OMERO workshop
TOPIM TECH
Chania, July 2018
Will Moore, Petr Walczysko
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 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
Different clients for different jobs
OMERO clients
- OMERO.insight
- OMERO.webclient
- Browsing images
- Viewing metadata
- Data management
- Searching
- OMERO web apps
- OMERO.iviewer
- OMERO.figure
- OMERO.parade
OMERO.iviewer
OMERO.parade
OMERO.web framework is extensible
Open with... Web apps
OMERO Python scripts
Fiji
CellProfiler and R in Jupyter notebooks
Orbit
Tomorrow's workshop
Tomorrow's workshop
- Please bring your laptops
- We have an OMERO server prepared:
- Everything is web-based except:
- Fiji. Google Fiji OMERO
- Orbit. www.orbit.bio
Thank you
