Error in writing ome.tiff files using the command line. I have a .lif file with several of z stacks and two channels each. I used the bfconvert- https://docs.openmicroscopy.org/bio-formats/5.7.1/users/comlinetools/conversion.html to batch convert lif files to ome.tiff files. I wanted to separate all channels and all series into separate files. One tiff file for each channel z stack.
Bf-convert could convert the first series correctly, but all the other series were corrupted.
I used the below command with respective input and output paths:
./bftools/bfconvert ‘/media/xxx/xxx/xxx_files/Project001.lif’ ‘/media/xxx/xxx/outputname_series_%s_C%c.ome.tiff’
How can i solve the files getting corrupted.
I see the below error in fiji.
I can find it in 3d as random lines (3d view in morphographx)
How can i also include the file name for the individual series from the lif file on the output file? Below is the typical lif file that we have with several series. The lif files are aquired as 12 bit images and have the voxels as in the file name.