Hello,
I have been using ImageJ (FIJI) to convert image stacks to 3D models (wavefront .obj format). Currently I am trying to determine how to automate this process. Currently I: 1) manually adjust the brightness/contrast, 2) merge the channels, 3) convert the stack to RGB, 4) convert the image to binary, 5) render the image in the 3D viewer, 6) save as a wave front file.
The problem is that I cannot find a utility in ImageJ that can bring out the features of the 3d image better than I can. I have tried deconvolution, and other utilities however I cannot remove myself from step 1. Would you recommend a different work flow, or do you have suggestions on different ways I can distinguish the background from the data?
Thanks!
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