Version history¶
6.5.1 (2020 July)¶
File format fixes and improvements:
- Aperio SVS / Aperio AFI
fixed a Null Pointer Exception when exposure time is not defined
- Big Data Viewer
corrected series indexes for non flattened multi resolution images
- Cellomics
physical sizes are now set for all series rather than just the first
- Imspector OBF
file format version and stack version are now recorded as part of global metadata
- MetaMorph
improved wavelength parsing using Metamorph XML or original metadata
- Mikroscan TIFF
stricter format recognition now used to prevent erroneous use of the reader
- Ventana BIF
added support for LEFT overlap direction (thanks to Joan Gibert)
- Zeiss CZI
fixed a bug to ensure Channel Illumination Type is not overridden by display settings
Documentation improvements:
added link from OME-TIFF page to commercial partners page
updated links for Biplane to now use Oxford Instruments
fixed a number of broken hyperlinks in documentation
Component updates:
jxrlib was upgraded to 0.2.4
Bio-Formats improvements:
fixed a bug in bfconvert for multi-series files with varying image sizes
removed the logging OMERO IDs passed to FormatReader and ImageReader
6.5.0 (2020 April)¶
File format fixes and improvements:
- Big Data Viewer
improved performance of tiled reading
- DeltaVision
implemented additional sanity check to header to ensure correct panel count
- DICOM
improved performance of initialization of multi-file datasets. Files spread across multiple directories are now handled by a DICOMDIR file that groups the dataset
- Imspector OBF
added support for OBF Version 6 stacks (thanks to Nils Gladitz)
added support for OBF Version 4 stack flush points (thanks to Nils Gladitz)
- MetaMorph
ensured dimension metadata read from tags and/or .nd file rather than allowing the underlying TIFF reader to treat each IFD as a series
- MetaXpress
added support for single site HCS variant
- Zeiss CZI
fixed the position count when only one position is present and the starting index is greater than 0
- Various Readers
reviewed and updated readers to prevent potential cases of integer overflow
OME-Model updates:
version of
OME-Model
has been updated to 6.1.0added support for Python 3.8 and make code-generation Python 3 only (thanks to Roger Leigh)
added getters and setters for OME@Creator attribute for ome.xml metadata interfaces and implementations (thanks to Nils Gladitz)
removed unmaintained C++ OME-XML implementation (thanks to Roger Leigh)
updated code-generation for building on Python 3.6, 3.7 (thanks to Roger Leigh)
uncapped the Sphinx version for OME-Model documentation
Documentation improvements:
fixed a number of broken links within the documentation
added a new format page for MetaXpress
added a reference to public OBF sample images in the format page
6.4.0 (2020 March)¶
File format fixes and improvements:
- Applied Precision CellWorX
added support for multiple Z sections
- DeltaVision
added and updated objective metadata based on values from softWoRx 7.2.0 (thanks to David Pinto)
- Hamamatsu NDPI
added support for JPEG-XR compression
added full support for files larger than 4 GB
improved support for a number of additional metadata tags
the Hamamatsu NDPI reader improvements are provided via work from Glencoe Software Inc.
- InCell
inverted Y coordinate in plane/field positions to correct stitching of tiles
- PerkinElmer Vectra QPTIFF
plane position values will now be populated on OME-XML
- TIFF
values for XPosition and YPosition in original metadata will now be more accurately stored as doubles
implemented a fix to prevent integer overflow when reading from a large tile greater than 2 GB
- Ventana BIF
improved handling of physical sizes for pre-stitched TIFFs
- Zeiss CZI
added a fix for uncompressed pixels incorrectly flagged as JPEG-XR
fixed a bug so that line-scans are now read correctly (thanks to Stephan Wagner-Conrad)
improved parsing of detector metadata
Bio-Formats tools improvements:
added a new
nobigtiff
option tobfconvert
to disable automatic switching to BigTiff based upon the number of pixel bytes (TIFF files larger than 4GB). This may be useful when converting using a compression codec so that the output file size is less than 4GBfixed a bug in
xmlvalid
tool to properly handle lowercasing of file namesadded new bfGetPlaneAtZCT function to MATLAB toolbox to retrieve a particular plane at a ZCT coordinate (thanks to Mark Kittisopikul)
added a new bfTestInRange helper function to MATLAB toolbox with improved performance and error handling (thanks to Mark Kittisopikul)
fixed a bug when using
bfconvert
on multi-series files with only a single timepoint, channel or Z slice selected
Bio-Formats API updates:
version of
jxrlib
has been updated to 0.2.2version of
ome-codecs
has been updated to 0.3.0 which includes performance upgrades for LZW compression (thanks to Alexander Popiel)moved JPEG-XR codec and service from
formats-gpl
toformats-bsd
componentTiffParser and TiffSaver have now been updated to implement Closeable
added a documentation note to use one IFD instance per plane with
saveBytes
inTiffWriter
FormatWriter will now create output file’s parent directory if needed
FakeReader now allows for DeltaT to be set in INI file
FakeReader now handles INI files in plates created by
mkfake
fixed a number of deprecation warnings in various readers
6.3.1 (2019 December)¶
File format fixes and improvements:
- ICS (Image Cytometry Standard)
prevented a potential error when writing ICS files with physical units which could not be converted
- Imspector OBF
fixed a bug with incorrect dimensions being parsed for some Imspector OBF files
- Leica LAS AF LIF (Leica Image File Format)
fixed a NullPointerException in some variants of the LIF file format
- TIFF
improved the performance of tiled writing
- Zeiss CZI
fixed issues with tile stitching and position size
Bio-Formats tools improvements:
fixed a potential NullPointerException in SpringUtilities for Bio-Formats plugins (thanks to July Chen)
updated URL for fetching ImageJ upgrades in
ijview
fixed the XY coordinates for cropped images in
bfconvert
fixed a bug when using a cropped multi-series file in
bfconvert
(thanks to Matthieu Moisse)fixed issues in
bfconvert
when writing separate tiles with additional optionsadded documentation of tile output patterns to utility help in
bfconvert
6.3.0 (2019 October)¶
File format fixes and improvements:
- Big Data Viewer
added support for parsing of physical sizes
- DeltaVision
added a new RCPNL reader which is a variant and split out of the DeltaVision format
- Hamamatsu NDPI
fixed population of the nominal magnification from the SourceLens TIFF tag
- ICS (Image Cytometry Standard)
fixed a bug when using tiles to read files from SVI-Huygens
- Imspector OBF
fixed an IndexOutOfBoundsException exception when using DummyMetadata (thanks to Nils Gladitz)
- JPEG 2000
added support for sub-resolutions
- Leica LIF
updated to parse attachments to determine if XY positions should be flipped or swapped
- MetaMorph
improved file name construction and plate detection logic
- Nikon ND2
updated to use floating point for 32 bit values
- OME-TIFF
reduced memory usage when reading files and memo file size for cached files
- PerkinElmer Operetta
improved handling of empty fields to prevent series from having X or Y set to 0
API updates:
added overwriteIFDValue signature that takes an IFD offset to TiffSaver
added a new getRequiredDirectories method to FormatTools
new FakeReader keys added for sleepOpenBytes and sleepInitFile
Build updates:
updated deployment mechanism for SNAPSHOT and Release to use Travis CI
increased the strictness of AcquisitionDate checks in FormatReaderTest
improved test coverage of companion file datasets
Component updates:
ome-common was upgraded to 6.0.4
updated DateTools to attempt to parse invalid dates with Locale.US
DateTools documentation updated to clarify expected units for timestamp passed to convertDate
Documentation improvements:
added documentation for sleep options when generating test images
fixed broken external links in documentation
corrected suffixes used for JPEG 2000
6.2.1 (2019 August)¶
File format fixes and improvements:
- Applied Precision CellWorX
corrected plane positions for series index > 0 rather than reusing positions from the first series
- DeltaVision
added objective info for new Applied Precision 100X/1.4 lensID
updated so that date from dv file will override log file date to avoid locale-dependent dates
- Leica LAS AF LIF (Leica Image File Format)
fixed units and indexing for tile-based plane positions
- TIFF
fixed a potential exception in MinimalTiffReader when the TIFF is stored using very large tile/strip dimensions
- Zeiss CZI
fixed a potential index out of bounds exception when populating positions
Bug fixes and improvements:
bfconvert has been updated so that when the dimensions of a sub-resolution are smaller than the requested tile size then they default to the size of the sub-resolution
fixed a bug in the execution of bfsave in the GNU Octave environment
Codec updates:
ome-codecs was upgraded to 0.2.5
JPEG codec updated to reduce decompression time for 8-bit RGB images
Huffman codec updated to allow the decoding tree to go all the way down to the 16-bit depth required by the standard (thanks to Aaron Avery)
Lossless JPEG codec updated to provide better compliance with the LJPEG standard (thanks to Aaron Avery)
Documentation improvements:
added instructions for building Bio-Formats with IntelliJ IDEA
corrected command-line tools documentation for the novalid and noncore options
updated broken links to Barre’s Medical Imaging Samples
updated the imagej.net link for Zeiss LSM toolbox plugin
- added links to public sample files for the following formats:
6.2.0 (2019 July)¶
New file formats:
- Mikroscan TIFF
a new reader for Mikroscan TIFF files has been contributed with thanks to Jim Crowe, Mikroscan Technologies, Inc.
- Ventana BIF
added a new reader for Ventana BIF files which has been commissioned via Glencoe Software
File format fixes and improvements:
- Cellomics
fixed indexing for plates with a single well or missing fields
- DeltaVision
added support for the reading of the new panel count field (provided through a collaboration between GE Healthcare and Glencoe Software Inc.)
