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.

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. ⚡🔥⚡

Transformer based region discovery in spatial transcriptomics (but mostly MERFISH) datasets

For scientific volumetric data visualization in Blender.

3D/4D volumetric rendering of microscopy data

simple standalone BigDataViewer for multiple N5 (or HDF5) datasets

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and appar…

Read and write Neuroglancer datasets programmatically.

Unsupervised Learning for Image Registration

making montage or combine tiff images of different sizes