OME-Zarr Viewer

OME-Zarr is the viewer's home format. It opens in place: nothing is converted and nothing is uploaded. New to the format? Why OME-Zarr Is Taking Over Microscopy covers what it is good for.

• OME-NGFF versions 0.3, 0.4, 0.5 and 0.6.
• Zarr v2, uncompressed or compressed with blosc, zlib or gzip.
• Zarr v3, sharded or not, compressed with blosc, zstd, gzip or zlib.
• Single images, and datasets with several series from bioformats2raw.
• HCS plates, with plate, well and field views. See OME-Zarr Plates.
• Labels in the image's labels/ group. They load with the image. On a plate, press Discover. See Labels.

How It Opens

• A folder on your disk, in Chrome and Edge. See Local Files.
• One zipped file (.ozx or .zip), in any browser, from your disk or its address. See A Dataset in a Single File.
• An address: https://, s3:// or gs://. See Remote URLs.
• Private data, with a private link or a token. See Private Images and Slides.

Local or remote? Your OME-ZARR Storage Setup Is Slowing You Down helps you pick.

A Z-stack can also be viewed in 3D, whichever of these it was opened from. A folder still needs Chrome or Edge. See 3D Rendering.

A Dataset in a Single File

An OME-Zarr dataset is thousands of small files in nested folders. That shape is what makes it fast to read one region without reading the whole image. It is also what makes it awkward to send someone or carry on a stick.

The format has an answer: pack the whole dataset into one ZIP archive. Name it .ozx, or leave it as .zip. Both open here.

To open one, drop it onto the viewer, or click Open Image and then Choose File on the Local Files tab. It opens the way a folder does, with the same plate navigation, the same channels and the same speed. The viewer reads pieces of the archive as it needs them, so a large dataset never has to be unpacked first.

This route works in every browser, Safari and Firefox included. It is the only way to open an OME-Zarr dataset from your own disk in those two.

Making one

The quickest way is the one your computer already has. Right-click the dataset folder and choose Compress on macOS, or Send to › Compressed (zipped) folder on Windows. The zip holds the folder itself, and it opens here as it is.

For the smallest and fastest archive, zip the contents of the folder from the command line instead:

cd your-dataset.ome.zarr
zip -r -0 ../your-dataset.ozx . -x '.DS_Store' '*/.DS_Store'

That is the whole recipe. Three details in it matter.

. rather than the folder name puts zarr.json at the top of the archive, which is the .ozx layout other tools expect. The viewer opens it either way.

-0 stores the files instead of compressing them. Zarr chunks are already compressed, so compressing them again costs time on both ends and saves almost nothing. Stored entries are also the fastest to read a piece of.

The -x at the end drops the hidden files macOS leaves in any folder you have opened in Finder. They are harmless, and without it a plate picks up one in every row. Leave it off on Linux and Windows.

Any tool works. Name the result .ozx or .zip, whichever you prefer.

Check it opened the way you meant

Drop the archive on the viewer. If it opens, it is right. If you see a message that it holds no dataset the viewer can find, the dataset is neither at the top of the archive nor in a single folder there. Two datasets zipped side by side is the usual cause.

Double-click to open

Install the viewer in Chrome or Edge and it registers .ozx, so double-clicking one in Finder or Explorer opens it straight in the viewer. No browser window to find first, no dragging.

Only .ozx is registered, never .zip. A microscopy viewer claiming every archive on your machine would be presumptuous, and most zips you double-click are not datasets. Rename a .zip to .ozx if you want this for it.

If the viewer is already open, the file opens in that window and asks before it replaces whatever you were looking at.

To install: open the viewer in Chrome or Edge and use Install in the address bar. See Installing and Offline for what else that gives you.

Nothing is unpacked, and nothing is copied

Opening an archive does not read it. The viewer reads the ZIP index, then only the pieces it needs, seeking straight to them inside the file.

Opening the 96-well plate used for testing this, 10 MB with 205 entries, reads 0.08 MB to open it, 0.10 MB to work out the whole plate layout, and 0.41 MB by the time the first field is on screen. That is 3.9% of the file. The rest is never touched until you navigate to it. A dataset far too large to fit in memory opens exactly as fast, because size was never the thing being read.

Your data stays on your disk. It is not uploaded, and it is not copied into the browser either.

From an address

A zipped dataset opens from its address too. Paste the address and click Load from URL. It opens in 2D and in 3D, like a folder.

The viewer reads the file's table of contents from its end, then only the parts it needs for the view. It does not download the whole file. The server must allow CORS and answer range requests. See What the Server Needs.

A Dropbox file link works too, but Dropbox takes several seconds per read. See Dropbox file links.

Public Data to Try

The Image Data Resource (IDR) hosts thousands of public microscopy datasets in OME-Zarr. Browse the IDR, find a dataset, and copy its Zarr address to open it here.

https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0001A/2551.zarr

Most public OME-Zarr servers, such as the IDR and the BioImage Archive, already allow CORS. Or click Open Example on the landing page for datasets known to work well.

Related guides

• Supported Formats: every format the viewer opens.
• Local Files and Remote URLs: the two ways in, for every format.