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2. Contruction_ROI_Boxes.md

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Color Deconvolution

  1. Find proper islet and make squared ROI box.
  1. Open the SAM API extension and apply SAM with click Run for selected to the ROI box and designate as Islet Class.
  1. Make square box at the non-islet area and designate as Background Class.

4.Train pixel classifier

  • Classify -> Pixel classification -> Train pixel classifier

  • Features -> Edit -> Channels (set Insulin, Glucagon, CD3+)

  • Region -> Any object bounds(fast)

  • Save classifier named {#slide}_classifier

  • Check with Live Prediction

  • Click Create objects

  1. Apply trained classifier after removing all Annotation squares in image.

  • Classify -> Pixel classification -> Load pixel classifier

  • Choose model

  • Region -> Everywhere

  • Create objects

  • New object type = Annotation

  • Minimun object size 20um^2

  • Check Split objects and Run

  • Remove all the Annotation (Background)

  1. Run the script 2_get-bounding-box.groovy, and it turns all the annotation boxes into Red squared ROI boxes.

  2. Manual modification the ROI boxes.