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EMBL BioImage Data Analysis

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@EntraCod @COSTprogramme @NEUBIAS_COST Yes everyone indeed. Thanks for the suggestion.
About 2 hours, 21 mins ago by: Kota Miura (@cmci_)

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RT @SimonFlyvbjerg: Fresh off Springer's open access press: "Bioimage Data Analysis Workflows" - the book! #BioImageAnalysis https://t.co
About 7 hours, 5 mins ago by: Kota Miura (@cmci_)

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@COSTprogramme @NEUBIAS_COST Thanks to the authors and editors: @perrinepgil Sébastien Tosi Julien Colombelli… https://t.co/GVlRWoqGxr
About 7 hours, 47 mins ago by: Kota Miura (@cmci_)

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Now online, "Bioimage Data Analysis Workflow". https://t.co/stW12drKaS Thanks to the support by @COSTprogramme ,… https://t.co/pgJck70nW6
About 7 hours, 53 mins ago by: Kota Miura (@cmci_)

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RT @Datascience__: Dynamic allocation of computational resources for deep learning-enabled cellular image analysis with Kubernetes https://…
About 3 days, 8 hours ago by: Kota Miura (@cmci_)

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RT @mariana_deniz: Many thanks to the @NEUBIAS_COST instructors and organizers for an exciting and stimulating course on image analysis 😁😁…
About 3 days, 13 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 05:46 (external edit)