Find Nuclei Viewer

Interactive microscopy data, anywhere on the web

Live Demo

Two lines of HTML


<!-- Load once per page -->
<script src="https://find-nuclei.github.io/embed/v1/viewer.js"></script>

<!-- Place anywhere -->
<find-nuclei-viewer
  url="https://your-storage.org/cells.zarr"
  labels="on"
  width="100%"
  height="500"
></find-nuclei-viewer>

Works in any web page: journal articles, LIMS, data repositories, wikis, presentations.

3D Nuclear Segmentation

Blin et al. (2019) · IDR-0062 · Mouse tissue · LaminB1 + DAPI · 236 Z-slices · Try: scrub the Z-slider, toggle the label overlay

Setting the starting view


<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>

Channel names, colors, and intensity ranges are read from OME-ZARR metadata automatically.

Live Imaging · Zebrafish Heart Regeneration

McDole et al. (2018) · IDR-0079 · lynEGFP (membranes, green) · NLStdTomato (nuclei, red) · Try: turn off green to isolate nuclei

Controlling channels and position


<find-nuclei-viewer
  url="https://...idr0079_images.zarr"
  channels="0:on:00FF00:8:90,1:on:FF0000:7:80"
  x="500" y="350" zoom="-0.5"
  width="100%"
  height="500"
></find-nuclei-viewer>

channels format: id:on|off:RRGGBB:min:max — override as many or as few as you need.

Brightfield Histology

Schaadt et al. (2020) · IDR-0073 · Human tissue · Tertiary lymphoid organs · RGB detected automatically

Brightfield and RGB images


<find-nuclei-viewer
  url="https://...9798462.zarr"
  background="white"
  width="100%"
  height="500"
></find-nuclei-viewer>

RGB color model is detected automatically. White background, unified brightness slider, no per-channel controls.

Coming soon: Stories

Compose a sequence of named chapters in the standalone viewer. Each chapter captures a region, channel setup, and a short description.

Readers step through at their own pace and explore the data freely at any point. Perfect for walking reviewers through a published figure, guiding students through a real dataset, or presenting results without leaving your slides.


<find-nuclei-viewer
  url="https://data.lab.org/cells.zarr"
  story="https://data.lab.org/cells-story.yaml"
></find-nuclei-viewer>

Try it yourself

Free to embed. No account required.

find-nuclei.github.io/docs/guides/embedding.html

info@find-nuclei.com