OMERO workshop
Smithsonian Tropical Research Institute, Panama
June 2024
OME TeamOutline
- 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 > 160 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
Integration
Open with... Web apps
OMERO setups - community
- Implementation of OMERO at the Münster Imaging Network, setup from Zobel et al. 2022:
idr.openmicroscopy.org
IDR is based on OMERO
Integrate IDR with other repositories
Your own trainings on OMERO
What do I need for an OMERO training?
- Guides for participants
- Server
- Server setup
- 3rd party software setup
- Analysis environments
- Server cleanup or re-deployment strategy
What can I get from OME Team?
- Data and DB in a zip? ✓
- OMERO.guides? ✓
- Servers? 🌓 ⚠
- Blueprint for setting up your training server? ✓
- Image data? ✓
- The setup scripts for
- Users/Groups ✓
- Image imports ✓
- Metadata import and handling ✓
- Creation of annotations ✓
- Scripts for cleanup of the server? ✓
- Analysis and 3rd party tools environments? ✓
OMERO guide
- Workshop content is in OMERO guides
https://omero-guides.readthedocs.io
What should OME user know ?
- See the OMERO guide for facility managers
- Especially see getting users started guide
- See the OMERO guide for users
- Videos
- See Train-the-trainer presentation
Routine training and user inductions
Attracting users to OMERO
Support on image.sc - community
Read-annotate setup example
Import: Desktop Application
Read the import guide or watch the import video
Import: Advanced options
Read the import guides
Thank you
