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VERSO (Verso allows Easy Registration of Sections, Obviously)
BrainBox is a web application that lets you annotate and segment 3D brain imaging data in real time, collaboratively.
a place to work on a specification for skeletons
A repository to organize data models and code for creating a pilot common connectivity matrix for BRAIN CONNECTS
Reconstructing True 3D Spatial Omics at Single-Cell Resolution
Use claude code and codex for free in the terminal, VSCode extension, and discord like OpenClaw (voice supported)
Vim-fork focused on extensibility and usability
[Nature Communications] Adaptive Riemannian Optimization for Multi-Scale Diffeomorphic Registration
Interactive 3D Allen CCF mouse brain atlas viewer with DANDI dataset integration
Official implementation of MuViT (CVPR 2026), a ViT-based architecture for multi-scale modelling of gigapixel microscopy images.
Python package for analysis and visualization of functional ultrasound imaging data.
An API for accessing atlas registered 3D volumetric data.
Python package for the openMINDS metadata models. The package contains all openMINDS schemas as Python classes in addition to schema base classes and utility methods.
Data and code supporting Hansen et al., 2026, PLOS Biology "Synapse types are spatially associated with regional hemodynamics in the mouse brain"
Derotate images acquired via multiphoton calcium imaging
Automated and reproducible analysis of multiphoton imaging datasets
A tile server for WSI stored in S3-compatible object storage.
SAM-Med3D: An Efficient General-purpose Promptable Segmentation Model for 3D Volumetric Medical Image
A fluid, morphing config for your Linux desktop
A fluid, morphing shell for your Linux desktop
Omnipose: a high-precision solution for morphology-independent cell segmentation
A mouse brain histology tool for neuroscientists.