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--- documents:101124locibioformats_bftoolstip [2010/11/24 12:50] – created kota
+++ documents:101124locibioformats_bftoolstip [2016/05/24 12:46] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== Using LOCI Bio-Format Command line tools ======
-For converting .lif files to separate tif files:
+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:
@@ Line 8: / Line 10: @@
 </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:
@@ Line 13: / Line 24: @@
 bfconvert -series s laminedapi23012.lif testS%s.tif
 </code>
-if LIF file consists of stack series, each stack has multiple channels and to separate them as each tiff stack with separated channel:
+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
+   ...