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MMPB.md

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Instructions how to transform files for MMPB

  • Login to the cluster login node.

  • Generate a text file (job script) with below content (modifying the export statements as described below ).

#!/bin/bash

export TRAFO="/g/cba/exchange/platy-trafos/linear/TransformParameters.BSpline10-3Channels.0.txt"
export OUT="/g/cba/cluster/tischer/elastix-job-000.out"
export ERR="/g/cba/cluster/tischer/elastix-job-000.err"
export INPUT_IMAGE="/g/cba/tischer/tmp/ProSPr6_Ref.tif"
export OUTPUT_IMAGE="/g/arendt/EM_6dpf_segmentation/EM-Prospr/ProSPr6_Ref-SPM.xml"

srun --mem 16000 -n 1 -N 1 -c 8 -t 30:00 -o $OUT -e $ERR /g/almf/software/Fiji.app/ImageJ-linux64 --ij2 --headless --run "Transformix" "elastixDirectory='/g/almf/software/elastix_v4.8', workingDirectory='$TMPDIR', inputImageFile='$INPUT_IMAGE',transformationFile='/g/cba/exchange/platy-trafos/linear/TransformParameters.BSpline10-3Channels.0.txt
',outputFile='$OUTPUT_IMAGE',outputModality='Save as BigDataViewer .xml/.h5',numThreads='1'"
  • Save this file, e.g. with the name transformix.job.
  • Submit the file as a job: sbatch transformix.job

The export statements have to be adapted for your gene and user.

  • TRAFO
    • the transformation to be used
    • SPMs: /g/cba/exchange/platy-trafos/linear/TransformParameters.BSpline10-3Channels.0.txt
      • uses linear interpolation
    • MEDs: /g/cba/exchange/platy-trafos/nn/TransformParameters.BSpline10-3Channels.0.txt
      • ueses nearest neighbor interpolation
  • OUT
    • text output
    • use: some file where you have write access
  • ERR
    • text output of errors
    • use: some file where you have write access
  • INPUT_IMAGE
    • the input image, make sure that the calibration is correct, otherwise the transformation will fail!
  • OUTPUT_IMAGE
    • the output image, must be in folder /g/arendt/EM_6dpf_segmentation/EM-Prospr/
    • MEDs: must end with -MED.xml
    • SPMs: must enfd with -SPM.xml

Alternative

Notes

  • Faster transformation for testing: TransformParameters.Similarity-3Channels.0.txt

Issues

  • I did not manage yet to specify a cluster job specific tmp dir. I tried using $TMPDIR, but it did not work. Like this, jobs running on the same node will screw up each other.