- PerkinElmer Operetta
images with smaller XY dimensions than all other TIFF files in dataset will now be padded
- TIFF
updated functionality for overwriting IFD values to ensure that previous value is completely overwritten and no orphaned tags are left
- Zeiss CZI
expanded support for auto-stitching of tiles
Bug fixes and improvements:
added
-cache
,-cache-dir
and-no-sas
options tobfconvert
tooldeprecated broken TRUNK and DAILY builds from upgrade checker
disabled Oracle JDK from Travis CI checks
Documentation improvements:
fixed broken link for discontinued Dcraw software
updated links for Zeiss formats
6.1.1 (2019 June)¶
File format fixes and improvements:
- DeltaVision
added new lens definitions associated with rcpnl files
- Gatan Digital Micrograph (DM3/DM4)
now parsing the Montage tag to determine if tiles are present
- Leica LAS AF LIF (Leica Image File Format)
added fix to correctly read scale from polygon regions of interest (thanks to Sean Warren)
- PerkinElmer Columbus
improved handling of truncated TIFF files to return blank planes
- PerkinElmer Opera Flex
plate barcodes are now used to improve grouping and handling of truncated files
- TIFF (Tagged Image File Format)
improved parsing times for images stored as uncompressed contiguous strips
- Zeiss CZI
improved plane position metadata for many CZI datasets
Automated test changes:
format reader tests have been updated to handle PerkinElmer Columbus datasets with flex files
Documentation improvements:
added help for missing options in
bfconvert
command line tool
6.1.0 (2019 May)¶
New file formats:
- BDV
added a new reader for Big Data Viewer files
File format fixes and improvements:
- Applied Precision CellWorX
improved handling of thumbnail files
- DeltaVision
updated handling of rcpnl files to treat each file as a single timepoint
- FakeReader
removed header key from original metadata
- Hamamatsu VMS
removed header key from original metadata
- Hitachi S-4800
removed header key from original metadata
- ICS (Image Cytometry Standard)
fixed an issue reading .ics/.ids files written by SVI Huygens (thanks to Jan Eglinger)
- Imaris IMS
fixed issues with newer files which had been failing due to older netcdf version
- JPEG
improved the reading of EXIF data
- Lambert Instruments FLIM
added support for packed UINT12 datatype (thanks to Johan Herz)
- LEO
fixed a bug with the parsing of physical sizes
improved support for additional global metadata fields
- Olympus OIR
fixed a bug which would show empty pixels when more than 1000 timepoints
Automated test changes:
added additional tests for HCS/SPW datasets to ensure Plate, PlateAcquisition, Well, WellSample, and WellSample position values are configured where present
added a new file-leak-detector test to flag potential memory leaks
Bio-Formats API changes:
ImageConverter
as used inbfconvert
command line tool is now publicmade
ImageReader
more defensive against exceptions thrown when determining reader typefixed an issue when performing a non-sequential write for multi-resolution TIFF files
Component changes:
ome-common was upgraded to 6.0.3
perf4j was upgraded to 0.9.16
removed Guava dependency which will be pulled transitively from the upstream ome-common dependency
jhdf5 was upgraded to 14.12.6
metadata-extractor was upgraded to 2.11.0
xercesImpl version 2.8.1 was added as it is no longer a dependency of metadata-extractor
netcdf was upgraded to 4.6.13
6.0.1 (2019 March)¶
File format fixes and improvements:
- cellSens VSI
improved tag parsing resulting in fixes for missing or incorrect metadata
- Hamamatsu ndpi
improved handling of variants where a constituent NDPI has no wavelength
- LaVision Imspector
fixed a potential NullPointerException when ‘xyz-Table Z Resolution’ is false
- NRRD (Nearly Raw Raster Data)
added support for raw GZIP-compressed data files
- Olympus OIR
fix to ensure file path is normalized which fixes detection on Windows
- TIFF
improved handling of direct tile copying to prevent invalid images
improved handling of tiles in scenarios of an invalid offset or byte count of 0
- Documentation improvements:
added documentation for -noflat option to the showinf and bfconvert users pages
updated recommended minimal MATLAB version to R2017b
documented support for MATLAB versions prior to R2017b
links to MicroCT public datasets now point to the public archive rather than directly to the zip file
6.0.0 (2019 February)¶
Bio-Formats API changes:
Java 8 is now the minimum supported version
Sub-resolution reading:
added
MetadataList
andCoreMetadataList
classesadded a new
SubResolutionFormatReader
abstract class for handling pyramidal format readersupdated all pyramid format readers to use
SubResolutionFormatReader
deprecated
getCoreMetadataList
,seriesToCoreIndex
,coreIndexToSeries
,getCoreIndex
andsetCoreIndex
inIFormatWriter
Added a new
IPyramidHandler
interface with the resolution getter methodsSub-resolution writing changes:
IFormatWriter
now extendsIPyramidHandler
(breaking)added
setResolutions
andgetResolutions
methods toIFormatWriter
(breaking)added examples of using the sub-resolution writing API
Tiled writing API changes:
updated
IFormatWriter
to usesetTileSizeX(0)
andsetTileSizeY(0)
as a way to disable tiling (breaking)updated
FormatWriter
set 0 as the default values ofgetTileSizeX()
andgetTileSizeY
(breaking)
IFormatWriter.getCompressionTypes
now returns the types for the selected writer onlyMetadata handling:
added getter methods to
MetadataTools
for retrieving OME enumerations by valuedeprecated OME enumeration getter methods in
FormatReader
Refactor
FilePatternReader
logic in a newWrappedReader
abstract class
New file formats:
KLB
added a new reader for Keller Lab Block (KLB) files
CV7000
added a new reader for Yokogawa CV7000 datasets
GE MicroCT
added a new reader for GE MicroCT datasets
File format fixes and improvements:
Aperio SVS/AFI
removed pyramidal resolutions of mismatching pixel types
fixed exposure times, improved image naming of AFI datasets
displayed original metadata keys for each channel of AFI datasets
added support for multiple Z sections
DICOM
improved file grouping and file-to-series mapping for multi-file datasets
Fake
added support for multi-resolution test images
now populating WellSample positions when present using Plane data
Gatan Digital Micrograph
adjusted endianness and record byte count for long values
allowed ROIs to be stored in DocumentObjectList groups
no longer creating an empty ROI when an unsupported shape type is encountered
Image Pro
added support for Image Pro Plus .ips set
GE InCell
added support for parsing minimum and maximum pixel values
Lambert Instruments FLIM
fixed an integer overflow error with large files (thanks to Rolf Harkes)
Leica LIF
unified metadata parsing to use
DataTools.parseDouble
Leica SCN
improved support for Versa datasets
Micro-Manager
improved handling of very large
*_metadata.txt
filesprevented
NumberFormatException
for invalid double valuesadd support for parsing ChannelColor from
*_metadata.txt
files
Metamorph
added support for multi-dimensional .scan dataset created from Scan Slide (thanks to Jeremy Muhlich)
MRC (Medical Research Council)
fixed endian detection for old-style headers
Nikon ND2
prevented integer overflow when reading chunkmaps from files larger than 2GB
fixed handling of duplicate and incomplete exposure time lists
fixed chunk map handling when CustomData blocks are between ImageDataSeqs
OME-TIFF
added support for reading OME-TIFF with pyramidal resolutions stored as SubIFDs
added support for writing OME-TIFF with pyramidal resolutions
added support for companion OME-TIFF filesets where TIFF does not link back to the metadata file
improved handling of missing planes in TiffData
PerkinElmer Operetta
improved support to handle datasets generated by the Harmony software
TIFF
split IFDs into separate series if the dimensions or pixel type mismatch
restricted use case for legacy TIFF JAI reader
fixed a bug with FillOrder which resulted in 0 pixel values
Zeiss CZI
reduced duplicate original metadata when reading a pyramid file
Zeiss TIFF
added support for AVI files acquired with Keyence software
Zeiss ZVI
reuse stream for sequential calls to
openBytes
on the same plane
updated all pyramidal format readers to consume
SubResolutionReader
updated all readers to consume
MetadataTools
getter to retrieve enumerationsreviewed all readers and plugins to close open instances of
RandomAccessInputStream
fixed some deprecation warnings in a number of readers
for RGB images using
ChannelSeparator
all channel metadata is now copied instead of just names
ImageJ plugin improvements:
updated the updater message in the Fiji plugin (thanks to Jan Eglinger)
disabled LUT writing for any plane that has a default grayscale lookup table
added macro option to always skip LUT writing
MATLAB toolbox improvements:
improved performance of bfGetPlane by removing an unnecessary data copy (thanks to Cris Luengo)
Command-line tools improvements:
bfconvert
utilityadded
-no-flat
option to the command-line tools to convert files with sub-resolutionsadded
-pyramid-scale
and-pyramid-resolutions
options to generate sub-resolutions during conversionremoved
Plate
elements when-series
is passed as an optionextended usage to describe available formats, extensions and compressions
xmlvalid
utilityadded new
validate
methods toloci.formats.tools.XMLValidate
returning the validation statusadded a return code to
xmlvalid
Component changes:
ome-common was upgraded to 6.0.0
ome-codecs was upgraded to 0.2.3
ome-model was upgraded to 6.0.0
Automated test changes:
added
testng.allow-missing
property allowing to skip unconfigured filesetsadded
testUnflattenedSaneOMEXML
to compare series count to OME-XML images count when resolution flattening is disabledadded
test-equivalent
target to compare pixel data between two filesadded support for storing resolution index and resolution count in the configuration files used for automated testing
tests now fail when a configured file throws UnknownFormatException
Documentation improvements:
fixed the xmlvalid documentation page (thanks to Kouichi C. Nakamura)
improved the memory section of the MATLAB documentation page (thanks to Kouichi C. Nakamura)
extended
IFormatReader
Javadocs to reflect the reader guideadded reference to current Adobe TIFF specification
switched to image.sc as the reference location for public feedback
5.9.2 (2018 September 03)¶
File format fixes and improvements:
- AVI
added support for AVI files acquired with Keyence software
- Gatan
fixed a bug when reading a file with an empty tag of type 23
- Deltavision
extended the objective metadata support (thanks to David Pinto)
- MRC
fixed the reading of MRC files generated with FEI EPU software
- Zeiss LSM
improved the channel color detection for SIM data
Component changes:
All OME dependencies were upgraded mostly with build changes and documentation improvements:
ome-common was upgraded from 5.3.2 to 5.3.6
ome-poi was upgraded from 5.3.1 to 5.3.3
ome-mdbtools was upgraded from 5.3.1 to 5.3.3
ome-jai was upgraded from 0.1.0 to 0.1.3
ome-codecs was upgraded from 0.2.0 to 0.2.2
ome-stubs was upgraded from 5.3.0 to 5.3.2
ome-model was upgraded from 5.5.4 to 5.6.3
Documentation improvements:
added links to public sample files for Imaris IMS, DICOM, Leica-SCN, LEO, MRC, PNG, TIFF and Trestle formats
5.9.1 (2018 August 14)¶
File format fixes and improvements:
- Olympus OIR
fixed a bug to prevent incorrect files from being read when multiple datasets are in the same location
- LEO
updated parsing of metadata values for image pixel size, working distance, filament, EHT and date (thanks to David Mankus)
- DeltaVision
reader can now detect up to 12 channels
- Micro-Manager
now logs a warning when an image is acquired with an unsupported version
Documentation improvements:
added QuPath to the list of visualization and analysis applications
updated the link to the i3dcore library
updated the link to Slidebook
improved MATLAB documentation with information on Java heap memory preferences (thanks to Kouichi C. Nakamura)
corrected a number of permanently redirected URLs in the component and format pages
5.9.0 (2018 July 3)¶
File format fixes and improvements:
- MetaMorph
fixed a
NullPointerException
when a stage label is not presentensured that reported domain is now consistent with the existence of a Plate in OME-XML
fixed Metamorph RGB series channel count (thanks to Jeremy Muhlich)
- Leica LIF
improved handling of dimension order for non-RGB channels
- Imspector OBF
added support for FLIM datasets
- Inveon
updated to attempt to locate renamed data files
- Volocity
expanded image names to include the stack parent names
- Olympus OIR
added a fix for slow tag reading and a potential infinite loop
- TIFF
added support in
TiffWriter
for the writing of DEFLATE (zlib) compressiondeprecated
getIFDs()
inTiffParser
and addedgetMainIFDs()
andgetSubIFDs()
- Zeiss CZI
fixed an issue with big images when tiling is present but a pyramid is not
- Nikon NIS-Elements ND2
prevented integer overflow exception when reading a tile from a large image
- Amersham Biosciences Gel
prevented overflow issue when reading unsigned integer values
- Cellomics
fixed indexing when the field counts are variable
- Trestle
updated to ensure consistent ordering of used files
Bug fixes and improvements:
enabled building and testing with Java 9 and 10
added CI testing with Java 10 on AppVeyor and Travis
removed Java 7 from Appveyor matrix
updated a number of Maven plugins to current versions
corrected warnings in Maven configuration in sub-components
added a warning to clarify the behavior when passing metadata with
dimensionOrder
inbfsave
as part of the Bio-Formats MATLAB toolbox (thanks to Jonathan Armond)improved robustness in the detection of patterns as part of the file stitching
fixed a bug relating to dimension order in the Bio-Formats plugins Exporter
fixed download URLs in Bio-Formats command-line tools
updated use of
static final
to match Oracle’s recommendations and conventiondisabled upgrade checker when running unit tests
added support to data repo test suite for unconfigured tests
Documentation improvements:
fixed unstable links flagged by automated link checking
begun adding testing for breakages to memo files
clarified ordering expectation in
getUsedFiles
Javadocsadded documentation for dimensionOrder in bfsave with the MATLAB toolbox
fixed broken links in previous release notes
expanded documentation for command-line tools to cover undocumented options and environment variables
added a new license/copyright section to the About Bio-Formats page
updated the public format page for the Vectra QPTIFF format
5.8.2 (2018 April 23)¶
File format fixes and improvements:
- JPEG
large images with no restart markers now revert to using
DefaultJPEGReader
for improved decoding
- Micro-Manager
when available
PositionName
will be parsed and used as the image name
- Hamamatsu ndpi
updated image names to be more meaningful when resolutions are not flattened
- InCell 2000/6000
fixed an
IllegalArgumentException
and improved well and field indexing
- AVI
fixed a bug with padding for RGB images
- NIfTI
the
nDimensions
field is now used to read additional dimensions when size is greater than 4
- PerkinElmer Opera Flex
fixed a bug which resulted in an incorrect field count
- Zeiss CZI
improved handling of files with no extension
Bug fixes and improvements:
an error message is now logged by
ImageReader
when finding a reader for an empty fileadded a new protected helper method to
Memoizer
to check if a directory is writableimproved the rounding of
PlanePosition
values for data repo configuration testingprevented a null pointer exception when retrieving plane exposure time using Bio-Formats ImageJ macro extensions
updated
MinMaxCalculator
to account for unflattened multi resolution images
Documentation improvements:
decoupled the Bio-Formats documentation to the new ome/bio-formats-documentation GitHub repository
updated Adding format/reader documentation for the new decoupled workflow
improved link checking in automated builds
5.8.1 (2018 March 22)¶
File format fixes and improvements:
- TIFF
updated TiffWriter so that planes will no longer be split when using non-standard SamplesPerPixel e.g. images with 2 or 4 samples per pixel. This will ensure the
TiffData
elements represent the structure specified by the user. If users wish to split planes theChannelSeparator
andbfconvert
provide the means to do this explicitlyupdated TiffWriter to use the correct logic for index checking when writing tiled images
fixed a
ClassCastException
when theNEW_SUBFILE_TYPE
tag has a non-standard type or count such that the value is not inlinedupdated to also check the last IFD for an ImageJ comment in the scenario that the image has been processed by other software
- NRRD (Nearly Raw Raster Data)
added support for
space directions
andspace units
fields added in version 4
- Evotec/PerkinElmer Opera Flex
updated to read rather than calculate image offsets when a single tile is used
Bug fixes and improvements:
limited the number of exceptions in the Bio-Formats plugins exporter when an unsupported pixel type is found
fake test images now allow for per-plane ExposureTime{X,Y,Z} and Position{X,Y,Z} keys in the INI file (for further details see the documentation for Generating test images)
file patterns now have expanded support for multi-channel pyramids, allowing for the matching of at least two channels rather than three, and the stitching of files containing a pyramid has also been fixed
Documentation improvements:
improved testing of external links
5.8.0 (2018 February 21)¶
New file formats:
- Ionpath MIBI
added a new reader to support the reading of Ionpath Multiplexed Ion Beam Imaging (MIBI) files (thanks to Rachel Finck)
- PerkinElmer Vectra QPTIFF
added support for PerkinElmer Vectra QPTIFF files (The QPTIFF Bio-Formats reader is provided through a collaboration between PerkinElmer, Inc and Glencoe Software Inc.)
