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G'MIC

Command-line tools for rapidly processing image-based data on Linux systems using G'MIC. Includes a variety of useful operations including highly parallel maximum intensity projections, segmentation, smoothing, and more. Intially assembled by Dr. Philippe Roudot for operation on BioHPC, the high-performance computing facility at UT Southwestern Medical Center. Originally developed by Jérôme Boulanger.

Requirements1

Installation Directions

  • Clone the GMIC repository.
  • Navigate to the cloned repository
  • Right-click on installQuickMIPDisp.sh, select properties, and under permissions allow executing the file as a program.
  • Open a terminal, and drag and drop installQuickMIPDisp.sh to the terminal and hit enter2.
  • The command will be available on every newly opened terminal window3.

Example Operation

quickMIPMontage /path/to/your/3D/images

Brief Descriptions

  • quickMIPMontage - creates a 2D montage of maximum intensity projections of all of the data located within the provided folder.
  • quickMIPMovie - Presents the maximum intensity projections in an interactive viewer, saves maximum intensity projections to ~/gmic-video/test-images/frame.png, and saves a movie of the maximum intensity projections in an AVI format to /gmic-video.test.avi. Movie can be visualized with an appropriate media player, such as VLC.
  • quickMIPSwap - Often called as an intermediate function. Searches for all of the image files, lists them in the terminal, performs maximum intensity projection on each file, normalizes the intensity, and saves it to a cache directory in /tmp/gmic-cache/

Footnotes

  1. If you are operating this software on BioHPC, these dependencies are already installed. ↩

  2. If you open the file installQuickMIPDisp.sh you can see what Linux commands it is executing. Summarized briefly, the shell script is reating a directory called gmic-scripts-install in your HOME directory, copying the necessary files to this directory and changing their permissions to allow executing these files as program, and adding these files to your Linux PATH so that you can call them from a terminal. ↩

  3. When you update your Linux PATH, you will need to restart your terminal session in order for the changes to take place. ↩