PrerequisitesBefore starting this lesson, you should be familiar with:
OME-Zarr image file format (TODO)
Learning ObjectivesAfter completing this lesson, learners should be able to:
Render cloud (S3 object store) hosted OME-Zarr image data.
Access the pixel values of cloud hosted OME-Zarr image data.
Storing TB-sized image data locally and in multiple copies is either not possible or inefficient. Cloud storage enables efficient concurrent access to the same image data by multiple clients (scientists). OME-Zarr is the emerging community standard image file format for cloud (S3 object store) compatible image data storage. Thus it is important to know how to access S3 hosted OME-Zarr in various image analysis and visualisation platforms.
- Example URLs:
- https://s3.embl.de/i2k-2020/em-raw.ome.zarr (3D EM with label mask)
Show activity for:
ImageJ GUI MoBIE
- Install Fiji with MoBIE
- Start Fiji
- Open OME-Zarr from S3 in BigDataViewer:
- [ Plugins › BigDataViewer › OME ZARR › Open OME ZARR From S3… ]
- S3 URL: Choose one of the above example URLs
- Log chunk loading
Recommended follow-up modules: