Popular GitHub Repositories for Connectomics

Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)

An image enhancement and segmentation pipeline for generating connectomic reconstructions from X-ray holographic nanotomography, using CycleGANs, Local Shape Descriptors, and Mutex Watershed. Built with PyTorch, Daisy, and Gunpowder.

Flood Fill Network for 3d Electron Microscopy volume neuron segmentation. Adapt from google FFN-master add notes and custom variation and parallelization (for windows and our retina & LGN data)

Python package for CITS algorithm: Causal inference from time series data