Embedded Viewer for Publications

Two lines of HTML. No iframe. No install. See how journals can embed interactive OME-ZARR microscopy data directly in their pages.

IDR-0062

NesSys: Accurate Nuclear Segmentation in 3D

Blin G et al. (2019) PLoS Biology. Automated detection and segmentation of nuclei within intact mouse tissues and dense 3D cultures using confocal microscopy. View on IDR → · Open in Find Nuclei Viewer →

Mus musculus Confocal 3D Nuclear segmentation Multi-channel

Interactive Viewer

Embed Code

<!-- Load once in <head> --> <script src="https://find-nuclei.github.io/embed/v1/viewer.js"></script> <!-- Place anywhere in your article --> <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>
IDR-0066

mesoSPIM: Open-Source Light-Sheet Microscopy for Cleared Tissue

Voigt FF et al. (2019) Nature Methods. Mesoscale light-sheet imaging of large cleared tissue specimens including chicken embryo vasculature. View on IDR → · Open in Find Nuclei Viewer →

Chicken embryo Light-sheet (mesoSPIM) Cleared tissue MIP

Interactive Viewer

Embed Code

<!-- Load once in <head> --> <script src="https://find-nuclei.github.io/embed/v1/viewer.js"></script> <!-- Place anywhere in your article --> <find-nuclei-viewer url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpD_chicken_embryo_MIP.ome.zarr" width="100%" height="500" ></find-nuclei-viewer>
IDR-0073

Graph-Based Description of Tertiary Lymphoid Organs

Schaadt NS et al. (2020) PLoS Computational Biology. Neighborhood graph analysis of immune infiltrates in human tissue sections (breast cancer, kidney, lung) using bright-field immunohistochemistry. View on IDR → · Open in Find Nuclei Viewer →

Homo sapiens Bright-field histology Immunohistochemistry Tertiary lymphoid organs

Interactive Viewer

Embed Code

<!-- Load once in <head> --> <script src="https://find-nuclei.github.io/embed/v1/viewer.js"></script> <!-- RGB images auto-detect white background, or set explicitly --> <find-nuclei-viewer url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0073A/9798462.zarr" background="white" width="100%" height="500" ></find-nuclei-viewer>
IDR-0079

Cellular Architecture in the Developing Lateral Line Primordium

Hartmann J et al. (2020) eLife. 3D cell shape and organization analysis in the zebrafish posterior lateral line primordium using AiryScan confocal microscopy and automated segmentation. View on IDR → · Open in Find Nuclei Viewer →

Danio rerio AiryScan confocal 3D segmentation Z-stack

Series 0

Series 1

Series 2

Embed Code

<!-- Load once in <head> --> <script src="https://find-nuclei.github.io/embed/v1/viewer.js"></script> <!-- Use the image attribute to select a series --> <find-nuclei-viewer url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr" image="0" width="100%" height="400" ></find-nuclei-viewer>

Embed in Two Steps

Any journal, data portal, or institutional repository can add interactive OME-ZARR viewers to their pages. No backend, no API key, no build step.

Step 1 — Load the script (once per page)

<script src="https://find-nuclei.github.io/embed/v1/viewer.js"></script>

Step 2 — Place the viewer

<find-nuclei-viewer url="https://your-s3-bucket.com/dataset.ome.zarr" width="100%" height="500" ></find-nuclei-viewer>

Optional — Customize channels and Z-slice

<find-nuclei-viewer url="https://..." z="15" channels="0:on:00FF00:100:4000,1:on:FF0000:50:2000" theme="light" controls="minimal" ></find-nuclei-viewer>

Attributes Reference

Attribute Required Default Description
url Yes — ZARR store URL (HTTP or S3)
z No middle Initial Z-slice index
channels No auto Channel config: idx:on/off:hex:min:max,...
width No 100% CSS width (pixels or %)
height No 16:9 auto CSS height (pixels or %)
controls No minimal minimal or none
theme No dark dark or light
token No — Bearer token for auth sources

Want to embed interactive microscopy in your journal or data portal?

Try the Full Viewer → Read the Embedding Guide →

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