The Bio-imaging Data Analysis
Training Course 2021
Organizers: Dr. Kagayaki Kato, Dr. Hiroshi Koyama,
Dr. Takashi Murata, Dr. Yasuhiro Kamei, and Dr.
Shigenori Nonaka

Supervisors: Prof. Naoto Ueno, Prof. Toshihiko
Fujimori, and Prof. Shinji Takada

November 24 (Wed)–26 (Fri), 2021
The 9th Bio-imaging Data Analysis Training Course was
jointly held by the Exploratory Research Center on Life andLiving Systems (ExCELLS), JSPS KAKENHI Platforms
for Advanced Bioimaging Support (ABiS) and NIBB. Thiscourse was designed for biologists who are relatively newto analyzing datum obtained through advanced microscopy.
Therefore, the focus of the training was related to learning
about image processing and analytical techniques throughsolving simple problems with image analysis, and understanding appropriate methods and necessary preparation
when consulting experts in technically advanced problems
concerning imaging. 134 people applied for the course,which had an announced capacity of 16 participants. Given
the high demand for courses on these subjects, we accepted
33 participants.
This course's lectures were conducted with the aim ofguiding participants towards an awareness of the seriesof steps essential for fundamental image processing andanalysis while also obtaining images for eventual use (workflows). In addition to this, participants independently worked
on practical image analysis exercises using ImageJ; a typicalopen-source software package for biological image processing and analysis. Lectures were also given on how theprogramming of simple “macro language”, which uses theaforementioned workflows in ImageJ, allows for automation; a necessity for the large capacity and high-dimensional
throughput of microscopic imaging which has more becomecommon over recent years.
Upon the course’s conclusion, each student offered commentary about and discussed the methods taught by providing examples of images gleaned from their own research.
Unfortunately, although this year's course was held online
due to issues associated with COVID-19, we utilized technological innovations within the lectures and exercises, suchas a chat service to support individual participants, so as toallow them to feel as if the course was being held as an inperson event.
Every year following the course’s completion, participants
often report feeling pretty tired, but satisfied. In a similarvein, we believe that this course is beneficial to its participants thanks to the associated increase in their familiarity
with image analysis techniques. Thus, we expect that thiscourse will increase opportunities for joint research relating
to biological image analysis moving forward.
(Kagayaki Kato)

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Advanced Bioimaging Support(ABiS)
The demand for bioimaging has increased in recent years
in the field of life science. However, due to advances inimaging technologies, such as the diversification and specialization of imaging equipment, increasingly complex operations, increased equipment and running costs, as well as thegrowing need for image data analysis, individual research
institutes and universities are increasingly encountering difficulties related to the introduction, maintenance, and operation of imaging equipment.
ABiS was launched as one of the designated "Platforms for
Advanced Technologies and Research Resources" during
fiscal year (FY) 2016 under the new framework of the Grantin-Aid for Scientific Research on Innovative Areas (Leader:Prof. Masanobu KANO, NIPS/The University of Tokyo).
This program aims to contribute to the further development of academic research in Japan through the provisionof cutting-edge equipment and methodologies to individual
KAKENHI (Grants-in-Aid for Scientific Research) research
projects by the Ministry of Education, Culture, Sports,
Science and Technology (MEXT) under the Grant-in-Aid for
Scientific Research on Innovative Areas (FY2016-FY2021).
Cooperating with domestic partner organizations that own
and operate multiple types of advanced specialized imaging
equipment, ABiS provides cutting-edge instruments forlight microscopy, electron microscopy, magnetic resonanceimaging, and other methods through its network. It aims toprovide comprehensive support for advanced imaging in thefield of life science. NIBB, together with NIPS, contributes
as a core institute in the ABiS network. Among the various
support activities that ABiS performs, NIBB is tasked withthe following:■ Light microscopy• 4 D microscopy administered by Prof. Toshihiko
FUJIMOIRI• IR-LEGO microcopy administered by Assoc. Prof.
Yasuhiro KAMEI• D SLM administered by Assoc. Prof. ShigenoriNONAKA■ Imaging analysis• Development of image processing/analysis algorithmsfor biological data administered by Prof. Naoto UENO,Assist. Prof. Kagayaki KATO and Assist. Prof. Yusaku
OHTA.
■ Training• Training for image analysis administered by Prof. Naoto
UENO and Assist. Prof. Hiroshi KOYAMA.
To organize and coordinate ABiS activities, two secretariat offices were established at NIBB (Assoc. Prof. Shoji
MANO) and NIPS, respectively, under the control of thegeneral support group (Individuals in charge at NIBB;
Director-general Prof. Kiyokazu AGATA, Prof. Naoto
UENO, Prof. Shinji TAKADA, Assoc. Prof. Shoji MANO).
General support provided includes budget planning and management of ABiS activities. In particular, we promote ABiS
activities via its associated website and other media, so that

