ImageJ macros for Lightsheet microscope processing for Nicolas Chevrier

A set of ImageJ/Fiji macros to run headless on HPC under SLURM

Each of these headless macros should be invoked using the appropriate SLURM script:

Before running any of these, you must set LSPROCESSING_HOME to the base folder. E.g. export LSPROCESSING_HOME=/home/bfreeman/git/chevrier_lightsheet_processing

CZI to TIF conversion

    sbatch $LSPROCESSING_HOME/slurm/Z1_CZI_to_TIF_for_Timelapse_and_Multiview.headless.slurm params

where params =

    numChannels numAngles pathToFile outputDir

e.g.

    sbatch $LSPROCESSING_HOME/slurm/Z1_CZI_to_TIF_for_Timelapse_and_Multiview.headless.slurm \
        1 6 \
        /n/regal/bfreeman/11-14_-_1DPI_LSide_5xObj_wbeads_glycerol.czi \
        /n/regal/bfreeman/

Bead registration

    sbatch $LSPROCESSING_HOME/slurm/bead_registration.headless.slurm params

where params =

    numChan chan1Dir chan2Dir angleRange xyResolution zResolution

if only 1 channel, use 'not_used' for chan2Dir

e.g.

    sbatch $LSPROCESSING_HOME/slurm/bead_registration.headless.slurm \
        1 /n/regal/bfreeman/chevrier/green not_used 1-6 0.730 2.000

Multi-view fusion

    sbatch $LSPROCESSING_HOME/slurm/image_fusion.headless.slurm params

where params =

    chan1Dir angleRange

only 1 channel is assumed

e.g.

    sbatch $LSPROCESSING_HOME/slurm/image_fusion.headless.slurm \
        /n/regal/bfreeman/chevrier/green 1-6 

• current SLURM scripts use 16 cores, 2 hrs, and serial_requeue by default. Macros match the 16 cores used. This is hardcoded and will be removed.
• Dual/multi-channel stuff is not really wired in.
• App location is hard-coded into

Any questions, please contact Bob Freeman at robert_freeman [at] harvard.edu