Workshop: OMERO Setup and Configuration for Imaging Facility Managers

foundingGIDE BioImage Hackathon and Workshops

Workshop: OMERO Setup and Configuration for Imaging Facility Managers

Notice

Dear participants,

The OMERO setup and configuration workshop, originally scheduled for Nov. 4, will now be held over two days, Nov. 4 and Nov. 6. The gap in between is for participants who also join the ilastik workshop on Nov. 5. We apologize for any inconvenience caused by the changes to the schedule after registration.

The workshop on Nov. 4 will proceed as planned, focusing on the scheduled content. In addition, we decided to offer a second session covering the primary usage and operation of OMERO. The second session is particularly important for imaging facility staff, as understanding not only the setup and configuration of OMERO.server but also utilizing OMERO services is crucial. If your schedule permits, we also encourage you to attend the Nov. 6 session.

About OMERO

Are you working with large volumes of bioimaging data? Looking for a robust solution to manage, visualize, and analyze your datasets efficiently? Join our hands-on workshop focusing on the setup and configuration of OMERO, a powerful management platform for microscopy images. OMERO provides researchers with a flexible system to handle, organize, and analyze imaging data. This workshop will guide you through the complete setup of OMERO on your local or cloud infrastructure and provide best practices for configuring OMERO for optimal performance.

OMERO is a modern client-server software for managing, visualizing, and analyzing microscopy images and associated metadata.

• OMERO.server is a server software that manages a large number of microscopy images in their original format, and converts them on the fly into an easy-to-use format with Bio-Formats.
• OMERO.web is a web-based client software that allows users to access the data in OMERO.server from a browser. Users can also use OMERO.iviewer to preview microscopy images and change parameters.
• OMERO.figure is a tool for creating figures for paper publication from microscopy images in OMERO.server
• There are many OMERO clients, tools, and web apps for OMERO.

About the event

The OMERO Setup and Configuration for Imaging Facility managers offers some extensive programs for OMERO workshops, but it also includes basic OMERO introduction, installation, and how to use OMERO in the lab as the workshops:

• OMERO Open Workshop in Kobe 2018
• OMERO follow-on Webinar 2018
• ABiS-GBI 2023 course - Image data: image analysis, data management and reuse

Participation will be limited to about 15 people on Workshop 1: OMERO installation and configuration.

Participation will be limited to 40 people on Workshop 2: OMERO Imaging workflows, and Workshop 3: Advanced Analysis with OMERO

Event schedule

Schedule details

November 4th, Monday

Workshop 1: OMERO installation and configuration (Some IT background is advantageous)

• Installation, setup, and configuration of OMERO
  • Step-by-step guidance on installing OMERO on local machines or institution cloud.
  • Learn how to manage users, set permissions, and organize imaging data for multi-user environments.
  • Explore how OMERO handles image data imports, file formats, and efficient organization of large datasets with rich metadata.
• Deployment of OMERO.web and how to install the OMERO web apps

Workshop 2: OMERO Imaging workflows (This would be for facility managers and scientists with no IT background)

• Working with data in OMERO.web (data management)
• Analysis with OMERO using QuPath and Fiji connections,
  • Learn how OMERO connects with tools like ImageJ/Fiji, QuPath for image analysis
• Making figures with OMERO.figure
  • A deep dive into the OMERO.figure tool for creating publication-ready figures directly from OMERO.
• Publication with OMERO,
• General “best practices” on running OMERO in the facility described in plain English on examples from actual OMERO instances:

November 6th, Wednesday

Zoom link for Nov 6th (Workshop 2/3 and supplements for workshop 1)

• When: Nov 6, 2024 09:00 AM Osaka, Sapporo, Tokyo
• Register in advance for this meeting: https://riken-jp.zoom.us/meeting/register/tJ0kcO6vrzsoEt0sD8UoAsrG1HI1tseMa6Ho After registering, you will receive a confirmation email containing information about joining the meeting.

(For the Nov. 6th workshop, we will provide a hybrid session or recorded format for the attendees.)

Depending on the interest of attendees, conduct the topics in Workshop 2:

Workshop 3: Advanced Analysis with OMERO

• Python API
  • Explore leveraging the OMERO API to automate custom image management or analysis workflow.
• Analysis: CellProfiler, Cellpose, Stardust using Jupyter notebooks
  • Learn how OMERO connects with tools like CellProfiler, Cellpose, and StarDist for seamless image analysis workflows.

Place

8th Floor, RIKEN Integrated Innovation Building in Kobe, Japan

Requirements

This workshop is ideal for:

• Imaging scientists and researchers dealing with large datasets.
• Imaging core facility managers (non-IT specialists).

This workshop requires:

• You should bring your laptop; any kind of OS is welcome
• Installation, setup, and configuration of OMERO needs knowledge for Command Line Interface (CLI) for Linux
• You must take an e-learning course on RIKEN for using Linux virtual machines; we will give the instructions later
• Basic understanding of imaging workflows

Registration

Please register at foundingGIDE BioImage Hackathon Remember to check the box to confirm your attendance at the OMERO workshop, and provide a brief motivation.

Deadline for registration

October 4th 6th (Extended), 2024 (JST) with travel support application
Application for Workshop 1 is already closed

Additional calls for Workshop 2 OMERO Imaging workflows and Workshop 3 Advanced Analysis with OMERO.
October 19th, 2024 (JST)
(As the event date is coming, the application for additional call here will be accepted in first-come first-served)

Selection

Mostly based on your short motivation. This is not a first-come first-serve event; we evaluate all applications after the deadline. We will notify the selected individuals via the email they registered with by October 9th (JST).

The selection results for Workshop 1, Nov 4, have been sent via email. If you have not received it, please contact us at onami-sec@riken.jp

Travel Funds

Application for the travel funds is already closed

There is some travel support available. If you wish to do so, please state in your motivation statement that you are also applying for Travel Funds. The deadline for the travel funds is also Nov. 6th.

For more information on OMERO, visit the OME website.

Venue

• Building: Integrated Innovation Building (IIB)
• Address: 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
• Access: Click here (RIKEN webpage)

Related events

• Workshop: Machine-learning-based image analysis with ilastik
• Hackathon on Bioimaging Metadata and Ontology