Deep-learning based pipeline for analysis of whole-brain light sheet microscopy images

A WebGPU-native out-of-core rendering system for large virtualized volumetric data.

Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

A deep-learning library for denoising images using Noise2Void and friends (CARE, PN2V, HDN etc.), with a focus on user-experience and documentation.)

AI coding assistant skill (Claude Code, Codex, OpenCode, Cursor, Gemini CLI, OpenClaw, Factory Droid, Trae). Turn any folder of code, docs, papers, images, videos, or YouTube links into a queryable…

A visual-based graph node editor for training computer vision models.

Pure MLX implementations of UMAP, t-SNE, PaCMAP, TriMap, DREAMS, CNE, MMAE, and NNDescent for Apple Silicon. Metal GPU for computation and video rendering.

HDF5 for iOS and OS X

Eigent: The Open Source Cowork Desktop to Unlock Your Exceptional Productivity. Local and Free Alternative to Claude Cowork.

Gesture-based Interactive Exploration of Single Cell Embeddings

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

This is a connectivity map viewer for the Spinal Cord project U01 Spinal cord.

Hardware documentation for mesoSPIM-Bechtop microscope project

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

An open-source Python toolkit for large-scale fluorescence microscopy data alignment and fusion.

A Python script that converts BigDataViewer HDF5 files into a list of sparse OpenVDB files.

3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK)

Awesome custom widgets made for QT Desktop Applications. Simplify your UI development process. These widgets can be used in QT Designer then imported to PySide code.

[Nature Communications] Adaptive Riemannian Optimization for Multi-Scale Diffeomorphic Registration

A tool for translating between common coordinate frameworks using deformation matrices.

This repository provides a 3D implementation of DINOv2 for self-supervised pretraining on volumetric (3D) medical images using Lightly, MONAI, and Pytorch Lightning!

Aleph One is the open source continuation of Bungie’s Marathon 2 game engine.

v1.2 GLSL volume rendering. Able to view NIfTI, DICOM, MGH, MHD, NRRD, AFNI format images.

A re-implementation of antsMultivariateTemplateConstruction2.sh using optimized image pyramid scale-space and qbatch support

SpriteKit Floating Bubble Picker (inspired by Apple Music) 🧲

Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

Stitch images taken on a diagonal using the SPIM microscope

AI Toolkit for Healthcare Imaging

PyTorch Lightning + Hydra. A very user-friendly template for ML experimentation. ⚡🔥⚡