Web Apps
Many of the tools we build are compact, robust, and modular. Combined in a thin browser-based interface, they make capable neuroimaging workflows available without a desktop installation or a remote compute service.
These applications run locally in the browser using WebAssembly and, where useful, WebGPU. Your data stays on your device: the computation uses your own CPU and graphics hardware rather than uploading sensitive images to a server.
Built from interoperable pieces
Small, focused tools can be combined into workflows that are easier to inspect, adapt, and deploy. The dwi2trx pipeline illustrates that approach: a lightweight wrapper connects proven tools for conversion, brain extraction, image processing, visualization, and tractography.
Explore the apps
Tools from our team and others that showcase how our building blocks can be combined for a wide range of uses.
- brain2printSegment NIfTI images and create printable 3D brain meshes in the browser.ITK-Wasm / niimath / NiiVue
- brainchopAI-powered brain segmentation that runs on local images in the browser.brainchop / NiiVue
- browserQCReview neuroimaging data and support quality-control decisions in the browser.brainchop / dcm2niix / niimath / NiiVue
- CALMaRAutomated stroke-lesion mapping, connectivity analysis, and reporting.NiiVue
- DefaceRemove facial features from structural images before sharing.brainchop / niimath / NiiVue
- dicompareCompare, validate, and share DICOM acquisition protocols across sites.none listed
- dwi2trxPrepare diffusion MRI tractography for interactive exploration and 3D output.brainchop / dcm2niix / GPUstreamlines / niimath ? NiiVue
- Easy MP2RAGE T1 MapCreate quantitative T1 maps from MP2RAGE acquisitions.NiiVue
- EdgeRegPerform local rigid and affine MRI registration directly in your browser.brainchop / niimath / NiiVue
- MuscleMapSegment and review whole-body or regional muscle MRI data.NiiVue
- NeurodeskEDULearn reproducible AFNI functional-imaging preprocessing through an interactive example.NiiVue
- niimathRun compact image-processing commands with an interactive local viewer.niimath / NiiVue
- niiNavExplore neuroimaging volumes and surfaces with a lightweight web viewer.NiiVue
- qMRustUse quantitative MRI methods from qMRLab in a browser-native app.NiiVue
- QSMblyRun a guided quantitative susceptibility mapping workflow from DICOM or NIfTI data.NiiVue / QSM-WASM
- SeedSegSegment intraprostatic gold fiducial markers in prostate MRI.NiiVue
- Spinal Cord ToolboxUse browser-based spinal cord MRI segmentation workflows.NiiVue
- VesselBoostSegment blood vessels from MRI angiography with guided local inference.NiiVue
Core building blocks
These reusable modules provide the capabilities leveraged by the web apps.
- brainchopFor brain extraction, segmentation and parcelation.
- dcm2niixDICOM to NIfTI image conversion.
- GPUstreamlinesConverts voxels to tracts.
- ITK-WasmProvides access to this legendary image processing library.
- niimathHigh performance image processing.
- NiiVueVisualization of voxels, meshes, connectomes and streamlines.
- QSM-WASMQuantifies of susceptibility weighted imaging.
References
- brain2print is described as a browser-based workflow for preparing neuroimaging data for 3D printing.
- Masoud et al. (2023) describe Brainchop, an in-browser MRI segmentation and rendering application.
- niimath provides compact, high-performance neuroimaging image processing.
- Dörig et al. (2026) describe NeurodeskEDU, an interactive and reproducible neuroimaging education resource.