connectomics

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.

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

Distributed, Versioned, Image-oriented Dataservice

Collaborative Annotation Toolkit for Massive Amounts of Image Data

PyTorch Connectomics: segmentation toolbox for EM connectomics

Graph theory analysis of brain MRI data

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

Read and write Neuroglancer datasets programmatically.

NeuroCraft Fly by Evan Sinclair Smith: an interactive fruit-fly connectome model in Minecraft. Public project home and release roadmap.

Scalable Optical Flow-based Image Montaging and Alignment

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

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

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.

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

A curated list of fruit fly connectome projects: MaleCNS, FlyWire, brain simulations, embodied models, games, and research tools.

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