Browser-based viewer for OME-ZARR (OME-NGFF) microscopy data with GPU-accelerated rendering.
Pre-release · Launch Viewer · Documentation · Watch Demos · Embed in Your Site
Opening data
- Local files, straight from disk. No upload and no server. Browse ZARR folders on your own machine and the data never leaves it.
- Remote URLs. Anything served over HTTPS with CORS and range requests: S3, R2, GCS, Azure Blob, your own nginx.
Looking at it
- Multi-channel display with per-channel colour, contrast, gamma and histograms.
- Auto-contrast from the pixel data, percentile based (2% to 98%), one click per channel or all at once.
- Grayscale and inverted modes. Inverted flips the backgroud and pixel intensity, which prints well and makes a coloured mask overlay far easier to read.
- Z-projection: maximum, mean and minimum, over a Z-range you choose.
- GPU-accelerated tiled rendering via deck.gl WebGL, comfortable on images past 100,000 pixels a side.
- HCS plates. Well picker grid, field view and plate overview for 96, 384 and 1536-well screens.
Working with it
- Annotations. Polygons, lines, points and distance measurements, with areas and lengths in real units. Auto-saved to browser storage, exportable as CSV or GeoJSON.
- Segmentation labels. Load them from inside the ZARR or attach them from a local folder or a URL. Opacity, colour modes, drag to reorder.
- Analytics and phenotyping. Attach a measurements table and colour objects by any column, as a continuous heatmap or one colour per category. Filter by value, and build named phenotype groups out of those filters.
- Annotation templates. Reusable bundles of colour, class label and keyboard shortcut, applied to everything you draw next.
- Shareable deep links. The URL tracks zoom, position, channels and Z-slice as you work, Google Maps style. Copy it to hand someone the exact view.
Throughout
- Privacy first, zero install. Everything happens in your browser. No account, and no data sent anywhere.
Full guides at find-nuclei.github.io/docs.
| Getting Started | Open your first image |
| Local Files · Remote URLs · Authenticated Sources | Getting data in |
| Channels · HCS Plates | Display and navigation |
| Labels · Analytics & Phenotyping · Analytics Data Format | Segmentation and measurements |
| Annotations · Templates | Drawing regions |
| Sharing Views · Embedding · Data Server | Publishing and hosting |
Click any link to open directly in the viewer:
| Example | Description |
|---|---|
| Nuclear segmentation, labels on | Image plus its segmentation mask, coloured per object |
| Chicken Embryo MIP | v0.5 sharded, single channel |
| Zebrafish Lateral Line | 3D multi-channel with labels |
| HCS Plate 190129 | v0.5 multi-well plate, 5 channels |
| HCS Plate 9512 | v0.4 multi-well plate, 2 channels |
| Large Image 9822152 | 144K×93K pixels, multi-resolution |
| RGB Image 9798462 | 3-channel RGB, 21K×16K |
All datasets from the Image Data Resource (IDR), read straight from its public bucket. Nothing is copied or re-hosted.
Embed an interactive OME-ZARR viewer in any web page with two lines of HTML:
<script src="https://find-nuclei.github.io/embed/v1/viewer.js"></script>
<find-nuclei-viewer
url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
labels="on"
width="100%"
height="500"
></find-nuclei-viewer>No iframe, no build step, no framework required. Works in any CMS (WordPress, Drupal, Ghost, PubPub). Full style isolation via Shadow DOM.
- Live Demo: see it in action with IDR datasets
- Embedding Guide: full attribute reference and examples
- Digital Pathology: whole slide imaging (WSI) for H&E and IHC slides
- Spatial Biology & Multiplexed Imaging: multi-channel IF, CODEX, MERFISH, seqFISH
- High-Content Screening: automated 96/384/1536-well plate imaging
- Confocal & Light-Sheet Microscopy: Z-stacks and time-lapse live-cell imaging
- Electron Microscopy: serial-section TEM and volume EM for connectomics
- Super-Resolution Microscopy: STORM, PALM, SIM
- Spatial Transcriptomics: Visium, Slide-seq, MERSCOPE
- Organoid & Spheroid Imaging: 3D cell culture with Z-stack support
- Live-Cell Imaging: dynamic cellular processes over time
- Tissue Clearing & 3D Imaging: CLARITY, iDISCO
- Format: OME-ZARR (OME-NGFF) v0.4 and v0.5, including sharded stores, plus
bioformats2rawlayouts. - Any modern browser for remote URLs, including Firefox and Safari.
- Chrome or Edge to open files and folders from disk. That path uses the File System Access API, which the other browsers do not implement yet.
All data is processed locally in your browser. No files are uploaded to any server.
Copyright (c) 2026 Find Nuclei. All rights reserved.
For licensing inquiries: info@find-nuclei.com
- GitHub: Find-Nuclei/find-nuclei.github.io
- Issues: Report a bug
- Email: info@find-nuclei.com