How to list surface voxels in a 3D ROI

I have 3D ROIs that select out cells in a 3D confocal stack. Using the 3D ROI manager, I can use the ‘List Voxels’ function to list all the voxels in my ROI. Can anyone suggest a means to extract just those voxels that make up the surface of the 3D ROI?



Hi @Whelan_Ian,

Maybe the simplest thing to do is to draw the 3D rois contours and then list the voxels :

  • From a labelled image draw the rois contour with the plugin 3D Draw ROIS (raw image is none and seg is your labelled image, Display 3D labelled rois must be checked).
  • Add the image LabelRoi to 3DManager and list voxels.