I have a strange issue using bfconvert (from within a python script) when converting a CZI image file. The script itself works fine and the output is:
Original ImageFile : C:\test_bfconvert\CH=3 ImageFile OME.TIFF : C:\test_bfconvert\CH=3.ome.tiff ImageFile OEM.XML : C:\test_bfconvert\CH=3.ome.xml Use CMD : bfconvert -no-upgrade -option zeissczi.attachments false -option zeissczi.autostitch true -option ometiff.companion "C:\test_bfconvert\CH=3.ome.xml" "C:\test_bfconvert\CH=3.czi" "C:\test_bfconvert\CH=3.ome.tiff" C:\test_bfconvert\CH=3.czi ZeissCZIReader initializing C:\test_bfconvert\CH=3.czi Unknown IlluminationType value 'Fluorescence' will be stored as "Other" Unknown IlluminationType value 'Fluorescence' will be stored as "Other" Unknown IlluminationType value 'Fluorescence' will be stored as "Other" [Zeiss CZI] -> C:\test_bfconvert\CH=3.ome.tiff [OME-TIFF] Converted 3/3 planes (100%) [done] 10.137s elapsed (60.0+345.33334ms per plane, 5818ms overhead)
And I also open the original CZI in Fiji (latest BioFormats) and saved it as an OME-TIFF.
But when I try to open the OME-TIFF (created by bfconvert) in ZEN I get error messages, while opening the OME-TIFF (created by Fiji) works fine in ZEN.
So my questions is what the difference is between creating an OME-TIFF using bfconvert vs. open the image in Fiji via BioFormats and exporting it as an OME-TIFF.