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.
• 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.

Resources

• 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.

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://uk1s3.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.