Research Data Management

OMERO.figure workshop

2021 OME Community Meeting

9th June 2021 | Will Moore

Outline

  • Intro: OME & OMERO
  • Workshop overview
  • Workshop...
  • Breakout Rooms
    • OMERO.figure UI
    • Scripting (Python & JavaScript)

OME: Interoperability

OMERO is a server with clients

OMERO API

Python | Java | Matlab | R | JavaScript

idr.openmicroscopy.org

Today's workshop:

Using data from Jonas Hartmann: idr0079 experimentA
Zebrafish embryo: posterior Lateral Line Primordium (pLLP)

"An image-based data-driven analysis of cellular architecture in a developing tissue"
eLife 2020

Using image metadata to build a figure:

  • Pixel sizes & Time-stamps
  • Channel Names
  • User Annotations (Tags, Key-Value pairs)
  • Regions of Interest (ROIs)
  • Analysis results

OMERO.figure scripting

  • Create figures with Python scripts on the server
  • Edit figures with JavaScript in the client (web browser)
More Info

Workshop content

Thank you