Tutorial

Utils

Tutorials showcasing how to use the utils folder.

Pipelines

Semi-automatic Annotation Pipeline

Demonstrate pulling data and pushing traced annotations.

Segmentation

Notebooks showing how to manually and automatically segment data.

Algorithms

Adaptive Thresholding

Demonstrate region growing methods using GMM and simple ITK.

Connecting Fragments

Demonstrate fragment path connections using Viterbi algorithm on a simple grid example.

Trace Analysis

Demonstrate estimation of curvature and torsion on simple curve, and fitting splines to a neuron.

Soma Detection

Demonstrate simple soma detection algorithm on known somas in Janelia dataset, brain1.

Preprocessing

Vizualization

These tutorials demonstrate tools to load and visualize data from s3 buckets or .swc files.