BrainLine: Whole-Brain Fluorescence Volume Analysis Pipeline

Leverage ilastik to perform axon detection and soma detection on brain images, and combine with CloudReg image registration for visualization and analysis.

Semi-automatic Annotation Pipeline

Demonstrate pulling data and pushing traced annotations.


Notebooks showing how to manually and automatically segment data.


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.


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