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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:
sh /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:
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#!/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
Example Commands for Bory and Christian
converting lif to tif stacks:
sh /g/almf/software/ij/lifcon.sh /g/haering/Pombescreen/test.lif
actual processing:
sh /g/almf/softwae/ij/clust5fullp.sh /g/haering/Pombescreen/test.lif_tifStack headlesstest3.ijm