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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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Loading of indica tiff files #4189

Open rharkes opened 1 month ago

rharkes commented 1 month ago

At the moment bioformats doesn't load indica tiff files. The python tifffile library can do it since version 2023.12.9.

The problem with the files is that they have 32 bit per pixel, but didn't set the TIFFTAG_SAMPLEFORMAT, so it defaults to UINT. However, it has to be SAMPLEFORMAT_IEEEFP.

See also: https://github.com/cgohlke/tifffile/blob/master/tifffile/tifffile.py#L8369 (the sampleformat is changed here) https://github.com/cgohlke/tifffile/blob/master/tifffile/tifffile.py#L10459 (this is how it is checked)

dgault commented 1 month ago

Thanks @rharkes for reporting the issue. Are there any sample Indica Tiff files that could be used for testing? If you have some suitable samples and need an upload location then we recommend using https://zenodo.org/

cgohlke commented 1 month ago

A sample file was posted at forum.image.sc. See also the comments regarding the file format.