File format fixes and improvements:
- cellSens VSI
added support for lossless JPEG compression
- Imspector OBF
improved the parsing of OBF files with embedded OME-XML metadata (thanks to Bjoern Thiel)
- Leica LIF
companion metadata files are now attached if present
- Micro-Manager
fixed a bug related to the parsing of the metadata closing block
- NRRD (Nearly Raw Raster Data)
added support for GZIP pixel stream contained within a .nrrd file
- Olympus OIR
added support for multi-file datasets
- OME-TIFF
when files are ungrouped the dimensions are corrected by checking the indexes for each associated TiffData
- PerkinElmer Operetta
added support for additional metadata fields such as
Instrument
,Wavelength
andExposure time
- TIFF
fixed a bug when printing IFD values of type
OnDemandLongArray
fixed a bug when writing tile sizes for multi-series images
- Zeiss CZI
when Z positions are not enumerated then values are calculated from a Z step
metadata for DisplaySetting will now be preserved in the original metadata table
Bug fixes and improvements:
removed unused ScreenReader in preparation for migrating it to be an external reader
fixed a bug with the generation of thumbnails in Bio-Formats plugins
updated the Maven POM to unify component version property names
tile size is now reported in the core metadata when using the showinf tool
added
setFilePatternIds
toImporterOptions
for use with Bio-Formats pluginsimproved the precision of format identification for MRC, I2I, and Zeiss LSM
Documentation improvements:
fixed and updated a number of external documentation links
added links to public NRRD samples
5.7.3 (2018 January 11)¶
File format fixes and improvements:
- TIFF
fixed a NullPointerException when reading a TIFF file from the root system directory
improved support for large images that are stored as a single uncompressed tile with multiple interleaved channels
- MRC (Medical Research Council)
added support in original metadata for the fields
ISPG
andIs data cube
- TillPhotonics TillVision
directory listings for .pst files are now sorted
- MetaMorph
directory listings are now sorted during file initialization
- Amira Mesh
now supports
Avizo
in the file header in addition to the existing support forAmiraMesh
- Becker & Hickl SPCImage
added a fix for IllegalArgumentException when reading files with compressed data
- Zeiss CZI
fixed an IndexOutOfBoundsException when creating ROI objects
Bug fixes and improvements:
removed unused target utils-formats-api from ant build
automated Memoizer tests updated to use UUID for generating unique memo file directories
detect and fix Findbugs’
SBSC_USE_STRINGBUFFER_CONCATENATION
using StringBuilderconfiguration files for the automated test suite now use raw physical size rather than formatted size
added first version of Dockerfile for running the automated test suite standalone
Documentation improvements:
added a support page to the Bio-Formats project
updated reference URLs for the Aperio ImageScope and Micro-Manager
documented issues with conflicts in the JAI ImageIO component
clarified the default values of HCS keys for fake images in the documentation for Generating test images
corrected external links which failed automatic link checking
5.7.2 (2017 November 21)¶
File format fixes and improvements:
Nikon ND2 - fixed a bug which would use the incorrect channel count for small-sized single channel images
- MetaMorph TIFF
changed the reader’s behaviour to populate exposure times for all planes when only a single exposure time is defined
- DeltaVision
improved parsing of the associated log files to add additional key value pairs to global metadata
- EPS (Encapsulated PostScript)
fixed an exception when reading pixel data in cases with embedded TIFF
- GIF
fixed a bug to display the correct data when reading planes out of order
Bug fixes and improvements:
fixed failures with Ant build from a clean Maven repository by updating Maven repositories to use HTTPS rather than HTTP
now using safe version checking for Bio-Formats plugins to prevent a bug with Java 9
updated the JPEG-XR codec to allow either interleaved or non-interleaved data to be returned
Documentation improvements:
added clarification regarding Bio-Formats version requirements for using Java 7 or above
updated download links to latest Bio-Formats release version
updated the link to the most active fork of JAI ImageIO
fixed a number of external broken links
added a Trello link for contributing external developers
added a link to the page Adding format/reader documentation pages to help those contributing to the documentation or supported formats pages
the Bio-Rad Gel page has been updated to add a link to biorad1sc_reader, an external python implementation (thanks to Matthew Clapp)
5.7.1 (2017 September 20)¶
File format fixes and improvements:
- Nikon NIS-Elements ND2
improved parsing of Z position values
- LaVision Imspector
corrected the value of time per FLIM channel
fixed a bug which saw the Z and T dimensions swapped
fixed a divide by zero exception
added a fix for incorrect time-base and number of channels
- TIFF
added support for handling files with a FillOrder of 2 in which the bits in each byte are reversed
improved support for multi-channel ImageJ TIFF files greater than 4GB in size
Performance improvements:
improved TIFF performance by using non-regexp String replacement (thanks to Thushara Wijeratna)
improved TIFF handling of Strings for large metadata (thanks to T. Alexander Popiel)
Documentation improvements:
updated documentation to reference support for ImageJ TIFFs
added links to format options page to user and developer index pages
5.7.0 (2017 September 4)¶
File format fixes and improvements:
- Imaris HDF
fixed resolution problems in which dimensions and resolution order were incorrectly calculated (thanks to Eliana Andreica)
- Nikon NIS-Elements ND2
fixed a bug in offset calculation when native chunk map is being used
- MetaMorph
corrected delta T and position Z values for multi-channel images when channels are split across multiple files
- Amnis FlowSight
better handling of exceptions in isThisType method (thanks to Claire McQuin)
- PicoQuant Bin
better handling of exceptions in isThisType method (thanks to Claire McQuin)
Bug fixes and improvements:
reviewed and corrected URLs throughout the Bio-Formats source code
updated Bio-Formats Macro Extensions list with a missing function
added a new option in Bio-Formats plugins to configure the slice label display using patterns
Documentation improvements:
added new format page for OMERO Pyramid
updated the developer page for Working with whole slide images
added new page for configuring options in Bio-Formats plugins
updated documentation sidebar to enable navigation of previous versions
5.6.0 (2017 August 14)¶
File format fixes and improvements:
- Zeiss CZI
added support for images from Elyra PALM system
prevented a potential infinite loop when a scene with a pyramid is missing
- cellSens VSI
a new option has been added to throw an exception rather than logging a warning if .ets file is missing. The option,
cellsens.fail_on_missing_ets
, can be used via the MetadataOptions API, as a parameter in the command line tools or via the Bio-Formats configuration dialog in ImageJ
- MetaMorph Stack (STK)
fixed an error with HCS style datasets always returning the first plane regardless of the requested index
updated to use stage labels starting with
Scan
to detect when a whole plate is saved in a single .stk filefixed a bug for
ArrayIndexOutOfBoundsException
when an image contains a single Z plane
- Gatan Digital Micrograph
added support for Z stacks and ROIs
fixed several bugs in tag parsing
- PerkinElmer Operetta
ensure TIFF files exist before reading
- JPEG
support added for images with more than
Integer.MAX_VALUE
pixels
Bug fixes and improvements:
- JPEGTileDecoder
class now implements AutoCloseable to prevent resource leaks
- Bio-Formats Plugin
improved performance when using options to concatenate multiple series together
- TiffSaver
made performance improvements to prevent the writing of a new IFD for each tile, resulting in significant file size reductions for images with a large quantity of tiles
Documentation improvements:
updated website and URL links for new OME Website website
added missing Andor SIF to supported formats page
added a new page Working with whole slide images outlining the API support for pyramids/resolutions
fixed broken documentation links for external resources which are no longer available
updated the style of Sphinx documentation
Component architecture changes/decoupling:
decoupled image encoding and decoding routines to the new ome/ome-codecs GitHub repository and consumed as ‘org.openmicroscopy:ome-codecs’ artifact from Maven Central
removed components/forks/jai - decoupled to the new ome/ome-jai GitHub repository and consumed as part of ‘org.openmicroscopy:ome-jai’ artifact from Maven Central
replaced components/formats-api/codecs classes with wrappers around ‘org.openmicroscopy:ome-codecs’
replaced components/formats-bsd/codecs classes with wrappers around ‘org.openmicroscopy:ome-codecs’
Updated build system:
ant now removes the build files of the bundles during ‘clean’ to prevent a mix of dependencies
5.5.3 (2017 July 5)¶
File format fixes and improvements:
- Zeiss CZI
fix to store Bézier ROIs as polygons, using the control points for the set of Bézier curves to form an approximation of the ROI
improved parsing of stage positions in metadata
improved parsing of detector gain values
removed OME-XML validation errors by fixing potential for duplicate detector IDs
removed invalid XML failures for Modulo label elements
time increment metadata now populated on
Pixels
elementfix to deal with consecutive empty planes in a series (thanks to Nicholas Trahearn)
- DICOM
no longer allow core metadata to be modified when determining if files belong to a DICOM dataset
- Nikon NIS-Elements ND2
fixed calculation for scanline padding
- Kodak BIP
stricter file type checking enforced by no longer relying only on the file suffix
- MINC MRI
improved parsing of metadata by correcting units for physical sizes, pixel type and capturing XYZ plane positions in OME-XML
- Bio-Rad Gel
fixed the width of pixel data offset field
- DeltaVision
improved accuracy of format detection checking for input streams
- Andor SIF
fixed support for cropped images by parsing bounding box of the stored image
Documentation improvements:
Olympus cellSens VSI updated to include list of available specifications
5.5.2 (2017 June 15)¶
File format fixes and improvements:
- Olympus FluoView FV1000
fix for
java.lang.ArrayIndexOutOfBoundsException
caused by filter names of “—” (thanks to Stefan Helfrich)refactored channel metadata population and increased usage of
DataTools
utility functions
- Zeiss CZI
fixed detection of Z line scans that caused incorrect dimensions in certain filesets
