Access S3 hosted OME-Zarr

Prerequisites

Before starting this lesson, you should be familiar with:

  • OME-Zarr image file format (TODO)

Learning Objectives

After 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.

Motivation

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.

Concept map

graph LR S3("S3 object store") --- O("Objects") O ---|are| C("Image parts/blocks/chunks") R("Read") -->|http| O

Figure




Activities


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

Assessment


Follow-up material

Recommended follow-up modules:

Learn more: