Insight Toolkit

Classes that bridgeITK code running in the Emscripten runtime environment with native JavaScript.

CPU, RAM, and load monitor for use with tmux

Cross compiling toolchains in Docker images

A docker image that supports rendering graphical applications.

Utilities and example for using CMake to build Cython modules - migrated to scikit-build

Docker image for running X GUI apps with OpenGL hardware acceleration via the nvidia driver.

CPU and memory usage monitoring programs for GNU Screen

Docker image for running X GUI apps with OpenGL hardware acceleration via the mesa drivers.

A plugin for craco to use vtk.js with create-react-app

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Modern, open source microCT methods to enhance accessibility, scalability, and reproducibility

A hello world project to demonstate Matlab mex file generation with CMake.

A debugger for CMake.

An Introduction to Docker for Research Software Engineers

Provides a sharded Zarr store

Presentation on basic ultrasound physics for medical imaging

Ultrasound image formation, processing, and analysis. Interfaces built off the ITKUltrasound library.

Matthew McCormick's curriculum vitae.

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Configuration files.

A multi-dimensional spatial image data structure for scientific Python.

Efficient and Effective 3D Visualization of Internal Neuroimage Structures with NiiVue for the Triangle Society for Neuroscience 2025 Conference

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Build CastXML and its dependencies (LLVM/Clang)

An ITK module to compute 3D image skeleton

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GitHub profile

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a WebGL2 based medical image viewer. Supports over 30 formats of volumes and meshes.

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CMake-based project providing macros and associated tools allowing to easily build Slicer CLI

A serverless application framework for large-scale data management and AI model serving

A registry of publicly available datasets on AWS

File IO with itk for napari.

Reproduce https://github.com/jupyter-book/mystmd/issues/2270

SCIFIO ImageIO plugin for ITK

A list of Free Software network services and web applications which can be hosted on your own servers

A staging area for patches to be pushed upstream to the official plastimatch repository, https://gitlab.com/plastimatch/plastimatch.git

ct2print for converting voxel images to mesh for 3D printing

The Polygon Mesh Processing Library

A template to start an ITK Module

Tools used to generate the SciPy conference proceedings

Notebooks for working with The Cancer Imaging Archive datasets. Have you written one? Submit a PR!

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High-throughput Application for Skeletal Imaging

Image analysis approaches to analyze the OAI magnetic resonance images

Simple site for displaying multiple articles and notebooks with a table of contents.

Template of open science publications to be submitted to the Insight Journal

ParaView Medical

A setup script to generate ITK Python Wheels

Pytest plugin for testing applications that use Pyodide

Zarr core protocol for storage and retrieval of N-dimensional typed arrays

Mesh triangle reduction using quadrics

EventEmitter3 - Because there's also a number 2. And we're faster.

Script to convert a TIFF to OME-Zarr while simultaneously converting the pixel type

Visualization of the Allen Mouse Common Coordinate Framework brain atlas with itk.js, vtk.js, and zarr.

Kitware Course in Biomedical Image Analysis and Visualization: ITK

Default GitHub community health files

http://trizpug.org/Members/cbc/mar-18-mtg

FltkImageViewer subtree from ITKApps.

ImageViewer subtree from ITKApps.

Open-source implementation of JPEG2000 Part-15 (or JPH or HTJ2K)

WebAssembly Python for servers and browsers. Built using Zig. Supports extension modules such as numpy and posix subprocesses.

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Source of the site

Workshop for compiled packaging

Multi-platform high-performance compute language extension for Rust.

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

SwiftShader is a high-performance CPU-based implementation of the Vulkan graphics API. Its goal is to provide hardware independence for advanced 3D graphics.

A minimal, type-safe, runtime-agnostic async DAG executor with compile-time dependency validation

Spatial omics analysis toolbox

PNG decoding and encoding library in pure Rust

A conda-smithy repository for conda-forge-pinning.

A conda-smithy repository for wasmtime-py.

A conda-smithy repository for itkwasm.

Official elastix repository

Repository for nvCOMP docs and examples. nvCOMP is a library for fast lossless compression/decompression on the GPU that can be downloaded from https://developer.nvidia.com/nvcomp.

A composite GitHub Action to build, test, and package, ITK remote modules

Insight Journal

awesome open list of pointers about open science for software and computational science

Command line tools for working with MyST Markdown.

pygccxml is a specialized XML reader that reads the output from CastXML or GCCXML. It provides a simple framework to navigate C++ declarations, using Python classes.

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

Sources for insightsoftwareconsortium.org website

http://www.insight-journal.org/browse/publication/213

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

Convert between itk and napari data structures.

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People that have contributed to OME-Zarr at some point

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cbor iwi and iwm interoperability package for NiiVue and ITK

brain2print

Demonstrate reading the platy dataset with ngff-zarr.

ITK-SNAP medical image segmentation tool

Re: https://github.com/InsightSoftwareConsortium/ITKElastix/issues/341

C-family Abstract Syntax Tree XML Output

Generation of a multi-scale spatial images for scientific imaging in Python

Iterative Hough Transform for 3D Line Detection

MyST is designed to create publication-quality, computational documents written entirely in Markdown.

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:zap: xarray data creation by data classes

A JavaScript toolkit for working with chunked, compressed, n-dimensional arrays

Interfaces for data (arrays and graphs) and storage formats (databases and file formats)

ITK Image IO for Scanco MicroCT .ISQ files

GitHub Action to check for consistency with ITK's Coding Style

Curated list of awesome things related to Deno

DICOM Web viewer using ITK reader and vtk.js for the rendering

The Open Data Platform for Sustainable, Accessible Lung Radiogenomics

A library to handle the *.meshb file format.

The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.

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ITK Doxygen nightly built with GitHub Actions and published to GitHub Pages

Python WebAssembly runtime powered by Wasmtime

a programming library with geometric algorithms

dcmqi (DICOM for Quantitative Imaging) is a free, open source library that implements conversion between commonly used imaging research formats and the standard DICOM representation: https://qiicr.gitbooks.io/dcmqi-guide

ITK Mesh IO for the MZ3 triangle mesh file format.

Multi-dimensional web-based image, mesh, and point set viewer

oneAPI Threading Building Blocks (oneTBB)

Cuberille Implicit Surface Polygonization for ITK

Create delightful python projects using Jupyter Notebooks

Package management made easy

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The ultimate cross-platform, bash-like shell

An ITK module to read DICOM spatial transforms.

image processing utilities

A temporary repository for updating the itkAnalyzeObjectMap

Implementations of ITK spatially-aware filters in PyTorch

Implement's Glenn Pierce's itk::FDFImageIO as an ITK Remote Module

http://insight-journal.org/browse/publication/953

External Module for Total Variation Algorithms, providing wrap for https://github.com/albarji/proxTV

An ITK module to read and write High-throughput JPEG2000 (HTJ2K) images.

A clean customizable documentation theme for Sphinx

A clean book theme for scientific explanations and documentation with Sphinx

ITK IO for images stored in zarr and n5 file formats

Filters for calculating higher order accurate numerical derivatives and gradients.

A Sphinx extension that automatically generates API documentation for your Python packages.

A test paper

Packages for creating MyST websites themes using React and Remix

Zarr Official Blog

Get Your Brain Straight Neuroimage Registration Workshops and Hackathons

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MeshIO class to read and write ITK meshes into STL files

Extremely fast, in memory, JSON and interface library for modern C++

A conda-smithy repository for spatial-image.

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MyST Plugin starter repo for ITK Widgets

Examples for the Insight Toolkit. http://itk.org/ITKExamples

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Run-length encoded memory compression scheme for an itk::Image

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ITK remote module from an IJ article at http://www.insight-journal.org/browse/publication/915

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Classes to perturb ITK mesh objects with Gaussian noise

Fast Point Feature Histogram

A napari plugin for itk-elastix

ITK routines for erosions/dilations using parabolic structuring functions

Parsing gigabytes of JSON per second : used by Facebook/Meta Velox, the Node.js runtime, ClickHouse, WatermelonDB, Apache Doris, Milvus, StarRocks

Real-world tests to benchmark ITK performance.

A framework for distributed large-scale image registration

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👩‍🎤 Headless, type-safe, UI components for the next generation Web3.Storage APIs.

Sources for the ITKSoftwareGuide.

WASI-enabled WebAssembly C/C++ toolchain

CBOR protocol implementation for C

Kitware Style Checker

zlib replacement with optimizations for "next generation" systems.

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SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

Read and write OME-Zarr in 3D Slicer

NVIDIA Clara Viz is a platform for visualization of 2D/3D medical imaging data

Official DCMTK Github Mirror

A Rich-compatible library for writing pixel images and ASCII art to the terminal.

Chatbot to retrieve information to response to users' query about the BioImage Model Zoo.

KvikIO - High Performance File IO

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Your Gateway to Open-Source Collaboration.

GitHub Action to set up micromamba

A web file browser for managing data on remote jupyter servers.

A pytest plugin to fetch test data from IPFS HTTP gateways during pytest execution.

A next generation Python CMake adaptor and Python API for plugins

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CMake ExternalData module with InterPlanetary File System support.

ZSTD (Zstandard) decoder for Web and Node.js, using WebAssembly.

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OpenJPH wrapper for medical imaging

Github Actions for Pyodide

Official repository of the OpenJPEG project

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Website: https://ormircommunity.github.io

A python render engine running on wgpu.

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Java or JVM-language binding for Wasmtime

Data Archive Manager

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Resources for teaching/preparing to teach bioimage analysis

XState Web Component Reactive Selector Controller