improved exception handling of truncated/invalid files
- Veeco AFM
fixed reading of tiled images
- Hamamatsu ndpi
prevented potential memory leak by ensuring all
TiffParser
streams are closed
Bug fixes:
- OMEXMLServiceImpl
improved exception handling to deal with potential
java.lang.NullPointerException
when unable to locate OME-XML version while attempting to transform to the latest version
Documentation improvements:
updated documentation to be compatible with the latest version of Sphinx 1.6
fixed the usage/references of the option markup in documentation
fixed the table in the Micro-Manager user page
updated metadata ratings for supported formats
Updated build system:
- OME-Model version bump
the ome-model component has been updated to 5.5.4 which includes improvements to performance, documentation and the C++ model implementation
5.5.1 (2017 May 25)¶
File format improvements:
- CellH5
fix for
HDF5SymbolTableException
when recycling an IFormatReader to reopen another CellH5 filebug fix related to opening of subsets of CellH5 files, namely
openBytes(r, no, x, y, w, h)
for y>0
- Zeiss CZI
fix pyramid resolution indexing for pyramids of different depths
fix for incorrect channel names and colors
- Zeiss AxioVision ZVI
correct parsing of epoch for Zeiss TIFF and Zeiss ZVI
Bug fixes:
- Command line tools
fix for
java.lang. NegativeArraySizeException
caused by incorrect dimensions when using showinf via command line with options set to autoscale and crop
- Format tools
fix for
java.lang. IndexOutOfBoundsException
when usinggetFilename
with an image containing multiple samples per pixel channels and a single effective channel
Updated build system:
- Autogen jobs
fix for
gen-meta-support
to locate availableorg.openmicroscopy:ome-xml
sources from the Maven repository following the decoupling of the model components
- FileHandleTest
exclude JHDF5 native libraries from
FileHandleTest
to enable CellH5 files to be included in daily tests
Documentation improvements:
added a new example file for reading and writing of XZ and YZ orthogonal planes
5.5.0 (2017 May 8)¶
New file formats:
- Olympus OIR
added support for Olympus .oir data (funded by a partnership between Glencoe Software and OLYMPUS EUROPA SE & Co. KG)
- PerkinElmer Columbus
added support for PerkinElmer Columbus data
File format improvements:
- Andor Bio-Imaging Division (ABD) TIFF
fixed acquisition date format from
MM/dd/yyyy
todd/MM/yyyy
- Nikon NIS-Elements ND2
corrected logic used to determined
PixelType
by parsing uiBpc tags
- Hamamatsu ndpi
improved handling of channels in NDPIS datasets (thanks to Manuel Stritt)
- Imspector OBF
fix for
SAXParseException
when description field in metadata is empty
Documentation improvements:
added links to public sample files for Cellomics
added links to public sample files for InCell 3000
5.4.1 (2017 April 13)¶
File format improvements:
- MIAS (Maia Scientific)
added a fix for a possible exception when image files are not found under channel-specific subdirectories
- BD Pathway
added fix to check if
Experiment.exp
is a directory or an experiment file
- Imspector OBF
enabled forward compatibility for future versions, as the OBF format is backwards compatible (thanks to Bjoern Thiel)
Documentation improvements:
updated external homepage link for FocalPoint
removed Imago from list of visualization and analysis applications as it is no longer available from the Mayachitra website
added links to public sample files for Hamamatsu NDPI and Hamamatsu VMS
listed OpenSlide as available software for supported formats
added a new developer page detailing in-memory reading and writing
updated the Bio-Formats API versioning policy, which now follows strict semantic versioning
a new options page has been added, detailing the usage of configurable format-specific options for readers and writers. Links to the available options are also included under the relevant supported formats
5.4.0 (2017 March 21)¶
File format improvements:
- DICOM
added support for DICOMDIR files, which allow multiple DICOM files in a single directory to be opened as a single dataset
plane position values for values X, Y and Z are now being set in OME-XML
correctly read the physical size X and Y values based on the available specification
- Nikon NIS-Elements ND2
performance improvements based on reading chunkmap. Processing of the chunkmap can be disabled via the MetadataOptions API using the boolean option
nativend2.chunkmap
. For ImageJ users this option can be accessed via a checkbox in the Nikon ND2 section of the Bio-Formats configuration dialog (thanks to Christian Sachs)
- OME-TIFF
added an option to save an OME-TIFF dataset as a binary TIFF and companion XML. This can be used via the bfconvert command line tool by setting the value of option
ometiff.companion
to the name of the companion file to use. For examplebfconvert -option ometiff.companion outputFile.companion.ome inputFile.tiff outputFile.ome.tiff
- CellVoyager
metadata fixes specifically the naming of plates. Additional refactoring of the reader for general maintainability
- Gatan Digital Micrograph
previously missing Image-Instrument reference has been added to OME-XML
- TiffSaver
ensure open resources are closed under all possible scenarios
- Zeiss CZI
improved performance of large uncompressed images. When tiles from a large uncompressed image with no internal tiling are requested, only the specific tile specified in the call to
openBytes
is read from disk, instead of the entire image being read and then copied
- Zeiss AxioVision ZVI (Zeiss Vision Image)
ensure that the
bitsPerPixel
field is always set to match the final pixel type, and populate any channel colors that were parsed in the metadata. The bits per pixel update should only affectuint16
orint16
files where the acquisition bit depth is not a multiple of 8, and the RGB channel count is greater than 1
Updated build system:
updated dependency for NetCDF to 4.3.22
updated copyright headers from 2016 to 2017 and reviewed and fixed any incorrect header descriptions
documentation has been migrated to use
.rst
file format for Sphinx filesreviewed and cleaned up warnings such as unused variables and imports
added CellVoyager datasets to automated testing via continuous integration
unified the semantics for creating temporary directories within unit tests
Documentation improvements:
fixed link for PerkinElmer UltraVIEW system
fixed links for NIfTI public specification and data sets
available software for Hamamatsu ndpi has been updated from NDP.view to NDP.view2
5.3.4 (2017 February 21)¶
Bug fixes:
- ImageJ
fix for a NullPointerException when exporting images that were not opened via the Bio-Formats importer, and thus do not have a complete OMEXMLMetadata store
- Java 1.9
fix compile and runtime errors to enable building with Java 1.9
- ECAT7
update to add support for different versions of ECAT7 files (thanks to Torsten Stöter)
Updated build system:
updated dependency for ome-model in the POM to version 5.4.0. This allows for improved ROI handling by enabling support for Shape objects with Transform attributes. OME-XML schema version remains unchanged as OME schema 2016-06
Documentation improvements:
new public sample files added for ECAT7 (thanks to Torsten Stöter)
new public sample files added for Leica LIF (thanks to Michael Goelzer)
new specification document (Version 3.2) for Leica LIF
updated links to OMERO documentation as a result of decoupling
5.3.3 (2017 February 2)¶
Bug fixes:
- ImageJ
fix for issue when exporting from an ImagePlus that represents signed data. The pixel type will now remain unchanged as will the pixel values which had previously been scaled incorrectly
- Command line tools
fix for
java.lang.IllegalArgumentException
when using bfconvert via command line with option set to only convert a single time-point, channel or Z section
- Tiff writing
using TiffWriter to write tiled images now supports the writing of BigTIFF datasets
File format fixes:
- Applied Precision CellWorX
fix to now display the correct plate name and dimensions
- NIFTI
a few fixes for problems with byte alignment when reading non-core metadata from NIFTI headers
- Leica LIF
added support for timestamps of LIF files created with LAS AF 3.1 or newer. In the case of a halted acquisition only non-null timestamps are stored in the OME metadata (thanks to Michael Goelzer)
the physical pixel height and width were incorrectly calculated by dividing by the number of pixels. This has now been corrected to match the official Leica LIF specification documents by dividing by the number of pixels minus one (thanks to Michael Goelzer)
for backwards compatibility an option to preserve pre-5.3.3 physical sizes has been added. This can be set either via command line tools, through the API with the
loci.formats.in.DynamicMetadataOptions
class, or in the Bio-Formats plugin configuration in ImageJ
- Improvision TIFF
channel colors are now being read and if present set correctly in image metadata
- MetaMorph
fix for
java.lang.OutOfMemoryError
exceptions when reading large Metamorph TIFF plates
Updated build system:
version history file added to MATLAB bundle as NEWS.rst
increased TiffWriter test coverage
added test coverage framework for command line tools including new ImageConverterTest
Documentation improvements:
improved documentation and new examples for using tiled writing
updated developer documentation for use of Bio-Formats as a Maven, Gradle or Ivy dependency
documentation for Leica LIF bug fixes and use of backward compatibility options
fixes for a number of broken links
5.3.2 (2017 January 9)¶
Bug fixes:
- ImageJ
fixed race condition when opening multiple series from a dataset, as introduced by thumbnail loading changes in 5.3.0
updated thumbnail generation to be faster for datasets containing an image pyramid
- Metamorph
updated to read the refractive index and set
RefractiveIndex
onObjectiveSettings
in the generated OME-XML (thanks to Marc Bruce)
- Metamorph TIFF
fixed Z and channel dimension counts when each channel has a unique Z position
updated to read the emission wavelength and set
EmissionWavelength
onLightSourceSettings
in the generated OME-XML
- QuickTime
fixed incorrect image data when reading of tiles from single channel files
- file grouping
fixed handling of
loci.formats.in.MetadataOptions
objects by theloci.formats.FileStitcher
reader
Documentation improvements:
fixed extensions listed for Zeiss TIFF
simplified markdown for creating tables
5.3.1 (2016 December 19)¶
File format fixes:
- TIFF
fixed invalid IFD values when writing TIFF or OME-TIFF files with Bio-Formats 5.3.0. This bug affected the writing of TIFF and OME-TIFF via client code using
loci.formats.TiffWriter
, converting to a TIFF or OME-TIFF using ‘bfconvert’ command line tool or exporting to TIFF or OME-TIFF using ImageJ/FIJI Bio-Formats exporter.
