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12th Annual Users Meeting 2017

The 12th Annual OME User's Meeting was held at the University of Dundee on May 31st to June 2nd 2017.

Useful links

Day 1 — Wednesday 31st May, 2017 - Dalhousie Lecture Theatre

09.30-10.00 Morning registration with tea/coffee
10.00-11.30 Lightning Talks by members of the community
11.30-12.00 Glencoe Software Update — Chris Allan, Glencoe Software
12.00-13.00 Lunch
13.00-13.10 Welcome
13.10-13.45 OME Project Summary and Progress — Jason Swedlow, OME
13.45-14.15 Machine Learning-based Whole Slide Analysis with Orbit — Manuel Stritt, Actelion Pharmaceuticals Ltd
14.15-14.45 Molecular profiling of adverse skin reactions to cancer immunotherapy — Zoltan Maliga, Harvard Medical School
14.45-15.15 OMERO in the Cloud: A BD2K Project — Douglas Russell, Harvard Medical School
15.15-15.45 Coffee
15.45-16.15 PLoS Data Policy — Emma Ganley, PLoS
16.15-16.45 The Image Data Resource: Working with Linked Datasets — Josh Moore and Eleanor Williams, OME
16.45-17.15 SSBD: Systems Science of Biological Dynamics Database — Shuichi Onami, RIKEN
17.15-17.45 Towards open data in cell migration research — Paola Masuzzo, University of Ghent
17.45-18.00 One-minute poster talks
18.00-19.00 Poster session with refreshments
19.00 Dinner

Day 2 — Thursday 1st June, 2017 - Dalhousie Teaching Rooms

The workshops will feature a mixture of presentations and more informal discussion topics. Please feel free to approach a member of the team with your questions or to request a demonstration of the OMERO clients or specific functionality.

09:00 - 09:15 Arrival with tea/coffee
09:15 - 09:30 Introduction
09:30 - 10:45 Workshops - Round 1
 
  • Room 1 - Using OMERO
    • Informal demonstrations of OMERO.clients, especially OMERO.web
    • Informal demonstrations of web apps: figure, iviewer, webtagging etc.
    • Informal demonstrations of other tools developed by the OME consortium e.g. mtools, ImageJ
    • Discussions as requested on integrating your own tools: Java, Python etc.
    • Discussions as requested on using/customizing training materials
  • Room 2 - Working with OME Files and Bio-Formats (developer-aimed session)
  • Room 3 - IDR annotations tour (please bring laptop)
    • Search for annotations in the IDR web user interface
    • Query and retrieve annotations using the web API
    • Annotation querying and analysis using Jupyter notebooks
    • Annotating your own images in OMERO (if time allows)
 
10:45 - 11:15 Coffee & refreshments
 
 
11:15 - 12:30 Workshops - Round 2
 
  • Room 1 - OMERO DevOps / OMERO @scale
    • Introduction to OMERO @Scale
    • Tools for configuration, testing and deployment management (e.g. Docker)
    • Image Data Resource (IDR) case study (OpenStack, GPFS, public web, caching)
  • Room 2 - Import CLI
    • CLI import: advanced import and extensible import
    • Import options review, Import As
    • OME.smuggler: queue your imports (w/ Andrea Falconi, Montpellier)
  • Room 3 - Rocket: a flexible, modular, cloud-based platform for the management of heterogeneous information from acquisitions and tools for biomedical research (Chong Zhang, Neubias)
    • Introduction about the Rocket platform design architecture and technology
    • Use cases: 1. collaborative clinical data manager 2. bioimage analysis task manager
    • Demo and play
 
12:30 - 13:45 Lunch
 
13.45 - 15.00 Workshops - Round 3
 
  • Room 1 - OMERO for AWS (Douglas Russell, Harvard)
    • Introduction to Docker and AWS
    • Building archives locally with Docker
    • Dehydrating an archive to S3
    • Hydrating an archive in AWS with Cloudformation
  • Room 2 - Analyzing data in OMERO
    • Introduction to IDR and Jupyter
    • Analyzing data in OMERO using Python and R
    • Working through use-cases including image features
  • Room 3 - OMERO.web apps
    • Intro to OMERO.web framework
    • new JSON API
    • App overview: figure, iviewer, mapr, etc.
    • Available extension points
 
15:00 - 15:30 Coffee & refreshments
 
15:30 - 16:45 Workshops - Round 4
 
  • Room 1 - Resources for devs
  • Room 2 - Workshops re-runs as requested
  • Room 3 - Workshops re-runs as requested
 
17:00 Wine Tasting

Day 3 - Friday 2nd June, 2017 - Life Sciences Complex

Informal day of meetings and coding sessions with the OME development teams.

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