The Open Microscopy Environment

Today we are releasing Bio-Formats 7.0.1 which includes a number of format improvements.

The full list of changes included in this release are as follows:

File format fixes and improvements:

Amersham Biosciences Gel
- improved format detection
Aperio SVS
- fixed a NullPointerException when attempting to read the magnification metadata
- physical sizes and positions are now calculated for full resolution label and macro images
- fixed a regression from Bio-Formats 6.8.0 which saw label and macro images incorrectly indexed
DICOM
- the DICOM writer will now throw an exception if the provided tiles don’t match the expected tile size
Gatan DM3
- fixed a StringIndexOutOfBoundsException when parsing acquisition mode
Hamamatsu NDPI
- corrected for potential integer overflow in stored restart marker tag
IVision
- improved the version and data type checks in isThisType
Leica LIF
- improved the exception handling if no images are found
Olympus OIR
- fixed issue with XML block reading that resulted in missing pixel blocks
OME-TIFF
- reader will now fail fast and throw a FormatException if an invalid file is found
TIFF
- a FormatException is now thrown for unsupported 64-bit int data
- for all TIFF based formats the IFD entry offset is now checked before seeking
TillVision
- improved metadata parsing and detection of .pst files
Ventana
- fixed tile arithmetic for smallest resolutions
Zeiss CZI
- unified channel color parsing so that retrieving lookup tables now allows RGB and ARGB colors

Bio-Formats improvements:

URLHandle will fall back to resetting stream if resetting to a mark fails
an exception will now be thrown if the TurboJPEG library fails to load (thanks to Can Gokhan Dogan)
fixed a Bio-Formats plugin bug when attempting to export a file after reducing the range of channels
reviewed and updated a number of file headers
updated GitHub Actions from checkout v2 to v3

Component updates:

Documentation improvements:

Release of Bio-Formats 7.0.1