Tutorials

Running Notebooks Locally

1. Install PySNT following the installation guide

2. Download notebooks: Find them in the ./docs/notebooks/ directory of PySNT’s source code, or use the download button (↓) at the top of each notebook page

3. Open in Jupyter Lab or your preferred IDE within your pysnt environment

Note

If you haven’t installed PySNT’s GUI dependencies, you’ll need to install ipykernel first:

pip install ipykernel # or mamba install -n pysnt ipykernel

See also

• Install - Installation instructions

• Quickstart - Get started quickly

• Overview - Tour of pysnt’s architecture

• Limitations and Quirks - Known limitations and workarounds

Available Tutorials

•  T01: Single Cell Analysis
•  T02: Hemisphere Analysis
•  T03: Volumetric Quantifications
•  T04: Spatial Intersection Between Trees
•  T05: Visualizing Reconstructions in napari
•  T06: Unsupervised Classification of Projection Neurons
•  T07: Curvature Optimization with Automated Path Tracing