CellProfiler

Description

CellProfiler website  

CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Required Modules

Serial

• CellProfiler

System Variables

• HPC_CELLPROFILER_DIR
• HPC_CELLPROFILER_BIN

Additional Information

To run CellProfiler, you need to have X11 forwarding setup and an X11 emulator on your local computer. Please see the GUI Programs wiki page for information on this.

CellProfiler is primarily designed to be a GUI application. However, it does have a batch processing mode, which is how it is intended to be used at the Research Computing. To run CellProfiler in batch mode, you should include the -c or --run-headless option. Also, you want to use CELLPROFILER_USE_XVFB="1"

Here is a list of the CellProfiler command line options:

Usage: CellProfiler.py [options] [<output-file>])
    where <output-file> is the optional filename for the output file of measurements
          when running headless

Options:
 -h, --help            show this help message and exit
 -p PIPELINE_FILENAME, --pipeline=PIPELINE_FILENAME
                       Load this pipeline file on startup
 -c, --run-headless    Run headless (without the GUI)
 -r, --run             Run the given pipeline on startup
 --worker=WORKER_MODE_URL
                       Enter worker mode for the CellProfiler distributing
                       work at URL (implies headless)
 --worker-timeout=WORKER_TIMEOUT
                       Number of seconds the worker will continue trying to
                       find work before exiting.
 -o OUTPUT_DIRECTORY, --output-directory=OUTPUT_DIRECTORY
                       Make this directory the default output folder
 -i IMAGE_DIRECTORY, --image-directory=IMAGE_DIRECTORY
                       Make this directory the default input folder
 -f FIRST_IMAGE_SET, --first-image-set=FIRST_IMAGE_SET
                       The one-based index of the first image set to process
 -l LAST_IMAGE_SET, --last-image-set=LAST_IMAGE_SET
                       The one-based index of the last image set to process
 -g GROUPS, --group=GROUPS
                       Restrict processing to one grouping in a grouped
                       pipeline. For instance, "-g ROW=H,COL=01", will
                       process only the group of image sets that match the
                       keys.
 --html                Output HTML help for all modules. Use with the -o
                       option to specify the output directory for the files.
                       Assumes -b.
 --plugins-directory=PLUGINS_DIRECTORY
                       CellProfiler will look for plugin modules in this
                       directory (headless-only).
 --ij-plugins-directory=IJ_PLUGINS_DIRECTORY
                       CellProfiler will look for ImageJ plugin modules in
                       this directory (headless-only).
 --jvm-heap-size=JVM_HEAP_SIZE
                       This is the amount of memory reserved for the Java
                       Virtual Machine (similar to the java -Xmx
                       switch).Example formats: 512000k, 512m, 1g
 -b, --do-not-build, --do-not_build
                       Do not build C and Cython extensions
 --build-and-exit      Build extensions, then exit CellProfiler
 --do-not-fetch        Do not fetch external binary dependencies
 --fetch-and-overwrite
                       Overwrite external binary depencies if hash does not
                       match
 --ilastik             Run Ilastik instead of CellProfiler. Ilastik is a
                       pixel-based classifier. See www.ilastik.org for more
                       details.
 -d DONE_FILE, --done-file=DONE_FILE
                       The path to the "Done" file, written by CellProfiler
                       shortly before exiting
 --measurements        Open the pipeline file specified by the -p switch and
                       print the measurements made by that pipeline
 --data-file=DATA_FILE
                       Specify a data file for LoadData modules that use the
                       "From command-line" option
 -L LOG_LEVEL, --log-level=LOG_LEVEL
                       Set the verbosity for logging messages: 10 or DEBUG
                       for debugging, 20 or INFO for informational, 30 or
                       WARNING for warning, 40 or ERROR for error, 50 or
                       CRITICAL for critical, 50 or FATAL for fatal.
                       Otherwise, the argument is interpreted as the file
                       name of a log configuration file (see
                       http://docs.python.org/library/logging.config.html for
                       file format)

Citation

If you publish research that uses CellProfiler you have to cite it as follows:

• Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology 7:R100. PMID: 17076895

• Lamprecht MR, Sabatini DM, Carpenter AE (2007) CellProfiler: free, versatile software for automated biological image analysis. Biotechniques 42(1):71-75. PMID: 17269487

• Jones TR, Carpenter AE, Lamprecht MR, Moffat J, Silver S, Grenier J, Root D, Golland P, Sabatini DM (2009) Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. PNAS 106(6):1826-1831/doi: 10.1073/pnas.0808843106. PMID: 19188593 PMCID: PMC2634799

• Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE (2008) CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics 9(1):482/doi: 10.1186/1471-2105-9-482. PMID: 19014601 PMCID: PMC2614436