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EMBL BioImage Data Analysis



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... so don't think that you need to submit a full text.
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

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The deadline next week for NEUBAIS Gateway article is just for the **PROPOSAL.** you just need to fill and submit…
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

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I really like the article refers to the MoU of NEUBIAS. We made pretty much of efforts in polishing our initial "Ma…
About 2 days, 5 hours ago by: Kota Miura (@cmci_)

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recommendation to read
About 2 days, 10 hours ago by: Kota Miura (@cmci_)

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RT @florianjug: If you missed the webinar but are interested to have a look, a recording is now available: Thanks a…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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RT @SuperResoluSian: We've collated all the links from our @NEUBIAS_COST webinar on SMLM analysis into a post!⬇️ From here you can navigate…
About 1 week, 6 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

Example Commands for Bory and Christian

converting to tif:
sh /g/almf/software/ij/ /g/haering/Pombescreen/test.lif

actual processing:
sh /g/almf/softwae/ij/ /g/haering/Pombescreen/test.lif_tifStack headlesstest3.ijm

documents/101103imagej_cluster_short.1288801200.txt.gz · Last modified: 2016/05/24 05:46 (external edit)