【About the Course】
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 Dr. Ignacio Arganda-Carreras (Network of European BioImage Analysts [NEUBIAS]), Dr. Kagayaki Kato (NIBB, Japan) and Dr. Yusaku Ohta (NIBB, Japan) and two seminars featuring OMERO data management software and IDR image repository delivered by Open Microscopy Environment (OME) members, Dr. Jean-Marie Burel and Dr. 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 Dr. Matthew Hartley (EMBL-EBI, United Kingdom) and SSBD database delivered by Dr. Shuichi Onami (RIKEN BDR, Japan). This course will also provide opportunities for the participants to network with each other and instructors.
【Report】
The international training course, ABiS-GBI 2023 Course: Image Data - Image Analysis, Data Management, and Reuse, was held from July 3 to 7, 2023, at the Okazaki Conference Center (National Institute for Basic Biology) and the RIKEN Center for Biosystems Dynamics Research. The course focused on the theme of “Image Data Analysis, Data Management, and Reuse,” featuring both theoretical and practical sessions delivered by distinguished experts from Japan and abroad.
The first three days in Okazaki were led by Dr. Ignacio Arganda-Carreras from NEUBIAS—an international network dedicated to advancing cooperation and development in bioimaging analysis—and Drs. Jean-Marie Burel and Petr Walczysko from OME, an international collaborative initiative aimed at streamlining the management, sharing, and analysis of biological image data while promoting standardization and interoperability. Additionally, Dr. Kagayaki Kato and Dr. Yusaku Ohta from the National Institute for Basic Biology conducted theoretical and practical sessions on biological image analysis techniques.
The sessions, primarily utilizing ImageJ/FIJI, a widely adopted open-source platform for biological image processing and analysis, encompassed a broad spectrum of topics. These ranged from foundational knowledge, such as digital image properties and formats, to advanced techniques, including registration, image synthesis, visualization, segmentation, and image programming.
The teaching materials for the course, developed collaboratively and made publicly accessible on GitHub, served as the foundation for the sessions. This approach effectively linked material development with lecture delivery, optimizing the participants’ learning experience. By addressing a comprehensive array of biological image analysis methods, the course provided participants with opportunities to enhance their skills in alignment with their specific research needs.
Each session concluded with an “Assessment” designed to evaluate participants' comprehension through carefully crafted questions, followed by engaging Q&A discussions. Supplementary exercises were also introduced as needed, further reinforcing participants’ understanding of each topic.
We anticipate that this training course will significantly contribute to enhancing the quality of data analysis in future research endeavors and foster stronger networks among researchers in the biological sciences, both domestically and internationally.
Kagayaki Kato (Optics and Imaging Facility, National Institute for Basic Biology)