5.3.0 (2016 December 12)¶
New features/API:
added support for JPEG-XR compressed CZI data (funded by a partnership between Glencoe Software and ZEISS), adding ‘ome:jxrlib’ as a new dependency of Bio-Formats
- improved tile-based image writing
added new methods to the
loci.formats.IFormatWriter
interface allowing to set and retrieve the tile along the X and Y dimensionsadded default implementations to the
loci.formats.FormatWriter
abstract class defaulting to the entire image width/heightadded functionality to
loci.formats.TiffWriter
adding support for tiled images writing for TIFF and derived formats like OME-TIFFadded developer documentation and samples for tiled reading/writing
added a new
MetadataOptions
implementation supporting arbitrary key/value pairsupdated the display command line utility to support passing key/value options using
showinf -option
added two options to the CZI reader to disable autostitching and exclude pyramid file attachments. Added new checkboxes to the CZI configuration interface of the ImageJ plugin to activate these options
Bug fixes/deprecations:
deprecated
loci.formats.meta.MetadataConverter
in favor ofome.xml.meta.MetadataConverter
updated method deprecated in Octave 4.2.0 (thanks to Carnë Draug)
- OME-XML
fixed handling of Mask BinData elements
Component architecture changes/decoupling:
removed formats-common component - now decoupled to the new ome/ome-common-java GitHub repository and consumed as ‘org.openmicroscopy:ome-common’ artifact from Maven Central
removed ome-poi component - now decoupled to the new ome/ome-poi GitHub repository and consumed as ‘org.openmicroscopy:ome-poi’ artifact from Maven Central
removed specification, xsd-fu and ome-xml components - now decoupled to the new ome/ome-model GitHub repository and consumed as ‘org.openmicroscopy:{specification,ome-xml}’ artifacts from Maven Central
removed mdbtools component - now decoupled to the new ome/ome-mdbtools GitHub repository and consumed as ‘org.openmicroscopy:ome-mdbtools’ artifact from Maven Central
removed stubs components - now decoupled to the new ome/ome-stubs GitHub repository and consumed as ‘org.openmicroscopy:{lwf-stubs,mipav-stubs}’ artifacts from Maven Central
removed metakit component - now decoupled to the new ome/ome-metakit GitHub repository and consumed as ‘org.openmicroscopy:metakit’ artifacts from Maven Central
updated developer documentation for the decoupled components
Updated build system:
dropped embedded JARs and now use the Maven Ant Tasks plugin to unify the dependencies using the POM
improved Ant JAR and bundle target
dropped deprecated osgi targets, OME Tools bundle and ome-jxr component
removed PDF generation from the docs-sphinx target
added version number to Javadoc zip bundle name
migrated unit tests out of test-suite into formats-bsd
fixed test-suite targets, paths and symlink handling
fixed test-metadata and migrated it into test-suite
fixed mismatch between
ND2HandlerTest
package and locationcleaned up test-build to remove obsolete and decoupled components and folders
simplified Travis build
POM repositories clean-up to reduce complexity and use Maven Central as the first location to look for dependencies
now storing all versions in the top-level POM
updated build versioning from Maven by unified versioning strategy, reviewing meta information stored in the manifests of each JAR and introspecting this information in the
FormatTools
API to retrieve version and revision numbersupdated developer documentation on updated build system
5.2.4 (2016 October 18)¶
Java bug fixes:
- OME-TIFF
fixed regression when populating plane metadata
- CZI
populated series metadata with the scene/position information
5.2.3 (2016 October 5)¶
Java bug fixes:
- CZI
fixed imageCount for RGB images
- ICS writing
fixed ordering of image dimensions
- DeltaVision
fixed reading of large time dimensions
Command-line tools improvements:
bftools.zip
now includes the version history asNEWS.rst
(thanks to Gerhard Burger)
Code clean-up/improvements:
switched to String.indexOf(int) in GPL-licensed reader code so that a simpler library method can be used
strings now extended with characters where possible
completed deprecation of DataTools.sanitizeDouble()
deprecated unused OSGi and ome-tools bundle build targets
OME-XML changes/improvements:
bumped schema version number to 2 (schema namespace left unchanged)
added acquisition modes BrightField, SweptFieldConfocal and SPIM
added parsing for Laser Scan Confocal and Swept Field Confocal
Documentation improvements:
documented versioning policy
clarified supported versions for Micro-Manager and Olympus ScanR files
5.2.2 (2016 September 13)¶
Java bug fixes and improvements:
fixed a regression in which the DataTools number parsing API would not be thread-safe anymore
- InCell
improved handling of Analyzer 2000 datasets to find TIFF files
- FV1000
fixed preview names ordering
- OME-TIFF
enabled all BigTIFF extensions
various code cleanup across the Java code
added test coverage for all example codes in the developer documentations
added tests covering the semantics of the INI parser
ImageJ bug fixes and improvements:
fixed a bug in ImageJ when swapping dimensions of an image with multiple series of different dimensions
added an option to the exporter to pad filename indexes with zeros
Command-line tools improvements:
allowed the binaries to be symlinked (thanks to Gerhard Burger)
added an option to bfconvert to pad filename indexes with zeros
5.2.1 (2016 August 25)¶
Java bug fixes:
- Zeiss CZI
fixed NumberFormatException when the position object is not null but the values of child are null
- SimplePCI
made IniParser less stringent to allow reading of imperfectly formatted TIFF description headers
fixed stitching of file patterns in ImageJ to remove duplication of directory names in the file path
added an option to bfconvert to allow creation of OME-TIFF without lookup tables
addition of MetadataOnly elements containing no BinData or TiffData now handled via MetadataTools API in ImageInfo
example code in developer docs is now tested via a new Maven module
5.2.0 (2016 August 18)¶
Java format support improvements are listed below.
†Denotes a major breaking change to the reader (typically modification of core metadata). Code changes or re-import may be necessary in ImageJ/FIJI and OMERO.
added support (and public sample files) for Becker & Hickl .spc FIFO data
added support for Princeton Instruments .spe data
- bug fixes for many formats including:
- CellSens VSI†
fixes for correctly reading dimensions
- FlowSight
fixes to infer channel count from channel names (thanks to Lee Kamentsky)
- Hamamatsu VMS†
fixed dimensions of full-resolution images
- ICS writing
fixed dimension population for split files
- Kodak BIP
fixed handling of CCD temperature stored in hexadecimal
- Leica LIF
fixed incorrect plane offsets for large multi-tile files
- LiFlim
fixed
ExposureTime
check and units usage
- Micro-Manager
fixed handling of large datasets saved as image stacks and split over multiple files
added user documentation for file saving options
- MRC and Spider
fixed format type checking
- Nifti
fixed
planeSize
to prevent crashes when loading large files (thanks to Christian Niedworok)added support for gzipped compressed .nii.gz files (thanks to Eric Barnhill)
added public samples and updated documented supported file extensions
- OME-TIFF
fixed
Plane
population errorsfixed
NullPointerException
when closing reader for partial multi-file filesetsreduced buffer size for
RandomAccessInputStreams
to improve performancedeprecated
getMetadataStoreForConversion
andgetMetadataStoreForDisplay
methods
- OME-XML
fixed metadata store
- PicoQuant
updated reader to always buffer data
PNG writing
- SDT
performance improvements for loading of large files
- Slidebook
Slidebook6Reader is now completely external and fully maintained by 3i (see http://www.openmicroscopy.org/info/slidebook) and is specified as such in the
readers.txt
configuration file
- SVS
fixed
NumberFormatException
- Tiff
fixed integer overflow to read resolutions correctly
fixed handling of tiled images with tile width less than 64
- Zeiss CZI
fixed timestamp indexing when multiple separate channels are present
improved slide support - slides are now detected as a complete full-resolution image (instead of each tile being a separate series) and pyramid sub-resolutions and label/overview images are also detected
- Zeiss LSM
fixed
Plane
population errors
- Zeiss ZVI†
reworked image ordering calculation to allow for tiles
Top-level Bio-Formats API changes:
Java 1.7 is now the minimum supported version
the native-lib-loader dependency has been bumped to version 2.1.4
the xalan dependency has been bumped to version 2.7.2
all the ome.jxr classes have been deprecated to make clear that there is no JPEG-XR support implemented in Bio-Formats as yet
- the DataTools API has been extended to add a number of utility functions to:
account for decimal separators in different locales
parse a
String
intoDouble
,Float
,Integer
etchandle
NumberFormatException
thrown when parsing Unit tests
the Logging API has been updated to respect logging frameworks (log4j/logback) initialized via a binding-specific configuration file and to prevent
DebugTools.enableLogging(String)
from overriding initialized logger levels (see Logging for more information)helper methods have been added to FormatTools allowing a stage position to be formatted from an input
Double
and an input unitthe Formats API has also been updated to add a new validate property to
MetadataOptions
and support forMetadataOptions
has been moved to FormatHandler level to allow it to be used by both Readers and Writersinitial work on Reader discoverability extended the ClassList API to allow the
readers.txt
configuration file to be annotated using key/value pairs to mark optional Readers and specify additional per-Reader options
Other general improvements include:
improved performance of
getUsedFiles
fixes for
FilePatternBlock
,AxisGuesser
,FilePattern
fixes for the detection of CSV pattern blocks by
FilePatternBlock
bioformats_package.jar
now includes bio-formats-tools as a dependency soImageConverter
,ImageFaker
andImageInfo
classes are included in the bundlethe JACE C++ implementation has been decoupled as it does not function with Java 1.8 (see legacy repo)
- ImageJ fixes
to allow reader delegation when a legacy reader is enabled but not working
to allow ROIs to be imported to the ImageJ ROI manager or added to a new overlay
- MATLAB fixes
improved integration with Octave (thanks to Carnë Draug)
added logging initialization
- Command-line tools fixes
upgrade check no longer run when passing -version
common methods refactoring
showinf improvements to preload format
tiffcomment now warns that it requires an ImageDescription tag to be present in the TIFF file
added many automated tests and improved FakeReader testing framework
- documentation improvements include:
clarifying status of legacy Quicktime and ND2 readers
noting that the Gatan reader does not currently support stacks
more Java examples added to the developer documentation
new units page for developers
The Data Model version 2016-06 has been released to introduce Folders, and to simplify both the graphical aspects of the model and code generation. Full details are available in the OME Model and Formats Documentation. OME-XML changes include:
Map is now a complexType rather than an element and MapPairs has been dropped
extended enum metadata has been introduced to better support units
Shape and LightSource are now complexTypes rather than elements
BinData has been added to code generation to handle raw binary data
- various code generation improvements to:
simplify and standardize the generation process
remove a number of hard-coded exceptional cases allowing for easier maintenance and growth
allow for genuine abstract model types and enable C++ model implementation
updated OME-XML and OME-TIFF public sample files
The Bio-Formats C++ native implementation has been decoupled from the Java codebase and will be released as OME-Files C++ from now on, with the exception of OME-XML which is still within Bio-Formats at present (there is a plan to decouple both the Java and the C++ versions of OME-XML in future).
The following components have had their licensing updated to Simplified (2-clause) BSD:
XSL transforms
specification code
xsd-fu Python code
5.1.10 (2016 May 9)¶
Java bug fixes:
fixed warnings being thrown for ImageJ and other non-FIJI users on Windows (these warnings were triggered by the removal of the 3i Slidebook DLLs from the source code repository in Bio-Formats 5.1.9 and should now only be triggered when opening Slidebook files without the update site enabled - http://www.openmicroscopy.org/info/slidebook)
a fix in the ImageJ plugin for files grouped using the “Dimensions” option
a fix for writing TIFF files in tiles
5.1.9 (2016 April 14)¶
- Java bug fixes, including:
- SDT
fixed width padding calculation for single-pixel image
- Deltavision
fixed the parsing of the new date format
added support for parsing and storing the working distance in native units
- Micromanager
cleaned up JSON metadata parsing
- Olympus Fluoview
fixed null pointer exceptions while parsing metadata
- Leica LIF
fixed large multi-tiled files from having incorrect plane offsets after the 2GB mark
- EM formats (MRC and Spider)
added native length support for EM readers
- Gatan
fixed erroneous metadata parsing
added support for parsing and storing the physical sizes in native units
- OME-TIFF
improved handling of OME-TIFF multi-file fileset’s with partial metadata blocks
- Nikon ND2
fixed the parsing of emission wavelength
- Olympus CellR (APL)
fixed multiple parsing issues with the mtb file
- SlideBook
removed slidebook dlls from Bio-Formats repository
- Zeiss CZI
fixed parsing of files with multiple mosaics and positions
- Documentation updates, including:
improved documentation for the export of BigTIFFs in ImageJ
- C++:
no changes.
