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. ZARR folders open in Chrome and Edge. Zipped datasets (
.ozx,.zip) open in any browser. The data never leaves your machine. - Remote URLs. Anything served over HTTPS with CORS and range requests: S3, R2, GCS, Azure Blob, your own nginx.
s3://addresses. Pastes3://bucket/pathof a public bucket and the image or plate opens, as from its https address.- Opera Phenix and Yokogawa CellVoyager plates. Open an Opera Phenix plate exported by Harmony (V5
Index.idx.xmlor V6Index.xml), or a Yokogawa CellVoyager CV8000 or CV7000 measurement folder, straight from its TIFFs, by URL,s3://or a local folder. Nothing is converted. Guides: Opera Phenix Plates, Yokogawa CellVoyager Plates.
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 background 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.
- 3D. Turn a z-stack around as a volume, one click from the flat view. Two looks: MIP for bright, sparse signal, Composite for solid shapes. Side views (XY, XZ and YZ) sit next to it, linked by one crosshair. Your channels and annotations come along, and plate fields open in 3D too. Desktop browsers with WebGPU. Guide: 3D Rendering.
- Anatomical orientation. When an image records it (OME-NGFF RFC-4), 3D labels the axes superior and inferior, left and right, anterior and posterior, and shows the planes the radiological way.
- 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. See it on a plate with results.
- 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. With analysis results, it also keeps which masks are shown and how they are coloured. 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 |
| Supported Formats | What opens, and in which browser |
| Local Files · Remote URLs · Authenticated Sources | Getting data in |
| Channels · Z-Projection · 3D Rendering · 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 |
|---|---|
| Plate with analysis results | BBBC013, 96 wells: cells coloured by phenotype, nuclei on top, a measurement table behind every mask. Guide |
| Zebrafish lateral line in 3D | 3D, membranes and nuclei, with side views. Guide |
| Neurons in marmoset visual cortex, in 3D | 3D, maximum intensity projection of GFP neurons |
| Cerebral aneurysm, in 3D | 3D, rotational angiography in Composite |
| 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 |
BBBC013 is hosted here, in examples/, with our segmentation and measurements. Images from the Broad Bioimage Benchmark Collection (CC BY 3.0, Ilya Ravkin; Ljosa et al., Nature Methods 2012).
The marmoset neurons and the aneurysm come from OME-Zarr Open SciVis Datasets (McCormick 2025, doi:10.5281/zenodo.17495294, CC BY 4.0), courtesy of Frederick Federer (Moran Eye Institute, University of Utah) and of volvis.org and Philips Research, Hamburg.
The other datasets come 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. HCS instrument plates without conversion: Opera Phenix (Harmony V5 and V6) and Yokogawa CellVoyager (CV8000, CV7000). - 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.
- 3D: a desktop browser with WebGPU, and an image with more than one Z plane. It opens from a URL, a local folder (Chrome and Edge), an
.ozxor.zipfile, or a token-protected store.
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 2026-11-01. 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.
The Find Nuclei Viewer is free to use under the Terms of Use. It is proprietary software: its source code is not public, and the built files here may not be copied, modified, or redistributed except as the Terms of Use allow.
The JSON Schemas in schemas/ are licensed under CC BY 4.0, so anyone can read, validate, and write files in these formats. See schemas/LICENSE.
For licensing inquiries: info@find-nuclei.com
- GitHub: Find-Nuclei/find-nuclei.github.io
- Issues: Report a bug
- Email: info@find-nuclei.com