====== Using LOCI Bio-Format Command line tools ======

This is a command line examples of [[http://www.loci.wisc.edu/bio-formats/command-line-tools|"bfconvert" tool from LOCI Bioformats]]((within embl network, this tool is reachable by /g/almf/software/bin2/bfconvert)). 

For converting .lif file to separate tif files:

if LIF file consists of stack series, and to separate them as each tiff stack:
<code>
bfconvert laminedapi23012.lif testS%s.tif
</code>

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:
<code>
bfconvert -series s laminedapi23012.lif testS%s.tif
</code>

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:
<code>
bfconvert laminedapi23012.lif testS%s_C%c.tif
</code>

then the output would then be

   testS0_C0.tif
   testS0_C1.tif
   testS0_C2.tif
   testS1_C0.tif
   ...