Analyze data in OMERO Workshop

OME Community Meeting 2020

Dundee, May 2020
OME Team

Outline

  • What is OME?
  • What is OMERO?
  • Workshop overview

OME: Interoperability

OMERO is a server with clients

Image Data - Read by Bio-Formats

  • Support for reading > 150 image formats
  • Read pixel data and metadata
  • Includes 5D images, HCS data, Tiled WSI images
  • Domains: biological, medical, general (tiff, png, etc.)

Metadata

  • Stored in a Relational Database
  • Acquisition Metadata
  • User-added Annotations
  • ROIs / Segmentations

Search

  • Text and Annotations indexed with Lucene
  • Allows keyword searches

OMERO.tables

  • HDF5 tables for analysis results
  • Flexible columns

OMERO API

Python | Java | Matlab | R | C++

Integration

Fiji

Orbit

https://omero-guides.readthedocs.io/en/latest/api_usage.html

Today's workshop

  • Analyze data using Fiji scripting (Java API)
  • How to convert client-side script into server-side script (Python API)
  • How use the Python API
  • getPlane() vs Zarr (Python) (depending on time)
  • Parallel analysis (depending on time)

Thank you