How to perform cell-type contouring using ImageJ

How to perform cell-type contouring using ImageJ

Strategy for ROI selection on GeoMx® DSP

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About this course

The Cell-Type Contouring ImageJ script enables contouring around a morphology marker-based segment mask. 

This ImageJ script does the following:

  1. Creates a cell-type-specific mask within a given ROI based on a fluorescent marker of interest
    1. the user can select the fluorescent channel and tune their mask thresholding
  2. Creates a geometric ring contour mask around the developed cell-type mask
    1. the user can define the ring distance
  3. Creates a third mask that contains the remaining area in the given ROI
  4. The script will output three masks to upload into the GeoMx Control Center and one visual reference image for user reference displaying the masks together overlaid on the ROI.

Curriculum2 min

  • How to perform cell-type contouring using ImageJ (Note: No Audio) 2 min
  • Feedback Survey

About this course

The Cell-Type Contouring ImageJ script enables contouring around a morphology marker-based segment mask. 

This ImageJ script does the following:

  1. Creates a cell-type-specific mask within a given ROI based on a fluorescent marker of interest
    1. the user can select the fluorescent channel and tune their mask thresholding
  2. Creates a geometric ring contour mask around the developed cell-type mask
    1. the user can define the ring distance
  3. Creates a third mask that contains the remaining area in the given ROI
  4. The script will output three masks to upload into the GeoMx Control Center and one visual reference image for user reference displaying the masks together overlaid on the ROI.

Curriculum2 min

  • How to perform cell-type contouring using ImageJ (Note: No Audio) 2 min
  • Feedback Survey