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EMBL BioImage Data Analysis

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RT @EuroBioImaging: Last chance to present your bioimaging analysis work at 4th NEUBIAS conference 👇 https://t.co/D4jfEVfWGo
About 1 day ago by: Kota Miura (@cmci_)

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RT @f_levet: You have until next monday to submit an abstract to the @NEUBIAS_COST Symposium. It's your last chance ! Go go go !
About 1 day, 2 hours ago by: Kota Miura (@cmci_)

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Bioimage Analysis Lunch Heidelberg, Jan 2020 https://t.co/6FcCNzu1QJ
About 1 day, 2 hours ago by: Kota Miura (@cmci_)

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RT @Datascience__: DL@MBL: Deep Learning for Microscopy Image Analysis https://t.co/DT25zxxaRn #DeepLearning
About 2 days ago by: Kota Miura (@cmci_)

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@LauLauThom well done Laurent!
About 2 days, 4 hours ago by: Kota Miura (@cmci_)

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RT @LauLauThom: Another documentation gem for #ImageJ / #Fiji geeks https://t.co/GgC2rRSEYo https://t.co/Gce9E0o8Xt
About 3 days, 23 hours ago by: Kota Miura (@cmci_)
documents:101103imagej_cluster_short

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/doIJ.sh <fullpath to macro file> <fullpath to image file>

For example:

/g/almf/software/ij/doIJ.sh /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:

#!/bin/sh
#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 (cmci.embl.de)
#   20101103
#   ****************************************************
#
sh /g/almf/software/ij/doIJ.sh /g/almf/software/ij/getArgumentMacro.ijm /g/almf/miura/blobs.tif

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

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

Processing All Image Files in a Folder

Syntax is

sh /g/almf/software/ij/clust5fullp.sh </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/clust5fullp.sh /g/almf/miura/testsmalls headlesstest3.ijm
documents/101103imagej_cluster_short.1288800961.txt.gz · Last modified: 2016/05/24 05:46 (external edit)