Tutorial¶

Utils¶

Tutorials showcasing how to use the utils folder.

Pipelines¶

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.

Automatic and manual segmentation pipeline

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.

Soma detection notebook

Preprocessing¶

Vizualization¶

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