Browser-based viewer for OME-ZARR (OME-NGFF) microscopy data with GPU-accelerated rendering.
Pre-release — Launch Viewer · Watch Demos · Embed in Your Site
- Open local files directly from disk — no upload, no server. Browse ZARR folders from your computer. All data stays on your machine.
- Shape annotations with local persistence — draw polygons, lines, points, and distance measurements. Auto-saved to browser storage. Export as CSV spreadsheet or GeoJSON.
- Segmentation label overlays — load labels from the ZARR or link from your local or network drive. Adjustable opacity, color modes, drag-to-reorder rendering.
- Shareable deep links — URL tracks zoom, position, channels, Z-slice in real-time (Google Maps-style). Copy the browser URL to share an exact view.
- Multi-channel visualization — custom colors, intensity ranges, per-channel histograms.
- Auto-contrast from pixel data — one-click percentile-based (2%–98%) intensity optimization per channel.
- Z-projection — max, mean, and min intensity projections with configurable Z-range.
- HCS plate navigation — well picker grid, field view, plate overview for high-content screening datasets.
- GPU-accelerated multi-resolution rendering — handles 100K+ pixel images with tiled loading via deck.gl WebGL.
- Privacy-first, zero-install — all processing in your browser. No data leaves your machine. No account required.
Click any link to open directly in the viewer:
| Example | Description |
|---|---|
| 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).
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
- Browser: Chrome or Edge (full support with local file access). Firefox for remote URLs only.
- Format: OME-ZARR (OME-NGFF) v0.4 and v0.5, including sharded stores
All data is processed locally in your browser. No files are uploaded to any server.
Copyright (c) 2025 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