Publications: Embedded OME-ZARR Viewer Demo

Nuclei Mosaic

1,061,277 Cell Nuclei From 100 Experiments

Barkley RJR (2026). Nuclei mosaic, doi:10.5281/zenodo.18776682, CC BY 4.0. Every nucleus imaged across 100 experiments, cropped and stitched into one 263,936 × 263,680 pixel OME-Zarr with a 10-level pyramid, about 70 GB at full resolution, streamed from the Open Storage Network (doi:10.6075/J0RR1ZCR). Related preprint: Barkley RJR, Brodrick AJ, Parker JSL (2026). Reimag(in)ing representative images. Elemental Microscopy. doi:10.69761/ggmj4852 · Open in Find Nuclei Viewer →

The same field two ways, as shared links from the viewer: original contrast on black → · inverted on white →

Fluorescence Nuclei Single channel 1M objects Zarr v2

This work used the Open Storage Network through allocation BIO250450 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program, which is supported by U.S. National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296. doi:10.1145/3569951.3597559

Interactive Viewer

Time-lapse: the same lab's live imaging, playing on its own

Thirty timepoints, two channels (mNeonGreen, mCherry). With autoplay the figure moves as soon as it is on screen and pauses while scrolled away. Each frame is shown complete, so on a slow link the tempo drops rather than the frame tearing. Hover for the play button and the time slider.

Embed Code: time-lapse

                        
<find-nuclei-viewer
  url="https://nyu1.osn.mghpcc.org/barkley-replication/video.zarr"
  channels="0:on:00FF00:21:199,1:on:FF00FF:24:2121"
  autoplay fps="4"
  width="100%"
  height="500"
></find-nuclei-viewer>
                    

In a MyST article add "autoplay": true, "fps": 4 to the any:bundle JSON below.

Embed Code: HTML page

                        
<!-- 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://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr"
  channels="0:on:FFFFFF:0:240"
  x="2115" y="1688" zoom="-1.9"
  width="100%"
  height="500"
></find-nuclei-viewer>
                    

Embed Code: MyST article (Curvenote, Elemental Microscopy)

MyST sites render widgets inside a shadow root, so use the widget module instead of a script tag. Every key is an attribute of the viewer, same names as above. Add "invert": true for a white background with dark nuclei.

                        
:::{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 of this route, plus the iframe fallback: MyST and Shadow DOM.

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

Citing the Viewer

You are welcome to embed the viewer in a preprint, a journal article, or a data portal. Load the script from find-nuclei.github.io and cite the viewer as:

Find Nuclei (2026). Find Nuclei Viewer, release 2026-09-19. https://find-nuclei.github.io

Machine-readable form: CITATION.cff.

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

Try the Viewer → Read the Embedding Guide →

Free to use · No account required · No install

← Back to Find Nuclei Viewer

Embedded Viewer for Publications

1,061,277 Cell Nuclei From 100 Experiments

Interactive Viewer

Time-lapse: the same lab's live imaging, playing on its own

Embed Code: time-lapse

Embed Code: HTML page

Embed Code: MyST article (Curvenote, Elemental Microscopy)

NesSys: Accurate Nuclear Segmentation in 3D

Interactive Viewer

Embed Code

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

Interactive Viewer

Embed Code

Graph-Based Description of Tertiary Lymphoid Organs

Interactive Viewer

Embed Code

Cellular Architecture in the Developing Lateral Line Primordium

Series 0

Series 1

Series 2

Embed Code

Embed in Two Steps

Step 1: Load the script (once per page)

Step 2: Place the viewer

Optional: Customize channels and Z-slice

Attributes Reference

Citing the Viewer