CellProfiler

Introduction

CellProfiler is a free, open-source software for quantitative analysis of biological images. No prior experience in programming or computer vision is required

Module Information:

module use /apps/common/containers/modules
module spider CellProfiler

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CellProfiler:
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   Versions:
      CellProfiler/4.2.1
      CellProfiler/4.2.6

Interactive CellProfiler Sessions

In order to use the CellProfler application in GUI mode, connect to a graphical NX node using these instructions: Connecting to ARC NX nodes

Once connected to an NX desktop session, open a Konsole window, use cd to change directory to where your pipeline and image files are located and then type:

module purge
module use /apps/common/containers/modules
module load CellProfiler/4.2.6

cellprofiler

The CellProfiler application will then start interactively with full GUI access.

Non-interactive batch CellProfiler jobs

The following example SLURM submission script runs CellProfiler in batch (headless) mode. In this case, it assumes you have downloaded the Fruit Fly cells example ExampleFly and are submitting this from the extracted directory. i.e. the directory containing the ExampleFly.cppipe piprline file and images directory (the script creates an output directory).

For example creating a file named run_slurm.sh:

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
#SBATCH --time=00:05:00
#SBATCH --job-name=cellprofiler_test
#SBATCH --partition=devel

module purge
module use /apps/common/containers/modules
module load CellProfiler/4.2.6

mkdir -p output
cellprofiler -p ExampleFly.cppipe -c -r -i images -o output

To submit this to the scheduler:

sbatch run_slurm.sh