Hi all, I am trying to identify the cell boundaries of a binary image using the Analyze Particles feature of ImageJ. If I start with Image1 and use Analyze Particles, everything is mostly fine. The only issue is that adjacent cells do not share a boundary, and have some undetected space in between them (Image2). I would like adjacent cells to share a boundary because this will allow me to easily recognize which boundary points are common between adjacent cells and how that boundary changes overtime (for future analysis).
Potential solution #1: To overcome this I modified Image1 why by inverting the image, using the Skeletonize command, and inverting again -resulting in Image3. Now each cell has close to a single-pixel thick boundary, but the Analyze Particles command no longer detects cells, I think because some boundaries are not exactly single-pixel thickness (Image4). Is there a command different from Skeletonize that might be more appropriate? I don’t think Erode-Dilate operations would work for this?
Potential solution #2: I use Analyze Particles on Image1 to identify the centroids of all cells. Use Image3 to identify (x,y) coordinates of all boundary points (in matlab). Then, for each centroid, determine which boundary points belong to that centroid. This seems like a potential solution but I can’t think of what programming logic to use to know which (x,y) points belong to a particular cell?