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The field for bioimage analyst expanding. British museum! https://t.co/KClNvxP948
About 2 days, 6 hours ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Panel session: should I aim to become a bioimage analyst? With Robert Hasse @haesleinhuepf , Kota Miura @cmci_ and Arianne B…
About 3 days, 21 hours ago by: Kota Miura (@cmci_)

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RT @alex_paynedwyer: The one and only Kota Miura @cmci_ calling out all those dodgy contrast-mismatched figures #ethics in classic humorou…
About 4 days, 5 hours ago by: Kota Miura (@cmci_)

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RT @RekadZeinab: Kicking the last session of #CBIAS2022 with the great master @cmci_ on the challenges of doing image analysis at the inter…
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RT @MaKaefer: Fear not: there is something that can be done! Abide by the guidelines or report everything that has been done - whether it i…
About 4 days, 5 hours ago by: Kota Miura (@cmci_)
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
documents/101124locibioformats_bftoolstip.txt · Last modified: 2016/05/24 12:46 (external edit)