5.1.8 (2016 February 15)¶
- Java bug fixes, including:
- FEI TIFF
fixed stage position parsing and whitespace handling (thanks to Antoine Vandecreme)
- Pyramid TIFF
fixed tile reading when a cache (.bfmemo) file is present
- MicroManager
updated to parse JSON data from tags 50839 and 51123
fixed to detect
*_metadata.txt
files in addition tometadata.txt
filesfixed to handle datasets with each stack in a single file
- OME-XML
updated to make .ome.xml an official extension
- OME-TIFF
fixed to ignore invalid BinaryOnly elements
- TIFF
fixed caching of BigTIFF files
- Slidebook
fixed handling of montages in Slidebook6Reader (thanks to Richard Myers)
Performance improvement for writing files to disk (thanks to Stephane Dallongeville)
- Build system
fixed Maven POMs to reduce calls to artifacts.openmicroscopy.org
fixed bioformats_package.jar to include the loci.formats.tools package
- Documentation updates, including:
updated format pages to include links to example data
clarified description of Qu for MATLAB (thanks to Carnë Draug)
added installation instructions for Octave (thanks to Carnë Draug)
- C++:
Bugfixes to the OME-TIFF writer to correct use of the metadata store with multiple series
Ensure file and writer state consistency upon close failure
5.1.7 (2015 December 7)¶
- Java bug fixes, including:
Prevent physical pixel sizes from being rounded to 0, for all formats
- Metamorph
fixed calculation of Z step size
fixed detection of post-processed dual camera acquisitions (thanks to Mark Kittisopikul)
- OME-XML
fixed XML validation when an ‘xmlns’ value is not present (thanks to Bjoern Thiel)
- MINC
fixed endianness of image data
- Andor/Fluoview TIFF
fixed calculation of Z step size
- MATLAB
improved performance by reducing static classpath checks (thanks to Mark Kittisopikul)
- Gatan
fixed physical size parsing in non-English locales
- Automated testing
fixed handling of non-default physical size and plane position units
- Documentation updates, including:
updated MapAnnotation example to show linkage of annotations to images
- C++:
no changes, released to keep version numbers in sync with Bio-Formats Java
5.1.6 (2015 November 16)¶
- Java bug fixes, including:
- Updated to use native units for following formats:
IMOD
Analyze
Unisoku
Olympus CellR (APL)
- Metamorph TIFF
fixed handling of multi-line descriptions
added support for dual camera acquisitions
- Zeiss LMS
fixed exception in type detection
- Zeiss CZI
fixed detection of line scan Airyscan data
- Slidebook
fixed calculation of physical Z size
- ImageJ plugins
fixed handling of non-default units
fixed setting of preferences via macros
- Automated testing
fixed handling of non-default units for physical sizes and timings
- C++ changes, including:
allow relocatable installation on Windows
reduce time required for debug builds
- Documentation updates, including:
addition of “Multiple Images” column to the supported formats table
addition of a MapAnnotation example
5.1.5 (2015 October 12)¶
- Java bug fixes, including:
- ImageJ plugins
fixed use of “Group files…” and “Open files individually” options
fixed placement of ROIs
fixed size of the “About Plugins > Bio-Formats Plugins” window
- xsd-fu (code generation)
removed OMERO-specific logic
- Metamorph
fixed physical Z size calculation
- Gatan DM3/DM4
fixed physical pixel size parsing
- BMP
added support for RLE compression
- DICOM
updated to respect the WINDOW_CENTER tag
fixed image dimensions when multiple sets of width and height values are present
- Fluoview and Andor TIFF
fixed physical Z size calculation
- Imspector OBF
updated to parse OME-XML metadata (thanks to Bjoern Thiel)
- C++ changes:
TIFF strip/tile row and column calulations corrected to compute the correct row and column count
Several compiler warnings removed (false positive warnings in third-party headers disabled, and additional warnings fixed)
It is now possible to build with Boost 1.59 and compile with a C++14 compiler
The source release is now provided in both tar.xz and zip formats
- Documentation updates, including:
- substantial updates to the format pages
improved linking of reader/writer classes to each format page
improved supported metadata pages for each format
updated format page formatting for clarity
added developer documentation for adding and modifying format pages
5.1.4 (2015 September 7)¶
- Bug fixes, including:
- Command line tools
fixed display of usage information
- Automated testing
fixed problems with symlinked data on Windows
added unit tests for checking physical pixel size creation
- Cellomics
fixed reading of sparse plates
- SlideBook
fixed a few lingering issues with native library packaging
- SimplePCI/HCImage TIFF
fixed bit depth parsing for files from newer versions of HCImage
- SimplePCI/HCImage .cxd
fixed image dimensions to allow for extra padding bytes
- Leica LIF
improved reading of image descriptions
- ICS
fixed to use correct units for timestamps and physical pixel sizes
- MicroManager
fixed to use correct units for timestamps
- Gatan .dm3/.dm4
fixed problems with reading double-precision metadata values
- Hamamatsu NDPI
fixed reading of mask images
- Leica .lei
fixed reading of bit depth and endianness for datasets that were modified after acquisition
- FEI TIFF
updated to read metadata from files produced by FEI Titan systems
- QuickTime
fixed to handle planes with no stored pixels
- Leica .scn
fixed reading of files that contain fewer images than expected
- Zeiss .czi
fixed channel colors when an alpha value is not recorded
fixed handling of pre-stitched image tiles
- SDT
added support for Zip-compressed images
- Nikon .nd2
fixed to read image dimensions from new non-XML metadata
- OME-XML
fixed writing of integer metadata values
- Native C++ updates:
completed support for building on Windows
- Documentation updates, including:
updated instructions for running automated data tests
clarified JVM versions currently supported
5.1.3 (2015 July 21)¶
- Native C++ updates:
Added cmake superbuild to build core dependencies (zlib, bzip2, png, icu, xerces, boost)
Progress on support for Windows
- Bug fixes, including:
Fixed segfault in the showinf tool used with the C++ bindings
Allow reading from https URLs
- ImageJ
improved performance of displaying ROIs
- Command line tools
fixed bfconvert to correctly create datasets with multiple files
- Metamorph
improved detection of time series
fixed .nd datasets with variable Z and T counts in each channel
fixed .nd datasets that contain invalid TIFF/STK files
fixed dimensions when the number of planes does not match the recorded Z, C, and T sizes
- SlideBook
improved native library detection (thanks to Richard Myers)
- JPEG
fixed decompression of lossless files with multiple channels (thanks to Aaron Avery)
- Imspector OBF
updated to support version 2 files (thanks to Bjoern Thiel)
- Imspector MSR
improved detection of Z stacks
- PerkinElmer Opera Flex
improved handling of multiple acquisitions of the same plate
- Zeiss CZI
fixed error when opening single-file datasets whose names contained “(” and “)”
- TIFF
improved speed of reading files with many tiles
- AVI
updated to read frame index (idx1) tables
- Nikon ND2
fixed channel counts for files with more than 3 channels
- PNG
fixed decoding of interlaced images with a width or height that is not a multiple of 8
- PSD
improved reading of compressed images
- Documentation improvements, including:
updated instructions for writing a new file format reader
updated usage information for command line tools
new Javadocs for the MetadataStore and MetadataRetrieve interfaces
5.1.2 (2015 May 28)¶
Added OME-TIFF writing support to the native C++ implementation
OME-TIFF export: switch to BigTIFF if .ome.tf2, .ome.tf8, or .ome.btf extensions are used
Improved MATLAB developer documentation
Added SlideBook reader that uses the SDK from 3I (thanks to Richard Myers and 3I - Intelligent Imaging Innovations)
Preliminary work to make MATLAB toolbox work with Octave
- Many bug fixes, including:
- ImageJ
fixed regression in getPlanePosition* macro extension methods
fixed display of composite color virtual stacks
- Nikon ND2
improved parsing of plane position and timestamp data
- TIFF
reduced memory required to read color lookup tables
- Zeiss LSM
improved parsing of 16-bit color lookup tables
- Zeiss CZI
fixed ordering of original metadata table
fixed reading of large pre-stitched tiled images
- AIM
fixed handling of truncated files
- Metamorph/MetaXpress TIFF
improved UIC1 metadata tag parsing
5.1.1 (2015 April 28)¶
Add TIFF writing support to the native C++ implementation
Fixed remaining functional differences between Windows and Mac/Linux
Improved performance of ImageJ plugin when working with ROIs
TIFF export: switch to BigTIFF if .tf2, .tf8, or .btf extensions are used
- Many bug fixes, including:
fixed upgrade checking to more accurately report when a new version is available
- Zeiss CZI
fixed ordering of multiposition data
improved support for RGB and fused images
- Nikon ND2
improved ordering of multiposition data
- Leica LIF
improved metadata validity checks
improved excitation wavelength detection
- Metamorph STK/TIFF
record lens numerical aperture
fixed millisecond values in timestamps
- Gatan DM3
correctly detect signed pixel data
- Imaris HDF
fix channel count detection
- ICS export
fix writing of files larger than 2GB
5.1.0 (2015 April 2)¶
Improvements to performance with network file systems
Improvements to developer documentation
Initial version of native C++ implementation
Improved support for opening and saving ROI data with ImageJ
Added support for CellH5 data (thanks to Christoph Sommer)
Added support for Perkin Elmer Nuance data (thanks to Lee Kamentsky)
Added support for Amnis FlowSight data (thanks to Lee Kamentsky and Sebastien Simard)
Added support for Veeco AFM data
Added support for Zeiss .lms data (not to be confused with .lsm)
Added support for I2I data
Added support for writing Vaa3D data (thanks to Brian Long)
Updated to OME schema 2015-01
Update RandomAccessInputStream and RandomAccessOutputStream to read and write bits
- Many bug fixes, including:
- Leica SCN
fix pixel data decompression
fix handling of files with multiple channels
parse magnification and physical pixel size data
- Olympus/CellSens .vsi
more thorough parsing of metadata
improved reading of thumbnails and multi-resolution images
- NDPI
fix reading of files larger than 4GB
parse magnification data
- Zeiss CZI
improve parsing of plane position coordinates
- Inveon
fix reading of files larger than 2 GB
- Nikon ND2
many improvements to dimension detection
many improvements to metadata parsing accuracy
update original metadata table to include PFS data
- Gatan DM3
fix encoding when parsing metadata
fix physical pixel size parsing
- Metamorph
fix off-by-one in metadata parsing
fix number parsing to be independent of the system locale
- JPEG
parse EXIF data, if present (thanks to Paul Van Schayck)
- OME-XML/OME-TIFF
fix handling of missing image data
- PrairieView
improved support for version 5.2 data (thanks to Curtis Rueden)
- DICOM
fix dimensions for multi-file datasets
fix pixel data decoding for files with multiple images
- PNG
reduce memory required to read large images
- Imspector OBF
fix support for version 5 data (thanks to Bjoern Thiel)
- PCORAW
fix reading of files larger than 4 GB
- AIM
fix reading of files larger than 4 GB
- MRC
add support for signed 8-bit data
Fix build errors in MIPAV plugin
- ImageJ
fix export from a script/macro
fix windowless export
allow exporting from any open image window
allow the “Group files with similar names” and “Swap dimensions” options to be used from a script/macro
- bfconvert
fix writing each channel, Z section, and/or timepoint to a separate file
add options for configuring the tile size to be used when saving images
5.0.8 (2015 February 10)¶
No changes - release to keep version numbers in sync with OMERO
5.0.7 (2015 February 5)¶
- Several bug fixes, including:
ND filter parsing for DeltaVision
Timepoint count and original metadata parsing for Metamorph
Build issues when Genshi or Git are missing
LZW image decoding
5.0.6 (2014 November 11)¶
- Several bug fixes, including:
Pixel sign for DICOM images
Image dimensions for Zeiss CZI and Nikon ND2
Support for Leica LIF files produced by LAS AF 4.0 and later
5.0.5 (2014 September 23)¶
Documentation improvements
Support for non-spectral Prairie 5.2 datasets
5.0.4 (2014 September 3)¶
Fix compile and runtime errors under Java 1.8
Improvements to Nikon .nd2 metadata parsing
Added support for PicoQuant .bin files (thanks to Ian Munro)
5.0.3 (2014 August 7)¶
Many bug fixes for Nikon .nd2 files
- Several other bug fixes, including:
LZW image decoding
Stage position parsing for Zeiss CZI
Exposure time units for ScanR
Physical pixel size units for DICOM
NDPI and Zeiss LSM files larger than 4GB
Z and T dimensions for InCell 6000 plates
Export of RGB images in ImageJ
Improved metadata saving in MATLAB functions
5.0.2 (2014 May 28)¶
Many bug fixes for Zeiss .czi files
- Several other bug fixes, including:
Gatan .dm3 units and step count parsing
Imspector .msr 5D image support
DICOM reading of nested tags
Update native-lib-loader version (to 2.0.1)
Updates and improvements to user documentation
5.0.1 (2014 Apr 7)¶
Added image pyramid support for CellSens .vsi data
- Several bug fixes, including:
Woolz import into OMERO
Cellomics file name parsing (thanks to Lee Kamentsky)
Olympus FV1000 timestamp support (thanks to Lewis Kraft and Patrick Riley)
(A)PNG large image support
Zeiss .czi dimension detection for SPIM datasets
Performance improvements for Becker & Hickl .sdt file reading (thanks to Ian Munro)
Performance improvements to directory listing over NFS
Update slf4j and logback versions (to 1.7.6 and 1.1.1 respectively)
Update jgoodies-forms version (to 1.7.2)
5.0.0 (2014 Feb 25)¶
New bundled ‘bioformats_package.jar’ for ImageJ
Now uses logback as the slf4j binding by default
Updated component names, .jar file names, and Maven artifact names
Fixed support for Becker & Hickl .sdt files with multiple blocks
Fixed tiling support for TIFF, Hamamatsu .ndpi, JPEG, and Zeiss .czi files
Improved continuous integration testing
Updated command line documentation
5.0.0-RC1 (2013 Dec 19)¶
Updated Maven build system and launched new Artifactory repository (http://artifacts.openmicroscopy.org)
- Added support for:
Yokogawa CellVoyager (thanks to Jean-Yves Tinevez)
Woolz (thanks to Bill Hill)
Added support for populating and parsing ModuloAlong{Z, C, T} annotations for FLIM/SPIM data
Updated netCDF and slf4j version requirements - netCDF 4.3.19 and slf4j 1.7.2 are now required
Updated and improved MATLAB users and developers documentation
Many bug fixes including for Nikon ND2, Zeiss CZI, and CellWorX formats
5.0.0-beta1 (2013 June 20)¶
Updated to 2013-06 OME-XML schema
Improved the performance in tiled formats
Added caching of Reader metadata using https://github.com/EsotericSoftware/kryo
- Added support for:
- Many bug fixes, including:
Add ZEN 2012/Lightsheet support to Zeiss CZI
Improved testing of autogenerated code
Moved OME-XML specification into Bio-Formats repository
4.4.10 (2014 Jan 15)¶
Bug fixes including CellWorx, Metamorph and Zeiss CZI
Updates to MATLAB documentation
4.4.9 (2013 Oct 16)¶
Many bug fixes including improvements to support for ND2 format
Java 1.6 is now the minimum supported version; Java 1.5 is no longer supported
4.4.8 (2013 May 2)¶
No changes - release to keep version numbers in sync with OMERO
4.4.7 (2013 April 25)¶
Many bug fixes to improve support for more than 20 formats
Improved export to multi-file datasets
Now uses slf4j for logging rather than using log4j directly, enabling other logging implementations to be used, for example when Bio-Formats is used as a component in other software using a different logging system.
