OMERO workshop

TOPIM TECH
Chania, July 2018
Will Moore, Petr Walczysko

Today's workshop

Outline

  • 11:20 - 12:55 (1 hour 35 mins)
    • Introduction to OMERO
    • CellProfiler analysis
  • 13:25 - 14:10 (45 mins)
    • Image analysis in Orbit
    • Coding in Orbit
  • Lunch
  • 18:00 - 18:45 (45 mins)
    • Fiji analysis
    • Python script
    • R analysis
  • 19:10 - 20:15 (1 hour 5 mins)
    • OMERO.parade
    • OMERO.figure

Client-side vs Server-side analysis

Analysis data in OMERO

  • OMERO.tables
    • HDF tables
    • 1 row per Image / Well - flexible columns
    • Saved as a File-Annotation
  • Regions of Interest (ROIs)
    • Contain 1 or more Shape e.g. Polygon
  • Map Annotations
    • List of Key: Value pairs
    • Each map annotation linked to 1 object

Session 1: OMERO intro & CellProfiler

  • OMERO.webclient
    • Browse data
    • View images
    • Add annotations
  • CellProfiler

Session 2: Orbit

  • Orbit as an OMERO client, using Java API
  • Create a segmentation model in Orbit
    • Saved as a File Annotation to OMERO
  • Segment an Image, save Polygons as OMERO ROIs
  • Use Orbit script editor to access OMERO Java API

Session 3: Fiji, python scripts & R

  • Fiji as an OMERO client, using Java API
  • Segment images, save Polygons as OMERO ROIs
  • Python script on OMERO server summarises ROIs to OMERO.table
  • Analyse OMERO.table data in R, plot results

Session 4: OMERO.web: parade & figure

  • OMERO.parade: app for filtering and plotting data
    • Uses OMERO.table data from Fiji/Python scripts previously
  • OMERO.figure: tool for creating figures
    • Uses metadata for speed & accuracy
    • ROIs, Channel names, Pixel sizes, Tags etc.

Getting started

Importing Images...

Command-line import


$ bin/omero import image.lsm
CLI import docs

In-place import

Files remain in-place during import


# e.g. Transfer file using 'soft' link
$ bin/omero import -- --transfer=ln_s image.lsm
In-place import docs