search radius cluster algorithm
- fastest implimentation is hist3 with binsize = search radius
can easily require multiple molecules in the search radius by filtering:
so if we want 15 nm search radius, just make 15nm steps
M>3require at least 3 molecules in each 15 nm “search radius” (i.e. bin).
However this is going to crash the memory to generalize straight to 3D with same search radius — (matrix 4000 x 4000 is fine, 4000^3 is not).
so we use the above approach to 2D cluster the raw image data to ID initial clusters for investigation, and 3D histogram these guys.
matlabs morphological algorithms like bwareaopen, regionprops etc work in 3D!
simple extension of hist3 cluster algorithm. A beautiful inroad to all of matlabs image processing options, including regionprops, watershed, imfilter. Note though matlab lacks fspecial 3D there is a quality implementation here: fspecial3