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

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

Access to DVID API

This repository aims to make analysis on human brain tissue (EM data). This work is done within the chair of Lichtman Lab. at Harvard University.

Virtual Fly Brain blog and documentation site

MICrONS TA3 connectivity database

Final Project for CSCI 3397 - Biomedical Image Analysis. Using Pytorch Connectomics and 3D UNet model to implement 3D segmentation for synapse detection, using semi-unsupervised learning

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.

R tools for EM tracers

Code for processing DTI data and performing tractography analyses

Tools for accessing data from a catmaid server

Codebase for my master thesis titled "Cell Type Clustering in Volume EM Data: A Graph Neural Network Based Approach"

Examining the effect of proofreading on inferences in connectomics

Python client for clio-store

Code and data used in Bordt et al (2019) Synaptic inputs and connectivity of a sparsely branched ganglion cell in rabbit retina

This is the official C-PAC (Configurable Pipeline for the Analysis of Connectomes) brainlife.io app. Currently this app runs either the default pipeline or one of our preconfigured pipelines.

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

Visualize neural networks into a heirarchial graph using networkx. Weights and signs will be respected.

Classification of brain networks based on graph centrality measures