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.
Opening as a draft for now, as #4181 is higher priority. This may need some updates once #4181 is merged.
I would expect basic conversions such as bfconvert -noflat -precompressed -compression JPEG input.dcm output.ome.tiff to work, where the input DICOM is part of a whole slide dataset. Tile sizes should be correctly picked up without being specified in the bfconvert options.
A few outstanding things related to this PR and #4181:
-precompressed does still require the -compression option to be set correctly; removing that requirement could be done here
Opening as a draft for now, as #4181 is higher priority. This may need some updates once #4181 is merged.
I would expect basic conversions such as
bfconvert -noflat -precompressed -compression JPEG input.dcm output.ome.tiff
to work, where the input DICOM is part of a whole slide dataset. Tile sizes should be correctly picked up without being specified in thebfconvert
options.A few outstanding things related to this PR and #4181:
-precompressed
does still require the-compression
option to be set correctly; removing that requirement could be done here/cc @fedorov, @dclunie