README.md

Part 1

In this sections students will be guided through the the multiple ways neuronal processes are reconstructed in SNT. Exercises will focus on scripting the 'tracing' process.

Key Concepts

Path, Bidirectional A* search, Hessian analysis, Secondary image, Path fitting, Path filling

Exercises

1. Scripted tracing demo:

   1. Load the ddaC neuron sample image: File> Choose Tracing Image> From Demo... (Drosophila ddaC neuron (2D))
   2. Disable A* search (Main pane, auto-tracing widget)
   3. Make a straight-line path by clicking on the soma and a distal dendrite
   4. Drag and drop scripted-tracingResources.groovy into the main ImageJ window (or use File>New>Script... in Fiji, or simply press [)

2. intensity_profile.py

3. time_profile.py

4. Scripted tracing: In the Script Editor' look for the following script in Templates> Neuroanatomy> Tracings (source):

   1. Scripted_Tracing_Demo_(Interactive).py
   2. Scripted_Tracing_Demo.py

Homework

In this session we scripted an A* search from a manual path. Would would you modify the script to use a ROI (e.g., a line or a set of points) instead?

Library	Relevant Classes
ImageJ1	ImagePlus, Roi (including Line, and PointRoi)
SNT	SNTService, SNT, Path, PathAndFillManager, PointInImage

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Resources

SNT Manuscript | SNT Manuscript scripts | User Documentation | Forum | Source Code | API