4.4.6 (2013 February 11)¶
Many bug fixes
Further documentation improvements
4.4.5 (2012 November 13)¶
Restructured and improved documentation
- Many bug fixes, including:
File grouping in many multi-file formats
Maven build fixes
ITK plugin fixes
4.4.4 (2012 September 24)¶
Many bug fixes
4.4.2 (2012 August 22)¶
Security fix for OMERO plugins for ImageJ
4.4.1 (2012 July 20)¶
Fix a bug that prevented BigTIFF files from being read
Fix a bug that prevented PerkinElmer .flex files from importing into OMERO
4.4.0 (2012 July 13)¶
Many, many bug fixes
- Added support for:
.nd2 files from Nikon Elements version 4
PerkinElmer Operetta data
MJPEG-compressed AVIs
MicroManager datasets with multiple positions
Zeiss CZI data
IMOD data
4.3.3 (2011 October 18)¶
- Many bug fixes, including:
Speed improvements to HCImage/SimplePCI and Zeiss ZVI files
Reduce memory required by Leica LIF reader
More accurately populate metadata for Prairie TIFF datasets
Various fixes to improve the security of the OMERO plugin for ImageJ
Better dimension detection for Bruker MRI datasets
Better thumbnail generation for histology (SVS, NDPI) datasets
Fix stage position parsing for Metamorph TIFF datasets
Correctly populate the channel name for PerkinElmer Flex files
4.3.2 (2011 September 15)¶
- Many bug fixes, including:
Better support for Volocity datasets that contain compressed data
More accurate parsing of ICS metadata
More accurate parsing of cellSens .vsi files
- Added support for a few new formats
.inr
Canon DNG
Hitachi S-4800
Kodak .bip
JPX
Volocity Library Clipping (.acff)
Bruker MRI
Updated Zeiss LSM reader to parse application tags
Various performance improvements, particularly for reading/writing TIFFs
Updated OMERO ImageJ plugin to work with OMERO 4.3.x
4.3.1 (2011 July 8)¶
- Several bug fixes, including:
Fixes for multi-position DeltaVision files
Fixes for MicroManager 1.4 data
Fixes for 12 and 14-bit JPEG-2000 data
Various fixes for reading Volocity .mvd2 datasets
Added various options to the ‘showinf’ and ‘bfconvert’ command line tools
Added better tests for OME-XML backwards compatibility
Added the ability to roughly stitch tiles in a multi-position dataset
4.3.0 (2011 June 14)¶
- Many bug fixes, including:
Many fixes for reading and writing sub-images
Fixes for stage position parsing in the Zeiss formats
File type detection fixes
Updated JPEG-2000 reading and writing support to be more flexible
- Added support for 9 new formats:
InCell 3000
Trestle
Hamamatsu .ndpi
Hamamatsu VMS
SPIDER
Volocity .mvd2
Olympus SIS TIFF
IMAGIC
cellSens VSI
Updated to 2011-06 OME-XML schema
Minor speed improvements in many formats
Switched version control system from SVN to Git
Moved all Trac tickets into the OME Trac: https://trac.openmicroscopy.org
Improvements to testing frameworks
Added Maven build system as an alternative to the existing Ant build system
Added pre-compiled C++ bindings to the download page
4.2.2 (2010 December 6)¶
- Several bug fixes, notably:
Metadata parsing fixes for Zeiss LSM, Metamorph STK, and FV1000
Prevented leaked file handles when exporting to TIFF/OME-TIFF
Fixed how BufferedImages are converted to byte arrays
Proper support for OME-XML XML annotations
Added support for SCANCO Medical .aim files
Minor improvements to ImageJ plugins
Added support for reading JPEG-compressed AVI files
4.2.1 (2010 November 12)¶
Many, many bug fixes
- Added support for 7 new formats:
CellWorX .pnl
ECAT7
Varian FDF
Perkin Elmer Densitometer
FEI TIFF
Compix/SimplePCI TIFF
Nikon Elements TIFF
Updated Zeiss LSM metadata parsing, with generous assistance from Zeiss, FMI, and MPI-CBG
Lots of work to ensure that converted OME-XML validates
Improved file stitching functionality; non-numerical file patterns and limited regular expression-style patterns are now supported
4.2.0 (2010 July 9)¶
Fixed many, many bugs in all aspects of Bio-Formats
Reworked ImageJ plugins to be more user- and developer-friendly
Added many new unit tests
Added support for approximately 25 new file formats, primarily in the SPM domain
Rewrote underlying I/O infrastructure to be thread-safe and based on Java NIO
Rewrote OME-XML parsing/generation layer; OME-XML 2010-06 is now supported
Improved support for exporting large images
Improved support for exporting to multiple files
Updated logging infrastructure to use slf4j and log4j
4.1.1 (2009 December 3)¶
Fixed many bugs in popular file format readers
4.1 (2009 October 21):
Fixed many bugs in most file format readers
Significantly improved confocal and HCS metadata parsing
Improved C++ bindings
Eliminated references to Java AWT classes in core Bio-Formats packages
Added support for reading Flex datasets from multiple servers
Improved OME-XML generation; generated OME-XML is now valid
Added support for Olympus ScanR data
Added OSGi information to JARs
Added support for Amira Mesh files
Added support for LI-FLIM files
Added more informative exceptions
Added support for various types of ICS lifetime data
Added support for Nikon EZ-C1 TIFFs
Added support for Maia Scientific MIAS data
4.0.1 (2009 June 1)¶
Lots of bug fixes in most format readers and writers
Added support for Analyze 7.1 files
Added support for Nifti files
Added support for Cellomics .c01 files
Refactored ImageJ plugins
Bio-Formats, the common package, and the ImageJ plugins now require Java 1.5
Eliminated native library dependency for reading lossless JPEGs
Changed license from GPL v3 or later to GPL v2 or later
Updated Olympus FV1000, Zeiss LSM, Zeiss ZVI and Nikon ND2 readers to parse ROI data
Added option to ImageJ plugin for displaying ROIs parsed from the chosen dataset
Fixed BufferedImage construction for signed data and unsigned int data
4.0.0 (2009 March 3)¶
Improved OME data model population for Olympus FV1000, Nikon ND2, Metamorph STK, Leica LEI, Leica LIF, InCell 1000 and MicroManager
Added TestNG tests for format writers
Added option to ImageJ plugin to specify custom colors when customizing channels
Added ability to upgrade the ImageJ plugin from within ImageJ
Fixed bugs in Nikon ND2, Leica LIF, BioRad PIC, TIFF, PSD, and OME-TIFF
Fixed bugs in Data Browser and Exporter plugins
Added support for Axon Raw Format (ARF), courtesy of Johannes Schindelin
Added preliminary support for IPLab-Mac file format
2008 December 29¶
Improved metadata support for DeltaVision, Zeiss LSM, MicroManager, and Leica LEI
Restructured code base/build system to be component-driven
Added support for JPEG and JPEG-2000 codecs within TIFF, OME-TIFF and OME-XML
Added support for 16-bit compressed Flex files
Added support for writing JPEG-2000 files
Added support for Minolta MRW format
Added support for the 2008-09 release of OME-XML
Removed dependency on JMagick
Re-added caching support to data browser plugin
Updated loci.formats.Codec API to be more user-friendly
Expanded loci.formats.MetadataStore API to better represent the OME-XML model
Improved support for Nikon NEF
Improved support for TillVision files
Improved ImageJ import options dialog
Fixed bugs with Zeiss LSM files larger than 4 GB
Fixed minor bugs in most readers
Fixed bugs with exporting from an Image5D window
Fixed several problems with virtual stacks in ImageJ
2008 August 30¶
Fixed bugs in many file format readers
Fixed several bugs with swapping dimensions
Added support for Olympus CellR/APL files
Added support for MINC MRI files
Added support for Aperio SVS files compressed with JPEG 2000
Added support for writing OME-XML files
Added support for writing APNG files
Added faster LZW codec
Added drag and drop support to ImageJ shortcut window
Re-integrated caching into the data browser plugin
2008 July 1¶
Fixed bugs in most file format readers
Fixed bugs in OME and OMERO download functionality
Fixed bugs in OME server-side import
Improved metadata storage/retrieval when uploading to and downloading from the OME Perl server
Improved Bio-Formats ImageJ macro extensions
Major updates to MetadataStore API
Updated OME-XML generation to use 2008-02 schema by default
Addressed time and memory performance issues in many readers
Changed license from LGPL to GPL
Added support for the FEI file format
Added support for uncompressed Hamamatsu Aquacosmos NAF files
Added support for Animated PNG files
Added several new options to Bio-Formats ImageJ plugin
Added support for writing ICS files
2008 April 17¶
Fixed bugs in Slidebook, ND2, FV1000 OIB/OIF, Perkin Elmer, TIFF, Prairie, Openlab, Zeiss LSM, MNG, Molecular Dynamics GEL, and OME-TIFF
Fixed bugs in OME and OMERO download functionality
Fixed bugs in OME server-side import
Fixed bugs in Data Browser
Added support for downloading from OMERO 2.3 servers
Added configuration plugin
Updates to MetadataStore API
Updates to OME-XML generation - 2007-06 schema used by default
Added support for Li-Cor L2D format
Major updates to TestNG testing framework
Added support for writing multi-series OME-TIFF files
Added support for writing BigTIFF files
2008 Feb 12¶
Fixed bugs in QuickTime, SimplePCI and DICOM
Fixed a bug in channel splitting logic
2008 Feb 8¶
Many critical bugfixes in format readers and ImageJ plugins
- Newly reborn Data Browser for 5D image visualization
some combinations of import options do not work yet
2008 Feb 1¶
Fixed bugs in Zeiss LSM, Metamorph STK, FV1000 OIB/OIF, Leica LEI, TIFF, Zeiss ZVI, ICS, Prairie, Openlab LIFF, Gatan, DICOM, QuickTime
Fixed bug in OME-TIFF writer
Major changes to MetadataStore API
Added support for JPEG-compressed TIFF files
- Added basic support for Aperio SVS files
JPEG2000 compression is still not supported
Improved “crop on import” functionality
Improvements to bfconvert and bfview
Improved OME-XML population for several formats
Added support for JPEG2000-compressed DICOM files
EXIF data is now parsed from TIFF files
2007 Dec 28¶
Fixed bugs in Leica LEI, Leica TCS, SDT, Leica LIF, Visitech, DICOM, Imaris 5.5 (HDF), and Slidebook readers
Better parsing of comments in TIFF files exported from ImageJ
Fixed problem with exporting 48-bit RGB data
