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RT @jytinevez: LimeSeg on bioRXiv: LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation https://t.co/jECl7deOVG
About 9 hours, 22 mins ago by: Kota Miura (@cmci_)

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Impressive and swift moderation @helenajambor !
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz https://t.co/zOaMWvzd8k https://t.co/AXYBCeGyw6
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots https://t.co/QZE7xQtaa3
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RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp…
About 2 days, 23 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)