Open Zarr files in Fiji

October 25, 2022 1 minute read see also comments

By now, there are already two options to view images stored in Zarr files in Fijiꜛ: the N5 Viewer and the MoBIE plugin. Both plugins visualize the images via Fiji’s BigDataViewerꜛ.

Open local Zarr and OME-ZARR files via the N5 Viewer plugin

The N5 Viewerꜛ supports both Zarr and OME-ZARR files, that are locally stored on our hard drive. Just open the N5 Viewer via

    Plugins->BigDataViewer->N5 Viewer

and browse to the desired Zarr or OME-ZARR file.

No Zarr file at hand? Check out my previous post and quickly generate a sample file to play around with:

At the moment, N5 Viewer is not able to recognize the OME-ZARR specifications correctly. We have to select the first pyramid level within the OME-ZARR file, i.e., the 0 folder, to view the image:

Open OME-ZARR files via the MoBIE plugin

The MoBIE Fiji Viewerꜛ is currently only able to read OME-ZARR files, but supports the access to remotely stored files.

If it is not already there, you first need to installꜛ MoBIE:

Got to
```
  Help->Update...
```
In the ImageJ updater dialog, click on Manage update sites.
Here, search for MoBIE, enable its checkbox and click Close. If you can’t find it, you have to add its source URL by clicking on Add update site. In the input prompt, enter https://sites.imagej.net/MoBIE/ for the URL and MoBIE for the name. Enable its checkbox and click Close.
Back in the ImageJ updater dialog, click on Apply changes.
Restart Fiji.

Open a local OME-ZARR file via

    Plugins->BigDataViewer->OME ZARR->Open OME-Zarr From File System...

and browse to the desired OME-ZARR file on your hard drive.

To open a remotely stored OME-ZARR file, select

    Plugins->BigDataViewer->OME ZARR->Open OME ZARR from S3...

As an example source, enter “https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr”,

and the image is downloaded into the BigDataViewer:

For the screenshot above, I’ve additionally adjusted the brightness and colors of the image.

Other options

There is some rumorꜛ, that the OMEꜛ is working on a more native support for Zarr files in Fiji via bio-formatsꜛ. Whenever this becomes available, I will inform you on my blog.