12th Annual Users Meeting 2017

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

Tea/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

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)
• Overview of OME Model and Formats, Bio-Formats and OME Files
• Introduction to working with Bio-Formats
• Introduction to working with OME Files
• Small group breakout sessions

• 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

Tea/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 Cloud formation

• 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

Tea/coffee & refreshments

15:30 - 16:45

Workshops - Round 4

• Room 1 - Resources for devs
• Room 2 - Workshop re-runs as requested
• Room 3 - Workshop re-runs as requested

17.00

Wine tasting and buffet dinner