I am using the bioformats command line interface on Ubuntu (16.04) and I am encountering issues converting CZI images to TIFFs.
I can perform the conversion well enough using the following command:
bfconvert -compression LZW -separate -series 0 -channel 0 $czi_fn $tiff_fn to extract the first channel of the first scene of a CZI file. The issue is that the files are massive, nearly 20x bigger than when converted via imageJ and other software.
When using bioformats on windows I will recieve a 25MB tiff file, the expected size. When using the command line interface I get a 456MB file. This 456MB file, when opened in image processing software like GIMP and exported as tiff, is properly compressed to 25MB.
Has anyone else experienced this massive inflation of tiff files? Any suggested solutions? When I convert the czi -> tiff and disable LZW compression the files become well over a GB which is ridiculous.