python-bioformats icon indicating copy to clipboard operation
python-bioformats copied to clipboard

reading tif with >3 channels returns just 3 channels

Open tamkaho opened this issue 6 years ago • 0 comments

I have some tiffs with >3 channels which opens fine with imagej's bioformat. However if I open them with bioformats I keep getting 3 channels no matter what I put into c (as below). The tiffs are pyramidal tiled tiffs created with vips.

reader = bioformats.ImageReader("file.tif")
info = bioformats.get_omexml_metadata(path="file.tif")
o = bioformats.OMEXML(info)
o.image().Pixels.SizeC
>> 5
reader.read().shape
>> 3
reader.read(c=1).shape
>> 3
reader.read(c="anything").shape
>> 3

tamkaho avatar Jan 31 '20 23:01 tamkaho