KAKENHI researchers make full use of the ABiS platformto accelerate their research projects. In addition, we organize
technology training sessions, workshops, and symposia
to disseminate advanced imaging technologies and share
information about them. We also coordinate with the otherthree platforms (Platform of Supporting Cohort Study andBiospecimen Analysis, Platform of Advanced Animal Model
Support, and Platform for Advanced Genome Science) toprovide both multidisciplinary and international support.
Euro-Bioimaging (EuBI) is the largest and most well-established imaging network in Europe, and has been expanding
globally to form the Global Bioimaging (GBI) network
which boasts participants from areas such as India, Australia,
Singapore, the Republic of South Africa, Canada, Mexico,USA, and some Latin American countries. In 2018, ABiS
joined the GBI project representing the Japanese bioimaging
community. It is hoped that through GBI, ABiS will be ableto raise the quality of present support to that of the currently
accepted international benchmarks, and that further observations, data analyses and research methods will be able to bebetter shared globally. Furthermore, it is also hoped that thiscollaboration will lead to set up a better environment for bioimaging research in Japan. This will be achieved not only byproviding international training courses for young researchers and the staff of imaging facilities, but also throughdiscussions about the implementation of career paths; acommon problem in this field.
Since the ABiS project that spanned 6 years was finishedat the end of this fiscal year, we self-evaluated the past
ABiS activities and forecast the future demands, andapplied for the Grant-in-Aid for Transformative Research
Areas, Platforms for Advanced Technologies and ResearchResources (FY2022) as the next ABiS project. In February2022, our past activities were highly evaluated by the committee and plans for the next project have been approved forthe second phase of the ABiS project (FY2022-FY2027). Asin the past, the ABiS will continue to support light microscopy, electron microscopy, magnetic resonance imaging, andimage analysis as the core institute together with the Institutefor Physiological Sciences.

ABiS Symposium "Image Data
Analysis to Open Up A New Era
for Life Science"
March 1 (Tue) 2022
The ABiS symposium "Imaging Data Analysis toOpen Up A New Era for Life Science" was held thisyear as an online event. The following 8 researchers,
experts in image data analysis and database construction, gave lectures.
• N aomi KAMASAWA (The Max Planck Florida
Institute for Neuroscience Imaging Center)• N obuhiko OHNO (Jichi Medical University/
National Institute for Physiological Sciences)• Tatsumi HIRATA (National Institute of Genetics)• Kazuo IABA (Tsukuba University)• Naohiro OKADA (The University of Tokyo)• Saori TANAKA (Brain Information Communication
Research Laboratory Group)• Shu-ichi ONAMI (RIKEN Center for Biosystems
Dynamics Research)•Yo s h i t a k a K I M O R I ( F u k u i U n i v e r s i t y o fTechnology)
There were 168 participants, and a lively question
and answer session was held for each presentation. A
participant survey and other information about thissymposium is available on the website. (https://www.
nibb.ac.jp/abis/ev20220301/)

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