README.md

December 1, 2020 · View on GitHub

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?

LibraryRelevant Classes
ImageJ1ImagePlus, Roi (including Line, and PointRoi)
SNTSNTService, SNT, Path, PathAndFillManager, PointInImage

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Resources

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