NiiVue

NiiVue is web-based visualization tool for neuroimaging that can run on any operating system and any web device (phone, tablet, computer). This repository contains only the core NiiVue package that can be embedded into other projects. We have additional repositories that wrap NiiVue for use in jupyter notebooks, vscode, and electron applications.

News

The NiiVue iOS app is now available on iPhone and iPad.

Click here to see NiiVue live demos

What makes NiiVue unique is its ability to simultaneously display all the datatypes popular with neuroimaging: voxels, meshes, tractography streamlines, statistical maps and connectomes. Alternative voxel-based web tools include ami, BioImage Suite Web, BrainBrowser, nifti-drop, OHIF DICOM Viewer, Papaya, VTK.js, and slicedrop.

Local Development

To run a hot-loading development that is updated whenever you save changes to any source files, you can run:

git clone [email protected]:niivue/niivue.git
cd niivue
npm install
npm run dev

The command npm run demo will minify the project and locally host all of the live demos. The DEVELOP.md file provides more details for developers.

Developer Documentation

Click here for the docs web page

Projects and People using NiiVue

• Analysis of Functional NeuroImages (AFNI) Scientific and Statistical Computing Core (National Institutes of Health)
• BOOSTLET.js image processing plugins work with NiiVue.
• brainchop uses NiiVue for their drag-and-drop segmentation, brain extraction and parcellation tool
• BrainLife.io integrates NiiVue into ezbids
• CACTAS from Daniel Haehn's team is extending NiiVue drawing and segmentation capabilities
• ChRIS Research Integration System (ChRIS) from Boston Children's Hospital uses NiiVue
• Center for the Study of Aphasia Recovery (C-STAR) (University of South Carolina)
• Digital Brain Bank for navigating MRI datasets
• FMRIB's Software Library (FSL) Wellcome Centre for Integrative Neuroimaging (University of Oxford)
• FreeSurfer Laboratories for Computational Neuroimaging (Massachusetts General Hospital) uses NiiVue for FreeBrowse
• OpenNeuro.org uses NiiVue to visualize datasets
• neurodesk uses NiiVue for their QSMxT Quantitative Susceptibility Mapping toolbox
• Neuroinformatics Research and Development Group embeds NiiVue in tractoscope
• nilearn is extending ipyniivue
• niivue-vscode is a VSCode extension for displaying images
• QuantCo is using NiiVue in medical imaging workflows
• FSL Clinical is using NiiVue in brain imaging reports
• brain2print (from the NiiVue team) uses NiiVue for showing both volume data and converted meshes
• ct2print (from the NiiVue team) uses NiiVue for showing volume and mesh data
• ipyniivue allows NiiVue to be used in Jupyter Notebooks
• T2Lesion (from the NiiVue team) uses NiiVue to show input data and segmented lesion masks
• NiiVue Desktop (from the NiiVue team) uses NiiVue in a crossplatform Electron app
• NiiVue iOS (from the NiiVue team) uses NiiVue in a hybrid Swift + webView mobile app
• NiiVue Neglect uses NiiVue to visualise stroke lesion data in the spatial neglect severity prediction tool

Funding

• 2021-2022 P50 DC014664 NIH NIDCD NOT-OD-21-091
• 2023-2026 RF1 MH133701 NIH NIMH

Supported Formats

NiiVue supports many popular brain imaging formats:

• Voxel-based formats: NIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7, DSI-Studio SRC.
• Mesh-based formats: GIfTI, ASC, BYU/GEO/G, BrainSuite DFS, ICO/TRI, PLY, BrainNet NV, BrainVoyager SRF, FreeSurfer, MZ3, OFF, Wavefront OBJ, STL, Legacy VTK, X3D.
• Mesh overlay formats: GIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
• Tractography formats: TCK, TRK, TRX, TSF, TT, VTK, AFNI .niml.tract
• DICOM: DICOM and DICOM Manifests