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

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. 🤠

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

Read and write Neuroglancer datasets programmatically.

Visualize, share and annotate your large 3D images online

A performant, powerful query framework to search for network motifs

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

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.

Scalable Optical Flow-based Image Montaging and Alignment

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")

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

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.