connectomics

Flood-Filling Networks for instance segmentation in 3d volumes.

Distributed, Versioned, Image-oriented Dataservice

Collaborative Annotation Toolkit for Massive Amounts of Image Data

Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.

Graph theory analysis of brain MRI data

PyTorch Connectomics: segmentation toolbox for EM connectomics

Extraction of 3D skeletons from meshes.

Read and write Neuroglancer datasets programmatically.

Visualize, share and annotate your large 3D images online

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

Preprocessing and reconstruction of diffusion MRI

The ENIGMA Toolbox is an open-source repository for accessing 100+ ENIGMA statistical maps, visualizing cortical and subcortical surface data, and relating neuroimaging findings to micro- and macroscale brain organization. 🤠

KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.

Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute

A performant, powerful query framework to search for network motifs

Marching Cubes & Mesh Simplification on multi-label 3D images.

A unified environment for DNN-based automated segmentation of neuronal EM images

Performant, pure-Python subgraph isomorphism and monomorphism search (aka "motif search")

Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.

Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.