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.
Path, Bidirectional A* search, Hessian analysis, Secondary image, Path fitting, Path filling
-
Scripted tracing demo:
- Load the ddaC neuron sample image: File> Choose Tracing Image> From Demo... (Drosophila ddaC neuron (2D))
- Disable A* search (Main pane, auto-tracing widget)
- Make a straight-line path by clicking on the soma and a distal dendrite
- Drag and drop scripted-tracingResources.groovy into the main ImageJ window (or use File>New>Script... in Fiji, or simply press [)
-
Scripted tracing: In the Script Editor' look for the following script in Templates> Neuroanatomy> Tracings (source):
- Scripted_Tracing_Demo_(Interactive).py
- Scripted_Tracing_Demo.py
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 |
SNT Manuscript | SNT Manuscript scripts | User Documentation | Forum | Source Code | API