channels when they are split into separate windows
337* Fixed a bug with 4-channel datasets
3392006 Oct 31:
340* Added support for Imaris 5 files
341* Added support for RGB ICS images
3432006 Oct 30:
344* Added support for tiled TIFFs
345* Fixed bugs in ICS reader
346* Fixed importer plugin deadlock on some systems
3482006 Oct 27:
349* Multi-series support for Slidebook
350* Added support for Alicona AL3D
351* Fixed plane ordering issue with FV1000 OIB
352* Enhanced dimension detection in FV1000 OIF
353* Added preliminary support for reading NEF images
354* Added option to ignore color tables
355* Fixed ImageJ GUI problems
356* Fixed spatial calibration problem in ImageJ
357* Fixed some lingering bugs in Zeiss ZVI support
358* Fixed bugs in OME-XML reader
359* Tweaked ICS floating-point logic
360* Fixed memory leaks in all readers
361* Better file stitching logic
3632006 Oct 6:
364* Support for 3i SlideBook format (single series only for now)
365* Support for 16-bit RGB palette TIFF
366* Fixed bug preventing import of certain Metamorph STK files
367* Fixed some bugs in PerkinElmer UltraView support
368* Fixed some bugs in Leica LEI support
369* Fixed a bug in Zeiss ZVI support
370* Fixed bugs in Zeiss LSM support
371* Fixed a bug causing slow identification of Leica datasets
372* Fixed bugs in the channel merging logic
373* Fixed memory leak for OIB format
374* Better scaling of 48-bit RGB data to 24-bit RGB
375* Fixed duplicate channels bug in "open each channel in a separate window"
376* Fixed a bug preventing PICT import into ImageJ
377* Better integration with HandleExtraFileTypes
378* Better virtual stack support in Data Browser plugin
379* Fixed bug in native QuickTime random access
380* Keep aspect ratio for computed thumbnails
381* Much faster file stitching logic
3832006 Sep 27:
384* PerkinElmer: support for PE UltraView
385* Openlab LIFF: support for Openlab v5
386* Leica LEI: bugfixes, and support for multiple series
387* ZVI, OIB, IPW: more robust handling of these formats (eliminated
388  custom OLE parsing logic in favor of Apache POI)
389* OIB: better metadata parsing (but maybe still not perfect?)
390* LSM: fixed a bug preventing import of certain LSMs
391* Metamorph STK: fixed a bug resulting in duplicate image planes
392* User interface: use of system look & feel for file chooser dialog
393  when available
394* Better notification when JAR libraries are missing
3962006 Sep 6:
397* Leica LIF: multiple distinct image series within a single file
398* Zeiss ZVI: fixes and improvements contributed by Michel Boudinot
399* Zeiss LSM: fixed bugs preventing the import of certain LSM files
400* TIFF: fixed a bug preventing import of TIFFs created with Bio-Rad software
4022006 Mar 31:
403* First release
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