A package to trace filament like structures in 2D/3D images.
All the neccesssary Fiji junk is in the fijiScripts/ folder.
This currently calls Fiji from the command line with a pre-made Jython script BobNeuriteTracer_v2_.py
.
Our ultimate goal is to implement our own A* tracing between successive points.
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Fiji Tracing requires a system install of a lifeline version of the Fiji.app
Download from https://imagej.net/software/fiji/downloads#life-line-fiji-versions
You want the one referred to as:
Java 8, 2017 May 30, "Just prior to a sweeping update to nearly all components."
You need to put the lifeline version of Fiji.app (20170530) in the following folder where
<user>
is your username on macOS<user>/Documents/fiji_old/Fiji.app
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Please note, here we will be testing tracing by loading stack/annotations with PyMapManager.
python -m venv tracing_env
source tracing_env/bin/activate
pip install -e .
# this needs to be from
# branch 'cudmore-fix-interface'
pip install -e ../PyMapManager/.
In tests/test_fiji_tracing_pymapmanager.py, run test_tracing_pymapmanager()
.
Be sure to specify the corect path on your system.
tifPath = '/Users/cudmore/Sites/PyMapManager-Data/one-timepoint/rr30a_s0_ch2.tif'
The output should look like this. The red points are user defined control points. The yellow line/points is the full tracing coming back from Fiji - Simple Neurite Tracer.