Added logic to read multi-series datasets spread across multiple files
Improved channel merging in ImageJ - requires ImageJ 1.39l
Support for hyperstacks and virtual stacks in ImageJ - requires ImageJ 1.39l
Added API for reading directly from a byte array or InputStream
Metadata key/value pairs are now stored in ImageJ’s “Info” property
Improved OMERO download plugin - it is now much faster
Added “open all series” option to ImageJ importer
ND2 reader based on Nikon’s SDK now uses our own native bindings
Fixed metadata saving bug in ImageJ
Added sub-channel labels to ImageJ windows
Major updates to 4D Data Browser
Minor updates to automated testing suite
2007 Dec 1¶
Updated OME plugin for ImageJ to support downloading from OMERO
Fixed bug with floating point TIFFs
Fixed bugs in Visitech, Zeiss LSM, Imaris 5.5 (HDF)
Added alternate ND2 reader that uses Nikon’s native libraries
Fixed calibration and series name settings in importer
Added basic support for InCell 1000 datasets
2007 Nov 21¶
Fixed bugs in ND2, Leica LIF, DICOM, Zeiss ZVI, Zeiss LSM, FV1000 OIB, FV1000 OIF, BMP, Evotec Flex, BioRad PIC, Slidebook, TIFF
Added new ImageJ plugins to slice stacks and do “smart” RGB merging
- Added “windowless” importer plugin
uses import parameters from IJ_Prefs.txt, without prompting the user
Improved stack slicing and colorizing logic in importer plugin
- Added support for DICOM files compressed with lossless JPEG
requires native libraries
Fixed bugs with signed pixel data
Added support for Imaris 5.5 (HDF) files
Added 4 channel merging to importer plugin
Added API methods for reading subimages
Major updates to the 4D Data Browser
2007 Oct 17¶
Critical OME-TIFF bugfixes
Fixed bugs in Leica LIF, Zeiss ZVI, TIFF, DICOM, and AVI readers
Added support for JPEG-compressed ZVI images
Added support for BigTIFF
Added importer plugin option to open each plane in a new window
Added MS Video 1 codec for AVI
2007 Oct 1¶
Added support for compressed DICOM images
Added support for uncompressed LIM files
Added support for Adobe Photoshop PSD files
Fixed bugs in DICOM, OME-TIFF, Leica LIF, Zeiss ZVI, Visitech, PerkinElmer and Metamorph
Improved indexed color support
Addressed several efficiency issues
Fixed how multiple series are handled in 4D data browser
Added option to reorder stacks in importer plugin
Added option to turn off autoscaling in importer plugin
Additional metadata convenience methods
2007 Sept 11¶
Major improvements to ND2 support; lossless compression now supported
Support for indexed color images
Added support for Simple-PCI .cxd files
Command-line OME-XML validation
Bugfixes in most readers, especially Zeiss ZVI, Metamorph, PerkinElmer and Leica LEI
Initial version of Bio-Formats macro extensions for ImageJ
2007 Aug 1¶
Added support for latest version of Leica LIF
Fixed several issues with Leica LIF, Zeiss ZVI
Better metadata mapping for Zeiss ZVI
Added OME-TIFF writer
Added MetadataRetrieve API for retrieving data from a MetadataStore
Miscellaneous bugfixes
2007 July 16¶
Fixed several issues with ImageJ plugins
Better support for Improvision and Leica TCS TIFF files
Minor improvements to Leica LIF, ICS, QuickTime and Zeiss ZVI readers
Added searchable metadata window to ImageJ importer
2007 July 2¶
Fixed issues with ND2, Openlab LIFF and Slidebook
Added support for Visitech XYS
Added composite stack support to ImageJ importer
2007 June 18¶
Fixed issues with ICS, ND2, MicroManager, Leica LEI, and FV1000 OIF
Added support for large (> 2 GB) ND2 files
Added support for new version of ND2
Minor enhancements to ImageJ importer
Implemented more flexible logging
Updated automated testing framework to use TestNG
Added package for caching images produced by Bio-Formats
2007 June 6¶
Fixed OME upload/download bugs
Fixed issues with ND2, EPS, Leica LIF, and OIF
Added support for Khoros XV
Minor improvements to the importer
2007 May 24¶
Better Slidebook support
Added support for Quicktime RPZA
Better Leica LIF metadata parsing
Added support for BioRad PIC companion files
Added support for bzip2-compressed files
Improved ImageJ plugins
Native support for FITS and PGM
2007 May 2¶
Added support for NRRD
Added support for Evotec Flex (requires LuraWave Java SDK with license code)
Added support for gzip-compressed files
Added support for compressed QuickTime headers
Fixed QuickTime Motion JPEG-B support
Fixed some memory issues (repeated small array allocations)
Fixed issues reading large (> 2 GB) files
Removed “ignore color table” logic, and replaced with Leica-specific solution
Added status event reporting to readers
Added API to toggle metadata collection
Support for multiple dimensions rasterized into channels
Deprecated reader and writer methods that accept the ‘id’ parameter
Deprecated IFormatWriter.save in favor of saveImage and saveBytes
Moved dimension swapping and min/max calculation logic to delegates
Separate GUI logic into isolated loci.formats.gui package
Miscellaneous bugfixes and tweaks in most readers and writers
Many other bugfixes and improvements
2007 Mar 16¶
Fixed calibration bugs in importer plugin
Enhanced metadata support for additional formats
Fixed LSM bug
2007 Mar 7¶
Added support for Micro-Manager file format
Fixed several bugs – Leica LIF, Leica LEI, ICS, ND2, and others
Enhanced metadata support for several formats
Load series preview thumbnails in the background
Better implementation of openBytes(String, int, byte[]) for most readers
Expanded unit testing framework
2007 Feb 28¶
Better series preview thumbnails
Fixed bugs with multi-channel Leica LEI
Fixed bugs with “ignore color tables” option in ImageJ plugin
2007 Feb 26¶
Many bugfixes: Leica LEI, ICS, FV1000 OIB, OME-XML and others
Better metadata parsing for BioRad PIC files
Enhanced API for calculating channel minimum and maximum values
Expanded MetadataStore API to include more semantic types
Added thumbnails to series chooser in ImageJ plugin
Fixed plugins that upload and download from an OME server
2007 Feb 7¶
Added plugin for downloading images from OME server
Improved HTTP import functionality
Added metadata filtering – unreadable metadata is no longer shown
Better metadata table for multi-series datasets
Added support for calibration information in Gatan DM3
Eliminated need to install JAI Image I/O Tools to read ND2 files
Fixed ZVI bugs: metadata truncation, and other problems
Fixed bugs in Leica LIF: incorrect calibration, first series labeling
Fixed memory bug in Zeiss LSM
Many bugfixes: PerkinElmer, DeltaVision, Leica LEI, LSM, ND2, and others
IFormatReader.close(boolean) method to close files temporarily
Replaced Compression utility class with extensible Compressor interface
Improved testing framework to use .bioformats configuration files
2007 Jan 5¶
Added support for Prairie TIFF
Fixed bugs in Zeiss LSM, OIB, OIF, and ND2
Improved API for writing files
Added feature to read files over HTTP
Fixed bugs in automated testing framework
Miscellaneous bugfixes
2006 Dec 22¶
Expanded ImageJ plugin to optionally use Image5D or View5D
Improved support for ND2 and JPEG-2000 files
Added automated testing framework
Fixed bugs in Zeiss ZVI reader
Miscellaneous bugfixes
2006 Nov 30¶
Added support for ND2/JPEG-2000
Added support for MRC
Added support for MNG
Improved support for floating-point images
Fixed problem with 2-channel Leica LIF data
Minor tweaks and bugfixes in many readers
Improved file stitching logic
Allow ImageJ plugin to be called from a macro
2006 Nov 2¶
Bugfixes and improvements for Leica LIF, Zeiss LSM, OIF and OIB
Colorize channels when they are split into separate windows
Fixed a bug with 4-channel datasets
2006 Oct 31¶
Added support for Imaris 5 files
Added support for RGB ICS images
2006 Oct 30¶
Added support for tiled TIFFs
Fixed bugs in ICS reader
Fixed importer plugin deadlock on some systems
2006 Oct 27¶
Multi-series support for Slidebook
Added support for Alicona AL3D
Fixed plane ordering issue with FV1000 OIB
Enhanced dimension detection in FV1000 OIF
Added preliminary support for reading NEF images
Added option to ignore color tables
Fixed ImageJ GUI problems
Fixed spatial calibration problem in ImageJ
Fixed some lingering bugs in Zeiss ZVI support
Fixed bugs in OME-XML reader
Tweaked ICS floating-point logic
Fixed memory leaks in all readers
Better file stitching logic
2006 Oct 6¶
Support for 3i SlideBook format (single series only for now)
Support for 16-bit RGB palette TIFF
Fixed bug preventing import of certain Metamorph STK files
Fixed some bugs in PerkinElmer UltraView support
Fixed some bugs in Leica LEI support
Fixed a bug in Zeiss ZVI support
Fixed bugs in Zeiss LSM support
Fixed a bug causing slow identification of Leica datasets
Fixed bugs in the channel merging logic
Fixed memory leak for OIB format
Better scaling of 48-bit RGB data to 24-bit RGB
Fixed duplicate channels bug in “open each channel in a separate window”
Fixed a bug preventing PICT import into ImageJ
Better integration with HandleExtraFileTypes
Better virtual stack support in Data Browser plugin
Fixed bug in native QuickTime random access
Keep aspect ratio for computed thumbnails
Much faster file stitching logic
2006 Sep 27¶
PerkinElmer: support for PE UltraView
Openlab LIFF: support for Openlab v5
Leica LEI: bugfixes, and support for multiple series
ZVI, OIB, IPW: more robust handling of these formats (eliminated custom OLE parsing logic in favor of Apache POI)
OIB: better metadata parsing (but maybe still not perfect?)
LSM: fixed a bug preventing import of certain LSMs
Metamorph STK: fixed a bug resulting in duplicate image planes
User interface: use of system look & feel for file chooser dialog when available
Better notification when JAR libraries are missing
2006 Sep 6¶
Leica LIF: multiple distinct image series within a single file
Zeiss ZVI: fixes and improvements contributed by Michel Boudinot
Zeiss LSM: fixed bugs preventing the import of certain LSM files
TIFF: fixed a bug preventing import of TIFFs created with Bio-Rad software
2006 Mar 31¶
First release