# Bioimage Analysis Wiki

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documents:101124locibioformats_bftoolstip

# Using LOCI Bio-Format Command line tools

This is a command line examples of "bfconvert" tool from LOCI Bioformats1).

For converting .lif file to separate tif files:

if LIF file consists of stack series, and to separate them as each tiff stack:

bfconvert laminedapi23012.lif testS%s.tif


then the output would be

 testS0.tif
testS1.tif
testS2.tif
...

… such numbered stacks in the same directory.

All stacks will be extracted as tif stacks with the above command.
To extract only one of the stacks out of .lif file, then specify the series number:

bfconvert -series s laminedapi23012.lif testS%s.tif


If your LIF file consists of stack series, each stack has multiple channels and you want to separate them as each tiff stack with separated channel:

bfconvert laminedapi23012.lif testS%s_C%c.tif


then the output would then be

 testS0_C0.tif
testS0_C1.tif
testS0_C2.tif
testS1_C0.tif
...
1)
within embl network, this tool is reachable by /g/almf/software/bin2/bfconvert