Tracing

A package to trace filament like structures in 2D/3D images.

Fiji Tracing

Usage

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.

Install

1. 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
   

2. 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/.

Getting started

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.