User Tools

Site Tools


Sidebar

Top
Profile
Seminar
Courses -2016
Courses 2018-
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
Weblog
RSS aggregates
Discussions
Archives


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @NEUBIAS_COST: NEUBIAS Academy presents two webinars on KNIME for Image Processing March 4th & 11th at 15h30-17h00 CET Register now (si…
About 9 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @katpyxa: @KapiteinLukas @JurriensDaphne Also there was some help from another 3D image analysis expert https://t.co/Fbm09Hd4x8
About 9 hours, 10 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @haesleinhuepf: @microforum Or, consider linking, mirroring and joining https://t.co/NdXusRiqSU - it's open for collaborators 😃 Many peo…
About 1 day, 9 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

@haesleinhuepf @jmutterer @nevermore_78 I made a trial. setBatchMode("hide"); (or setBatchMode(true);) at the beg… https://t.co/zcd9PGvo3Q
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

@haesleinhuepf @jmutterer @nevermore_78 Maybe use “batch mode” in behind, just to suppress them to appear on the desktop?
About 2 days, 5 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

@haesleinhuepf @jmutterer @nevermore_78 Hi Robert, Great to have the markdown notebook! Just one thing: would it b… https://t.co/3aictxcfxa
About 2 days, 7 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)