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

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

Distributed, Versioned, Image-oriented Dataservice

Collaborative Annotation Toolkit for Massive Amounts of Image Data

Extraction of 3D skeletons from meshes.

Graph theory analysis of brain MRI data

PyTorch Connectomics: segmentation toolbox for EM connectomics

Preprocessing and reconstruction of diffusion MRI

Read and write Neuroglancer datasets programmatically.

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

Visualize, share and annotate your large 3D images online

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. 🤠

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

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

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

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