A curated list of resources, papers and articles for 3D volumetric segmentation of connectomics in EM Images.

Semantic segmentation of the connectomics volume with limited amount of labeled data. It is my research project at TU Dresden.

Volume Image Environment

Virtual Fly Brain blog and documentation site

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)

Study the connectome structure in C. Elegans by finding paths between a set of neuron classes present.

Repository for code built during 3 month internship with Barabasi Lab (Oct 22 - Jan 23). In this project, we aim to build a diffusion-based method for density-equalizing the 3D connectome. Supervisors: Albert-Laszlo Barabasi & Csaba Both.

interactive search and analysis for neuronal motifs

Graph Theoretical Network Analysis on the Drosophila Hemibrain Connectome provided by Google Research

Code for "Bayesian reconstruction of memories stored in neural networks from their connectivity" https://arxiv.org/abs/2105.07416

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

A (soon to be) lightweight Python package for accessing single-cell connectome networks with metadata.

Semantic segmentation architectures for connectomics.

Tools and wrappers for skeletonization.

Code for processing DTI data and performing tractography analyses

BRAPH 2.0 is a comprehensive software package for the analysis and visualization of brain connectivity data, offering flexible customization, rich visualization capabilities, and a platform for collaboration in neuroscience research.

Comparative Connectomics for Python

Metric learning and contrastive learning for neuron segmentation

Repo for the article on "Modeling the Neurocognitive Dynamics of Language across the Lifespan"

Tools for accessing data from a catmaid server