Raw Data Analysis

OME Users meeting
31th May 2018
Will Moore | Petr Walczysko
Jean-Marie Burel | Dominik Lindner

Outline

• OMERO: a platform for image analysis
• Client-side vs Server-side analysis
• Sample data: Study 21 from IDR
• Demo:
  1. Fiji as an OMERO client: Manual Analysis
  2. Jython scripts in Fiji
  3. Python scripts on OMERO.server
  4. R in a Jupyter notebook

OMERO: a platform for image analysis

• (Almost) no built-in analysis functionality
• But: lots of ways to store analysis results

Client-side vs Server-side analysis

Sample data: idr0021

Workshop Data preparation

See idr0021-data-prep.md for instructions:

• Download of the data from IDR
• Bulk import
• Populating Metadata

Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material

Steffen Lawo, Monica Hasegan, Gagan D. Gupta & Laurence Pelletier

Nature Cell Biology volume 14, pages 1148–1158 (2012)

Data from Figure 1

Analysis

1. Fiji: Manual analysis of particles and save to OMERO
2. Fiji: Scripted analysis of particles and save ROIs to OMERO
3. OMERO.script: Server-side processing of ROIs to create Map Annotations and OMERO.table
4. R: Jupyter notebook running R to analyse Metadata

Analysis Demo...