UB-SPEBT / image-reconstruction

Python implementation of the Maximum Likelihood Expectation Maximization (ML-EM) approach of emission tomography image reconstruction.

How to run on the CCR HPC cluster

Through SSH

• ssh to vortex.ccr.buffalo.edu
• git clone the repository
• cd image-reconstruction/MLEM-MPI
• submit the job with sbatch slurm-run.sh

Through UB CCR OnDemand

• Login to the OnDemand
• Open a command-line shell from the OnDemand dashboard (ccrsoft/legacy should be loaded automaticlly)

• git clone the repository
• cd image-reconstruction/MLEM-MPI
• submit the job with sbatch slurm-run.sh

The reconstruction configuration

The configuration is loaded from the config.yml file. You can change it for your need. (but do not push your change to the remote repository, unless necessary)