NiiVue

NiiVue is web-based visualization tool for neuroimaging that can run on any device (phone, tablet, computer).

Local Development

See the Documentation for usage. The easiest way to develop with NiiVue is to run a hot-loading page that is updated whenever you save changes to any source files:

git clone git@github.com:niivue/niivue.git
cd niivue
npm install
npm run dev

Projects using NiiVue

• Analysis of Functional NeuroImages (AFNI) uses NiiVue for afni_proc.py
• BOOSTLET.js image processing plugins work with NiiVue.
• brain2print uses NiiVue for showing both volume data and converted meshes
• brainchop uses NiiVue for drag-and-drop segmentation, brain extraction and parcellation tool
• BrainLife.io integrates NiiVue into ezbids
• CACTAS is extending NiiVue drawing and segmentation capabilities
• ChRIS Research Integration System (ChRIS) uses NiiVue
• ct2print uses NiiVue for showing volume and mesh data
• deepsyence by Thuy Dao
• FMRIB's Software Library (FSL) uses NiiVue for cloud tools and documentation
• FSL Clinical is using NiiVue in brain imaging reports
• fideus has developed the ITK-Wasm plugins.
• FreeSurfer Laboratories for Computational Neuroimaging uses NiiVue for FreeBrowse
• Galaxy is a web platform for research that embeds NiiVue
• huggingface integrates NiiVue.
• The Insight Journal uses NiiVue to embed interactive illustrations
• ipyniivue allows NiiVue to be used in Jupyter Notebooks including py.cafe
• LAMBADA (OpenBrainAtlas) – A reference atlas of the developing postnatal mouse brain, created using tissue clearing and light-sheet microscopy at the Paris Brain Institute (Institut du Cerveau). It uses NiiVue for 2D/3D visualization of brain structures, volume overlays, and mesh rendering.
• LINC Gallery uses NiiVue to showcase data from LINC, an NIH BRAIN CONNECTS center focused on mapping brain connections.
• neurodesk uses NiiVue for their QSMxT Quantitative Susceptibility Mapping toolbox
• NeuroFLAME uses federated learning to train models across locations while keeping data securely on-site.
• Neuroinformatics Research and Development Group embeds NiiVue in tractoscope
• neurosift NWB visualization and DANDI exploration
• neurosynth compose uses NiiVue for display
• nilearn is extending ipyniivue
• niivue-vscode is a VSCode extension for displaying images
• NiiVue Desktop uses NiiVue in a crossplatform Electron app
• NiiVue iOS is a Swift tool available on the Apple App store for MacOS and iOS
• NiiVue Neglect uses NiiVue to visualise stroke lesion data in the spatial neglect severity prediction tool
• OpenMedView uses NiiVue to valid image registration
• OpenNeuro.org uses NiiVue to visualize datasets
• Plurimedia uses NiiVue in client work for medical image visualization
• QuantCo is using NiiVue in medical imaging workflows
• Slice:Drop Reloaded uses NiiVue to extend the original slicedrop
• T2Lesion uses NiiVue to show input data and segmented lesion masks
• VoxLogicA-UI makes advanced medical imaging analysis intuitive

Funding

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

Supported Formats

NiiVue natively supports many popular brain imaging formats, with additional support for DICOM, MINC, and TIFF available via plugins:

• 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, WRL, X3D.
• Mesh overlay formats: GIfTI, CIfTI-2, MZ3, SMP, STC, FreeSurfer (CURV/ANNOT)
• Tractography formats: TCK, TRK, TRX, TSF, TT, VTK, AFNI .niml.tract