Share Your Microscopy Data With Your Team Without Sending Anyone a Hard Drive

You converted your CZI to OME-Zarr. You opened it in Find Nuclei Viewer. It looks great.

Now your collaborator at the other bench wants to see it. Your PI wants to check the segmentation before the lab meeting. The CRO you’re working with needs to review the plate before they proceed.

You could zip the folder and upload it somewhere. You could copy it to a shared drive and hope they have the right software. You could export a video and lose half the information in the process.

Or you could share a URL.

Step 1: Just open the local file

If you only need to look at the data yourself, drag the OME-Zarr folder directly into Find Nuclei Viewer. No upload, no account, no server. The viewer reads the chunks directly from your local filesystem using the browser’s File System Access API.

This works for any OME-Zarr store: a single image, a multi-series file, an HCS plate. If the folder contains multiple series the viewer detects them automatically and lets you pick which one to open.

Your data does not leave the machine. Full stop.

Step 2: Share with colleagues on the same network

Once you want someone else to see the data, you need HTTP. That sounds complicated. It is not.

Find Nuclei Data Server is a single Docker container. Point it at a directory of OME-Zarr files and it serves them over HTTP. One command:

docker run -p 3000:3000 -v /your/data:/data fn0000/fn-data-server

Your data is now accessible at http://your-machine:3000. Anyone on the same network can paste that URL into Find Nuclei Viewer and open the file directly in their browser. No install, no account, no waiting for a file transfer to finish.

The viewer generates a shareable deep link that captures your exact view: zoom level, channel settings, colors, Z-slice. Share that link and your colleague opens the viewer to exactly what you were looking at. Not “the file” — your exact view of the file.

Step 3: Add a token for sensitive or pre-publication data

If the data is sensitive or not ready to share with anyone who can reach the server, Find Nuclei Data Server supports bearer token authentication. Set a token when you start the server:

docker run -p 3000:3000 \
  -v /your/data:/data \
  -e FN_TOKEN=your-secret-token \
  fn0000/fn-data-server

When someone opens a protected URL in Find Nuclei Viewer, the viewer prompts for the token. Enter it once and the viewer stores it for the session. The token travels in the HTTP Authorization header — not in the URL, so it does not end up in browser history or server logs.

Share the URL and the token with exactly the people who should have access. Everyone else gets a 401.

What about cloud storage or a NAS?

If your data is already on S3, MinIO, or another S3-compatible store, you do not need the Data Server. Paste the HTTPS URL directly into Find Nuclei Viewer. Same deep-link sharing, same browser-based viewing, zero infrastructure to manage.

For a NAS or network share, the practical advice is: put an HTTP layer in front of it. nginx can serve a directory of Zarr files in a few lines of config. MinIO can sit in front of existing storage and expose it as S3-compatible. Either way, the result is a URL your colleagues can paste into any browser. The storage guide covers the performance tradeoffs in more detail.

The full picture

The format is the same in every case. OME-Zarr does not change. What changes is the layer between your storage and the viewer, and how much access control you need.

No hard drive required.