Try
xy = vertcat(a1RP.Centroid)
distances = pdist2(xy, xy)
Be aware that centroids are x,y, which is (column, row), not (row, column) -- just in case you ever need to do anything with the image itself. plot() should be okay though because it uses x & y.
So you did basically that and got a 100x100 array that gives the distances in pixels between every one of the 100 blobs in your image.
For the spatial calibration, what is 64 microns? What is "pitch"? Is that the distance between pixels, or the full field of view of the image?
If you used XData and YData options in imshow(), then pdist2 should give the output in microns already. If you didn't then the result in in pixels and you'll have to multiply those distances by the spatial calibration factor. Let's say that the pixel to pixel spacing is 64 microns, and you want the distance between the 34th blob and the 78th blob. You can do
dist = distances(34, 78) * 64;
If you want, you can convert the whole distances matrix at once so you don't have to do it one by one:
distances = pdist2(xy, xy) * 64 % ALL spacings will be in microns now.
