documents:101124locibioformats_bftoolstip
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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 | ||
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====== Using LOCI Bio-Format Command line tools ====== | ====== Using LOCI Bio-Format Command line tools ====== | ||
- | For converting .lif files to separate tif files: | + | This is a command line examples of [[http:// |
+ | |||
+ | For converting .lif file to separate tif files: | ||
if LIF file consists of stack series, and to separate them as each tiff stack: | if LIF file consists of stack series, and to separate them as each tiff stack: | ||
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</ | </ | ||
+ | then the output would be | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | ... | ||
+ | |||
+ | ... such numbered stacks in the same directory. | ||
+ | |||
All stacks will be extracted as tif stacks with the above command.\\ | 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: | To extract only one of the stacks out of .lif file, then specify the series number: | ||
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bfconvert -series s laminedapi23012.lif testS%s.tif | bfconvert -series s laminedapi23012.lif testS%s.tif | ||
</ | </ | ||
- | 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: | ||
< | < | ||
bfconvert laminedapi23012.lif testS%s_C%c.tif | bfconvert laminedapi23012.lif testS%s_C%c.tif | ||
</ | </ | ||
+ | |||
+ | then the output would then be | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | ... | ||
+ | |||
documents/101124locibioformats_bftoolstip.1290603000.txt.gz · Last modified: 2016/05/24 12:46 (external edit)