ABiS-GBI 2023 course - Image data: image analysis, data management and reuse

Okazaki and Kobe, Japan

Dates: 3-7 July 2023 (5 full days)

Locations: Okazaki, Japan (3-5 July); Kobe, Japan (6-7 July)

Venues:

  • National Institute for Basic Biology (NIBB): 3-5 July in Okazaki, Japan
  • RIKEN Center for Biosystems Dynamics Research (BDR): 6-7 July in Kobe, Japan

Event overview

This course is jointly organzied by Global BioImaging (GBI) and Advanced Bioimaging Support (ABiS), an imaging infrastructure in Japan. The course will feature an overarching topic of image data including image analysis, data management and image data reuse.

During 3-5 July, the course will kick-off at the National Institute for Basic Biology in Okazaki, Japan and will feature the following: an image analysis component, both theoretical and practical sessions (duration: 2-2.5 days) taught by Ignacio Arganda-Carreras (Network of European BioImage Analysts [NEUBIAS]), Kagayaki Kato (NIBB, Japan) and Yusaku Ohata (NIBB, Japan) and two seminars featuring OMERO data management software and IDR image repository delivered by Open Microscopy Environment (OME) members, Jean-Marie Burel and Petr Walczysko.

The image analysis topics that will be covered in Okazaki include the following:

  • Image acquisition, formats and handling images
  • Registration and stitching
  • Visualization
  • Segmentation and thresholding

During 6-7 July, the course will continue at RIKEN Center for Biosystems Dynamics Research in Kobe, Japan and will feature workshops on OMERO data management software and seminars featuring BioImage Archive image repository delivered by Matthew Hartley (EMBL-EBI, United Kingdom) and SSBD database delivered by Shuichi Onami (RIKEN BDR, Japan). This course will also provide opportunities for the participants to network with each other and instructors.

The course is open to image analysts who provide image analysis as a service and imaging facility staff and managers as well as service providers in imaging/microscopy and image analysis.

This course will also provide opportunities for the participants to network with each other and the speakers.

The program is available on the right hand side as a PDF document.

This course is limited to 25 places and will take place in-person only.

Event format

This event will take place in-person at National Institute for Basic Biology (3-5 July) and RIKEN Center for Biosystems Dynamics Research (6-7 July).

The possibility to join remotely will not be provided.

Registration fee

There are no registration costs associated with this event (free of charge)

Speakers and instructors

  • Aybuke Kupcu Yoldas (BioImage Archive, European Bioinformatics Institute EMBL-EBI, United Kingdom)
  • Ignacio Arganda-Carreras (University of the Basque Country, Spain)
  • Jean-Marie Burel (Open Microscopy Environment, University of Dundee, United Kingdom)
  • Kagayaki Kato (National Institute for Basic Biology, Japan)
  • Matthew Hartley (BioImage Archive, European Bioinformatics Institute EMBL-EBI, United Kingdom)
  • Petr Walczysko (Open Microscopy Environment, University of Dundee, United Kingdom)
  • Shuichi Onami (RIKEN Center for Biosystems Dynamics Research BDR, Japan)
  • Yusaku Ohta (National Institute for Basic Biology, Japan)

Prerequisites for application

  • You must be employed by a nonprofit research institution (institute, university, etc.)
  • Your day-to-day work must involve one or more aspects of image data, for example, image analysis, data management and/or data reuse
  • You work in imaging facility as an imaging facility manager or staff, as a junior image analyst or work with image data management systems/workflows
  • Experience with microscopy but no to little experience with image analysis
  • Basic knowledge of ImageJ or Fiji

Successful applicants will have to bring in their own laptops for the course.

Application form

Please complete the application form at the following link to be considered for this course: https://www.surveymonkey.com/r/ABiS-GBI-2023-course

Application deadline: the application is open until the course is full

Travel grants

Global BioImaging is providing a number of travel grants for successful applicants who do not have institutional travel support to attend this course. Applications for travel grants are invited by eligible persons (see prerequisites above).

Number of travel grants provided for this course: 8 travel grants. Eligible cost items include the following: travel costs (air travel, public transportation), accommodation costs (e.g. hotel) and visa application fees.

To apply for a travel grant, please visit the following webpage and complete a travel grant application form: https://globalbioimaging.org/international-training-courses/travel-grants-abis-gbi-2023-course

Application deadline: 8 April 2023

Successful travel award grantees: please note you will be expected to attend the entire course, 3-7 July 2023.

For US-based applicants: please note that we cannot provide travel grants to individuals based in US due to funding constraints.