View zarr file using MoBIE and BDV

Description

This section shows how to view ome.zarr files in Fiji using BigDataViewer and MoBIE.

We show:

Install Fiji on a local machine.
BigDataViewer is already included in Fiji.
To install MoBIE, go to Help>Update...
In the ImageJ updater dialog, click on Manage update sites.
The MoBIE` should already be listed. Select it and click Close.
Click Apply changes to install it.
If MoBIE` is not listed:
- Click Add update site.
- Enter for the name MoBIE (so you can identify it) and for the URL: https://sites.imagej.net/MoBIE/. See How to install an update site.
- Click Apply changes to install it.
Restart Fiji.

Samples images from the Image Data Resource (IDR) that have been converted into https://github.com/ome/ngff. A list of available files can be found here.
Script: Groovy script for opening the images in BigDataViewer using MoBIE.
- mobie_ome_zarr.groovy.
Watch an introductory video.

Launch Fiji.
Go to Plugins > BigDataViewer > HDF5/N5/Zarr/OME-NGFF Viewer
A dialog pops up.
In the text field, you can click Browse to open local data or enter the desired URL e.g.

https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr

If you Click the OK` button tbis will open the image in BigDataViewer. You can also click the Detect datasets button to inspect the content of the zarr file, such as individual pyramid arrays and labels. You can select multiple items, for example to open the (multiscales) image under labels alongside the parent (multiscales) image.
When the image is displayed in the BigDataViewer, select the dialog and press P to display the rendering controls.
Modify the settings as you see fit.

https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr