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EMBL BioImage Data Analysis



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RT @J_Cell_Sci: Read our Editorial about the launch of FocalPlane– a meeting place for the microscopy minded @focalplane_jcs:
About 1 day, 18 hours ago by: Kota Miura (@cmci_)

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RT @KuglerElisabeth: 🔥Preprint #3🔥 "3D #quantification of #zebrafish cerebrovascular architecture by automated image analysis of #lightShe…
About 1 day, 18 hours ago by: Kota Miura (@cmci_)

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RT @lmescu: Let's tile a bit the 3D space!!!!
About 1 day, 18 hours ago by: Kota Miura (@cmci_)

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RT @ferrandoelisa: Are you tired of searching through piles of image files? And do you want to start your working days here? Then apply for…
About 1 week, 1 day ago by: Kota Miura (@cmci_)

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Bioimage analysis lunch Heidelberg, July 2020 Topics: GPU temperature rise and how to deal with it, CentOS vs Ub…
About 2 weeks, 1 day ago by: Kota Miura (@cmci_)

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RT @mmvpgs: !!Last day to apply!! As part of its final dissemination action, NEUBIAS supports the article publication charges on the recent…
About 3 weeks, 3 days ago by: Kota Miura (@cmci_)

This is an old revision of the document!

Using Cluster (Quick Version)

Processing by ImageJ from Command Line

Command syntax is

/g/almf/software/ij/ <fullpath to macro file> <fullpath to image file>

For example:

/g/almf/software/ij/ /g/almf/software/ij/getArgumentMacro.ijm /g/almf/miura/blobs.tif

Processing Single Image file by ImageJ, throw the job to cluster

Above commands should be pasted in another shell script as follows:

#PBS -N ImageJProcess
#PBS -l walltime=1:00:00
# *** Script for single image file procesing by ImageJ ***
#   two arguments for full paths to (2) an image file and (1) a macro file is required
#   assuming that macro file takes the fisrt argument as the 
#   Kota Miura (
#   20101103
#   ****************************************************
sh /g/almf/software/ij/ /g/almf/software/ij/getArgumentMacro.ijm /g/almf/miura/blobs.tif

and then save the script as something like “”. Execute the job by following command in terminal

/usr/pbs/bin/qsub -q clusterng /g/almf/software/ij/

Processing All Image Files in a Folder

Syntax is

sh /g/almf/software/ij/ </full/path/to/dir> <File Name of Macro File>

For example, if you want to process all images under /g/almf/miura/testsmalls using an ImageJ macro file headlesstest3.ijm, then your command would be:

sh /g/almf/software/ij/ /g/almf/miura/testsmalls headlesstest3.ijm
documents/101103imagej_cluster_short.1288800961.txt.gz · Last modified: 2016/05/24 12:46 (external edit)