Advanced Bioimaging Support (ABiS) is a project to contribute to the further development of academic research in Japan through the provision of cutting-edge equipment and methodologies to individual KAKENHI (Grants-in-Aid for Scientific Research) research projects through a network of universities and research institutes that owned and operated multiple types of advanced specialized imaging equipment, with National Institute for Physiological Sciences (NIPS) and National Institute for Basic Biology (NIBB) as core institutions. ABiS provides 4 kinds of tailor-made support using advanced imaging equipment for light microscopy, electron microscopy, magnetic resonance imaging, and image data analysis to meet the needs of users. To date, ABiS has supported Grant-in-Aid proposals from researchers from young researchers to senior researchers, and many of them have led to research results. In addition, ABiS holds training courses on four types of support with the aim of disseminating bioimaging technology and fostering young researchers, and participates in the GBI project on behalf of the Japanese bioimaging community to collect information on cutting-edge technologies and discussing common issues worldwide.

Optical microscopes are one of the most widely used tools in biological and life science research. With recent advances in technology, various advanced microscopes have been developed and improved in performance and functionality, allowing observation at scales previously impossible, leading to new discoveries. However, a high level of expertise is required to select the most appropriate microscope for each application and to maximize its performance. In the ABiS Optical Microscopy Support Team, support staff stationed around the country work together to select the best microscope for the user’s purpose and use advanced technology to support everything from sample preparation to observation. We also conduct training courses to broaden the understanding of optical microscopy techniques within the research community. In addition, in cooperation with the image analysis support team, we are making progress in acquiring images suitable for quantitative analysis. We are working with global microscope users to standardize image data and create a database. Through these activities, we support life science research in a wide range of fields.

Imaging techniques of electron microscopy are critical to observe ultrastructure in life science. Advanced technologies, such as cryo-electron microscopy and 3D ultrastructural analyses using scanning electron microscopy, have enabled visualization of 3D structures at high resolution and at various scales, from molecular complexes to cells and tissues. In addition, various techniques for visualizing specific molecules and structures within the ultrastructure have also become indispensable, serving as a bridge between other modalities of life science research and ultrastructural analyses. The electron microscopy support of ABiS provides a platform to meet the needs in utilizing such electron microscopic technologies. It allows experts to guide the direction of experiments, suggest appropriate analysis methods, and provide support with advanced skills for necessary electron microscopic experiments, based on the research objectives and the data already obtained. Additionally, through training of electron microscopy as well as the provision of advanced imaging techniques, the platform enhances the quality of research and the capabilities of researchers. These efforts will facilitate more research projects in wide areas of life science and be expected to make electron microscopy more accessible to a broader spectrum of researchers.

Magnetic Resonance Imaging (MRI) is an imaging technology capable of extracting detailed anatomical and functional information from living organisms, including humans. Its data acquisition and analysis methods are advancing rapidly in the fields of human cognitive science and clinical medicine. The ABiS MRI Support Platform offers comprehensive support from experts in clinical and basic research, MRI image acquisition, data analysis, addressing individual issues, and providing tutorials. The platform aims to contribute to the publication of research findings and enhance researchers’ capabilities by offering techniques for image acquisition and analysis, advice and support, training in data analysis techniques, and assistance with technology transfer.

Rapid advances in microscopy technology have made it possible to observe multiple layers of biological phenomena and an important issue for life science is how to extract the biological meaning behind the morphology and dynamics of organisms from the vast amount of spatiotemporal image data acquired. The ABiS image analysis team consists of eight image analysis experts from seven research institutions, including Inter-University Research Institutes, national universities, and private universities. Each of the team members has a wide range of backgrounds in cell biology, developmental biology, systems biology, and information engineering, and they assist Grant-in-Aid recipients in extracting the biological meaning behind the image data acquired from multiple levels, such as molecules, cells, tissues, and individuals, and in the process of publishing their research papers. In the process, we provide tailor-made support by suggesting various observation methods and advising on the setting of image acquisition conditions using various microscopes, while engaging in in-depth interactive discussions with the recipient. In order to further improve the level of support, we develop applications and algorithms for image analysis while incorporating the latest AI technology.

Realizing CPS-type multi-functional measurements or building big data for artificial intelligence use requires a data format common for various instrument types. We concluded that such a format must have sufficient information to replicate the experiments from multiple aspects. We have developed an XML-based data structure called MaiML to realize this “independent usability,” also implementing modern mechanisms such as tamper-proofing and partial encryption. The format is in the process of JIS standardization and is hoped to be published in 2023. In this article, we present various aspects and situations around MaiML. Features like analysis process modeling and general-purpose data containers are in discussion. We also show a concrete image of the utilization process of the MaiML data reserved in data lakes.

Imaging through scattering media, such as biological tissues, atmospheric turbulence, and fog, has been a longstanding challenge in optics. Recent advancements in information science have led to the emergence of computational imaging, an optical imaging technique predicated on signal processing. Research in scattering imaging, a subset of computational imaging, is particularly active. Notably, this field enables light measurement and control through highly scattering media, where the presence of direct light cannot be assumed. Additionally, there is progress in non-invasive scattering imaging, moving closer to practical application. The miniaturization and enhancement of imaging systems that actively utilize scattering media have also been demonstrated. This article introduces the trends in scattering imaging within the optical field, focusing on our research.

Multiphoton excitation is a nonlinear optical process in which fluorescent molecules are excited by simultaneously absorbing multiple photons. Among microscopy techniques based on multiphoton excitation, two-photon microscopy (2PM) uses near-infrared pulsed lasers that penetrate well into highly light-scattering biological tissues and has exerted a profound impact on neuroscience, especially since the 2000s, as it allows for imaging of activity of complex neural circuits deep within the brain at single-cell resolution. On the other hand, typical 2PM scans the entire target volume with a focal point of about 1 μm³. This has limited its ability to observe the fast dynamics of neural circuit activity over a large brain area. To overcome this problem, recent 2PM takes advantage of various optical techniques to image a wider field of view at a faster sampling rate. Other technological innovations in multiphoton microscopy include three-photon microscopy to image the deeper brain more clearly, and miniaturized multiphoton microscopes that can be attached to the head of an animal to image brain circuit activity at a high resolution during freely-moving behavior.

Recent advancements in manipulation techniques, such as optical tweezers and magnetic tweezers, have facilitated precise manipulation of specimens under microscopic observation. This review introduces a three-dimensional (3-D) manipulation technique employing optical tweezers combined with the 3-D single-particle tracking method. Moreover, it highlights the cutting-edge research effectively utilizing these manipulation techniques.

The establishment of left-right (L-R) symmetry in the mammalian body relies on leftward fluid flow at the embryonic node, which activates nodal immotile cilia, referred to as the ‘antenna of the cell’, and activate left-side specific signal cascades. However, how the nodal flow activate the nodal immotile cilia were controversial. In our research, I and my colleagues utilized three-dimensional manipulation microscopy equipped with optical tweezers. Our findings revealed that nodal immotile cilia are responsive to mechanical stimuli, triggering calcium responses and Dand5 mRNA degradation. These events subsequently initiate left-side-specific signaling cascades responsible for the determination of left-right asymmetry.