In conventional pathology and physiology research, two-dimensional (2D) analysis—observing thinly sliced tissue sections—has been mainstream, making it difficult to comprehensively understand the distribution of cells across entire organs or throughout the whole organism. Therefore, a new analytical platform has been needed to quantitatively elucidate developmental processes of the organism, drug efficacy and adverse effects, and disease-related changes at the whole-organ or whole-body level.
To address this challenge, a research group led by Professor Hiroki R. Ueda of the Graduate School of Medicine, The University of Tokyo (also Specially Appointed Professor at Kurume University), Visiting Researchers Shota Y. Yoshida and Katsuhiko Matsumoto, has constructed a three-dimensional (3D) atlas (CUBIC Organ/Body Atlas)^*1 encompassing all cells across whole organs and the entire body.
This research group optimized the tissue-clearing technique (CUBIC Method)^*2 for application to individual organs as well as the entire body of neonatal mice while simultaneously developing a novel 3D imaging technology capable of high-resolution imaging over wide fields. Furthermore, from the acquired 3D images, the positional information of each individual cell was extracted, enabling the construction of 3D atlases consisting of all cells across entire organs and the whole body. As a result, it became possible to superimpose and compare the distribution of cells obtained from different individuals or experimental conditions using the same reference framework.
The 3D cellular atlases of all organs and the entire body constructed in this study is expected to serve as a fundamental technology for quantitatively evaluating changes in cell distribution and cell numbers at the whole-body scale in research fields such as developmental biology, physiology, and pathology. With this technology, analyses previously limited to local regions can now be compared and examined in the context of entire organs or the whole body. Furthermore, by combining the acquired 3D atlases data with existing gene expression data and 2D spatial omics data such as spatial transcriptomics, it becomes possible to advance toward integrated analyses of morphological and molecular information. Such integrated analyses may lead to a higher-precision understanding of diseases and the creation of novel indicators for pathological condition analysis. The analytical platform established in this study is anticipated for broad utilization across fields ranging from basic to applied research, as a foundational platform capable of evolving into next-generation 3D pathological diagnosis that complements and extends conventional 2D pathological diagnosis, while anticipating future applications to human tissues.

*1 3D Atlas (CUBIC Organ/Body Atlas)
Three-dimensional reference data across organs and the entire body Three-dimensional image data of organs and the whole body, to which positional information of organs and structures has been added. In this study, the positions of all cells present across entire organs or the whole body are recorded three-dimensionally and segmented into regions.
*2 Tissue-clearing technique (CUBIC Method)
A tissue-clearing technique developed at RIKEN in 2014 enabling 3D observation of organs and the entire body. By removing lipids and pigments from biological tissues and matching the refractive index, this technique enables 3D observation of internal structures while preserving the 3D architecture of entire organs or whole organisms. CUBIC stands for “Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis.”

This study was conducted collaboratively with the following various research groups: Senior Researcher Satoshi Takagi of the Cancer Chemotherapy Center, Japanese Foundation for Cancer Research; Professor Etsuo Susaki of the Graduate School of Medicine, Juntendo University; Professor Eiichi Morii of the Graduate School of Medicine, Osaka University; Professor Tetsuo Ushiku of the Graduate School of Medicine, The University of Tokyo; and Visiting Professor Yoshichika Yoshioka of the Institute for Biomedical Sciences, Iwate Medical University.

This achievement was supported by the Japan Science and Technology Agency (JST) Exploratory Research for Advanced Technology (ERATO) program, “Ueda Biological Timing Project*” (JPMJER2001).
*In this project, sleep-wake rhythms are used as a model system to develop “systems biology aimed at advancing the understanding of humans,” with the goal of elucidating “biological time” information that spans from molecules to individuals living in society.

Furthermore, this research was conducted with support from the JST Moonshot Research and Development Program (Project Number: JPMJMS2023), the Ministry of Education, Culture, Sports, Science and Technology (MEXT) Quantum Leap Flagship Program (Q-LEAP) (JPMXS0120330644), and the Japan Society for the Promotion of Science (JSPS) Grants-in-Aid for Scientific Research (JP20K06885, JP20K16626, JP23K27391, JP22H02824, JP22H04926, JP23K20044).

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