Train the trainer workshop
OME 2021 Community meeting
June 2021
OME Team
Aims of this workshop
Training landscape
Key questions
- What is important for a workshop?
- What can I get from the OME Team for my workshop?
- How does the OME Team run workshops?
- What does the community have and want? (Discussions)
- GitHub issue
- Breakout rooms
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?
- 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? ✓
OME Team: Public walkthroughs, presentations, guides
OMERO guides
- Walkthroughs, not a description of all functionalities
- Each guide is a separate project, bundled with code
OME: Main training servers
- All images are publicly available
- Accrued value approach
Training servers - alternative for you: #1
- Download IDR data using Aspera
Prepare training server - OME Team way
- Get a server, then deploy OMERO using ansible playbook
- Prepare groups and users as listed in the template sheet
- Rename users to have nice first and last names
- Import data in-place for all users using a bash script
- Can use a bulk file pointing to a list of paths of the image files for reproducibility.
$ ssh $SERVERNAME
$ su $USERNAME # Unix user with in-place import setup
$ OMEUSER=user NUMBER=50 # imports for each of the 50 OMERO users
$ PROJECTNAME=idr0079/experimentA # name of target container in OMERO
$ HOST=localhost
$ BULKFILE=/path/to//idr0079-experimentA-bulk.yml
$ bash /path/to/in_place_import_as.shPrepare training server - OME Team way
- Lightweight imports can be achieved by a python script copying images as pixeldata from IDR or other OMERO.servers.
- Import metadata, annotate images using training-scripts:
- Copy Key-Value pairs from IDR or other OMERO server.
- Add new Key-Value pairs.
- Calibrate images.
- Add timestamps.
- Propagate tags and ratings to all users.
- Import metadata from a CSV via OMERO.web or Command line.
- Create an analysis results table using a script run from a 3rd party tool.
Training servers - alternative for you: #2
Setup #1 - IDR and S3
- No setup required, all components ready ✓
- Limited audience, read-only server, only API workflows ⚠
Setup #2 - empty server
- Very little setup required, larger audience ✓
- Very limited workflows, low user satisfaction ⚠
Setup #3 - server with few images
- No IDR data import needed ✓
- Little setup, large audience, crucial workflows covered ✓
- Basic analysis, limited scripting, no OMERO.parade ⚠
Setup #4 - OME server copy
- Full audience, workflows and analysis ✓
- Need to import IDR data to match workflows ⚠
- Setup needs planning, space, maintenance ⚠
Training servers - for discussion
- A docker, possibly based on OME deployment examples
- A docker-compose with all the data included (a wish from community)
- Import of data (costly)
- Transfer of data between OMERO servers (not solved)
- Size of data and complexity (accrued value vs. lightweight setup)
- Keep indefinitely up and cleanup or spin up and delete
- Maintenance and upgrades
What now?
- General discussion
- Breakout rooms
- OME training servers
- Analysis environment
- ...
Thank you
