View zarr file using MoBIE and BDV

Description

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

We show:

  • how to install the required dependencies
  • how to view an ome.zarr file stored in S3 using the User Interface
  • how to view an ome.zarr file stored in S3 using the scripting editor of Fiji.

Setup

  • Install Fiji on a local machine.
  • Go to Help>Update...
  • In the ImageJ updater dialog, click on Manage update sites.
  • 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.
  • Restart Fiji.

Resources

Step-by-step

Opening an ome.zarr file from the User Interface

  1. Launch Fiji.
  2. Go to Plugins > BigDataViewer > OME ZARR > Open OME ZARR from S3….
  3. A dialog pops up.
  4. In the text field, enter the desired URL e.g.
https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/9836832.zarr
  1. Click the OK button.
  2. When the image is displayed in the BigDataViewer, select the dialog and press P to display the rendering controls.
  3. Modify the settings as you see fit.

Opening an ome.zarr file using a Groovy script

  1. Launch Fiji.
  2. Go to File > New > Script….
  3. A dialog pops up. In the Language menu, select Groovy.
  4. Copy the content of mobie_ome_zarr.groovy and paste it into the text script editor of Fiji.
  5. Click Run.
  6. When the image is displayed in the BigDataViewer, select the dialog and press P to display the rendering controls.
  7. Modify the settings as you see fit.