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) and inside a shadow root.
In a MyST article (Curvenote journals such as Elemental Microscopy), use the widget module. Every key is an attribute of the viewer:
:::{any:bundle} https://find-nuclei.github.io/embed/v1/widget.mjs
{
"url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr",
"channels": "0:on:FFFFFF:0:240",
"x": 2115, "y": 1688, "zoom": -1.9,
"height": "500"
}
:::- Live Demo: see it in action with IDR datasets and a 1M-nuclei mosaic
- MyST and Shadow DOM: the widget, the element in a shadow root, and the iframe fallback, side by side
- 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) v0.3, v0.4, v0.5 and v0.6 (the current spec), including sharded stores, plus
bioformats2rawlayouts. - Any modern browser for remote URLs, including Firefox and Safari.
- Any modern browser for a dataset zipped into a single
.ozxor.zipfile, opened in place with nothing unpacked. - Chrome or Edge to open a dataset folder from disk.
All data is processed locally in your browser. No files are uploaded to any server.
If you use the viewer in a publication, cite it as:
Find Nuclei (2026). Find Nuclei Viewer, release 2026-09-19. https://find-nuclei.github.io
The machine-readable form is CITATION.cff; GitHub's "Cite this repository" button reads it.
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