readme_compiling_JSIT.MD

Environment

These instructions are tailored for the environment on the "numbers" cluster using:

• MATLAB R2016a installed at /gsc/software/linux-x86_64-centos6/matlab-r2016a/
• No need for a license (i.e. activation code) after compiling — thanks to the MATLAB Runtime (MCR)
• Cluster jobs should call run_JSIT.sh, not the binary directly

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Step 1: Compile JSIT.m using MATLAB Compiler

From the directory /path/to/JSIT where JSIT.m is located, run:

/gsc/software/linux-x86_64-centos6/matlab-r2016a/bin/mcc -m JSIT_preproc_wrapper.m

Users should use JSIT_preproc_wrapper.m because JSIT expects some kind of fiducial alignment and preprocessing. Ignore JSIT_raw_wrapper.m.

This will generate the following files:

• JSIT — the compiled executable
• JSIT.ctf — compressed code archive (required at runtime)
• run_JSIT_preproc_wrapper.sh — helper script to run with MATLAB Runtime
• Other supporting files like readme.txt and requiredMCRProducts.txt

Make sure JSIT.ctf is in the same directory as JSIT and run_JSIT_preproc_wrapper.sh.

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Step 2: Set environment variables before running

The compiled binary requires the MATLAB Runtime (MCR) to be available.

Use this setup if calling JSIT manually:

export MCRROOT=/gsc/software/linux-x86_64-centos6/matlab-r2016a
export LD_LIBRARY_PATH=$MCRROOT/v901/runtime/glnxa64:\
$MCRROOT/v901/bin/glnxa64:\
$MCRROOT/v901/sys/os/glnxa64:\
$MCRROOT/v901/sys/opengl/lib/glnxa64:$LD_LIBRARY_PATH

These are set automatically when using run_JSIT_preproc_wrapper.sh — no need to export manually in SLURM.

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Step 3: Run JSIT via the helper script

Run the program using:

/path/to/JSIT/run_JSIT_preproc_wrapper.sh /gsc/software/linux-x86_64-centos6/matlab-r2016a \
  /path/to/aligned_images_{fov:03}_{z:02}.tiff.mat \
  /path/to/codebook.mat \
  /path/to/output_folder_{fov:03}_{z:02}

• Argument 1: path to MCR (always /gsc/software/linux-x86_64-centos6/matlab-r2016a)
• Argument 2: .tiff.mat input file
• Argument 3: codebook .mat file
• Argument 4: output folder (must exist or be creatable)

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Notes (1)

• Do not run ./JSIT directly — use run_JSIT_preproc_wrapper.sh
• You do not need a MATLAB license to run after compilation
• Make sure all input/output paths are accessible from compute nodes
• If you see a CTF not found error, make sure JSIT.ctf is in the same directory as JSIT

Notes (2)

Example code to run JSIT.m without compiling (using a MATLAB interpreter)

/gsc/software/linux-x86_64-centos6/matlab-r2016a/bin/matlab -nodisplay -nosplash -r "JSIT(/path/to/aligned_images_{fov:03}_{z:02}.tiff.mat', /path/to/codebook.mat, /path/to/output_folder_{fov:03}_{z:02}); quit;"