PySNT: Quantification of neuronal anatomy in Python#

PySNT

Trace, analyze, and quantify neuronal morphology — from Python.

PySNT brings SNT's tracing tools and neuroanatomy analytics to Python, providing a unified toolkit for morphometry that works interactively in notebooks or for automating large-scale studies.

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Getting Started

Set up your environment and run your first script with step-by-step guidance.

 Install
Morphometric Analysis

Quantify, transform, and compare neuronal morphology at single-cell and population levels.

 T01: Single Cell Analysis
Atlas & Circuit Analysis

Integrate reference brains, atlases, public databases, and whole-brain projectomes into your analysis.

 T02: Hemisphere Analysis
3D Visualization

Generate publication-ready figures and interactive 3D renderings of neuronal morphology.

 T03: Volumetric Quantifications
Geometric Analysis

Measure spatial extent, arbor overlap, and three-dimensional arrangements of dendritic and axonal trees.

 T04: Spatial Intersection Between Trees
Python Ecosystem

Interoperability with napari, pandas, NumPy, and the broader scientific Python stack.

 T05: Visualizing Reconstructions in napari
Classification of Cell Types

Cluster and classify neurons using morphometric and topological features.

 T06: Unsupervised Classification of Projection Neurons
ML Ground Truth Curation

Build quality-controlled training datasets: refine traces, detect crossovers, and validate reconstructions.

 T07: Curvature Optimization with Automated Path Tracing
And More

Sholl, Strahler, persistence diagrams, graph theory, growth dynamics, and full access to the SNT/Fiji ecosystem.

https://imagej.net/plugins/snt/#overview