I am trying to use Analyze skeleton to measure the total length of filamentous Cyanobacteria in lake water samples.
So far I have managed to get good results using skeletonize and Analyze skeleton. This way I get information about the length of the branches. If I then sum up all the lengths of all the branches I have the total length in my sample.
I have made a simple Macro in ImageJ:
run(“Convert to Mask”);
run(“Analyze Skeleton (2D/3D)”, “prune=[shortest branch] show display”);
This works great to get the information I need. However I would like to add something to the Macro to get only the data column of Branch length either saved to a .csv or excel file. I would like to have it in such a way that I will be able to run the macro on all the images inside a folder.
Is there anybody who could help me figuring out how to make a proper Macro for this?