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.
Watch an introductory video.
Step-by-step
Opening an ome.zarr file from the User Interface
Launch Fiji.
Go to Plugins > BigDataViewer > OME ZARR > Open OME ZARR from S3….
A dialog pops up.
In the text field, enter the desired URL e.g.
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/9836832.zarr
Click the OK button.
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.
Opening an ome.zarr file using a Groovy script
Launch Fiji.
Go to File > New > Script….
A dialog pops up. In the Language menu, select Groovy.
Copy the content of
mobie_ome_zarr.groovy
and paste it into the text script editor of Fiji.Click Run.
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.