@tferr I am having some trouble figuring out how to use the Fit Paths option in simple neurite tracer from a script.
I have a set of images and associated .traces files (100+) from a while back and I would like to apply the ‘Fit Paths’ option on the already traced paths and save the results.
The script would:
- open the image and associated traces file
- select all paths
- run Fit Paths… with diameter = X, optimization options 1) and 2) and replace nodes option.
- save traces
I am looking through the
traces javadocs and I assume
PathFitter (https://javadoc.scijava.org/Fiji/tracing/PathFitter.html) is the class I am looking for, but I am getting lost when trying to use it from a python script (for example, how to set the diameter and optimization options before running the
Any guidance or tips would be much appreciated!