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How to perform cell-type contouring using ImageJ (Note: No Audio) 2 min
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How to perform cell-type contouring using ImageJ
Strategy for ROI selection on GeoMx® DSP
The Cell-Type Contouring ImageJ script enables contouring around a morphology marker-based segment mask.
This ImageJ script does the following:
- Creates a cell-type-specific mask within a given ROI based on a fluorescent marker of interest
- the user can select the fluorescent channel and tune their mask thresholding
- Creates a geometric ring contour mask around the developed cell-type mask
- the user can define the ring distance
- Creates a third mask that contains the remaining area in the given ROI
- 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.