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

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

Extraction of 3D skeletons from meshes.

Distributed, Versioned, Image-oriented Dataservice

Collaborative Annotation Toolkit for Massive Amounts of Image Data

Graph theory analysis of brain MRI data

PyTorch Connectomics: segmentation toolbox for EM connectomics

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

Read and write Neuroglancer datasets programmatically.

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. 🤠

Visualize, share and annotate your large 3D images online

A performant, powerful query framework to search for network motifs

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

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

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

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

Scalable Optical Flow-based Image Montaging and Alignment

Brainconn - an R package for visualising brain connectivity data in 2D and interactive 3D

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