I am processing images of pumice for particle analysis. This means i have a series of binary images which contain glass (black) and void space (white) which accounts for the porosity of my samples.
I need to measure the total perimeter of my bubbles but due to the thin sectioning technique and thin nature of some of the bubble walls I have lost many of the thin bubble walls which reduces the overall “bubble perimeter”
842A63_100_4-connected.tif (192.9 KB)
Above is an original binary image with missing connections, examples of where connections should be made are shown in yellow.
I can apply the watershed to my binary image but this misses connections in some places and adds them where they dont belong in others. See image below.
842A63_100_4-watershed.tif (1.5 MB)
I tried using the Interactive Watershed plugin but found this to be less effective than the seperation achieved by the existing glass walls. Many objects were merged and no new ones created. No matter what I did to the various controls in the plugin.
not sure if I am just using the tools less well than I could be or whether what I want isnt do-able in Fiji…
I know this can be done on 2D and 3D datasets in Avizo using “separate objects” and you can alter the number of connections made by changing the neighborhood and the marker extent (see video https://www.youtube.com/watch?v=6tlABSI1e3A) but havent got access to this on my laptop.
I have at least 100 images like this so need something that is automated as a) it needs to be repeatable by others and b) i dont have the time to manually re-connect glass wals. Does anyone know how I can get better film reconstruction?