Puncta counting

Once you have a set of puncta labels you’re happy with, follow these steps to count them:

  1. Click on the Puncta labeling tab
  2. Select the image layer you want to count puncta for using the Select layer dropdown menu.
  3. Specify whether there’s a corresponding mask layer in the Select mask dropdown menu. If “None” is specified, all the puncta in your image will be counted.

  4. QuantPunc expects a puncta labels layer in the layer list named after the image you’ve selected in the first step with “_puncta” as its suffix, e.g., “your_image_puncta”.

    • If the base names don’t match, e.g. “your_image_processed” (name of selected layer) and “your_image_puncta” (name of puncta labels layer), nothing will get quantified.
  5. Click the Count puncta button.

To view your puncta counts and stats follow these steps:

  1. At the bottommost widget, choose the image layer you want to view your puncta stats for in the Select layer to display table dropdown menu.

  2. Click on the Counts tab if it hasn’t already been selected to view puncta counts.

    • The first column specifies the ROI ID and the second column specifies the puncta counts for each ROI.
    • If no masks were specified, the ROI ID for all counts is -1.

  3. Click on the Puncta stats tab to view the area, intensity, and associated mask for each puncta.

    • The area corresponds to the number of pixels a puncta label covers.
    • The intensity is the aggregate pixel intensity in a puncta label.
    • The associated mask is the mask a punctum is in.