The University of Tokyo develops whole-organ/whole-body mouse atlas

A research group led by Professor Hiroki R. Ueda from the Graduate School of Medicine, the University of Tokyo (also affiliated with Kurume University), along with Visiting Researchers Shota Y. Yoshida and Katsuhiko Matsumoto from the same university, has collaborated with the Japanese Foundation for Cancer Research (JFCR), Juntendo University, the University of Osaka, and Iwate Medical University to construct a three-dimensional atlas covering all the cells in every organ and the entire body of a mouse (CUBIC Organ/Body Atlas). This was achieved by optimizing the tissue clearing technique (CUBIC method) for application to individual organs and to the entire body of neonatal mice, developing an original three-dimensional imaging system capable of capturing wide areas at high resolution, and extracting the positional information of each individual cell from the resulting three-dimensional images. Ueda commented, "By using this atlas, it becomes possible to compare the distribution of cells obtained from different individuals and under different experimental conditions. I hope many researchers will make use of it." The study was published in Cell.

In conventional pathology and physiology research, two-dimensional analysis of thin tissue sections has been the dominant approach, making it difficult to comprehensively understand the arrangement and number of cells across an entire organ or body. However, since phenomena such as drug efficacy, side effects, immune responses, and developmental changes frequently span multiple organs and tissues, the need to capture cells throughout the whole body in three dimensions has been growing.

The research group had previously developed the CUBIC method and constructed and released an atlas covering all cells in the mouse brain. Ueda noted, "Initially, we thought that the brain would be the most complex and challenging part, yet that atlas has been used in a great deal of research. This time, when we tried to cover all cells in the entire body, it turned out to be more difficult than expected and required the development of several new technologies."

First, the CUBIC method was applied to both male and female neonatal mice and to all organs other than the brain in adult mice to achieve tissue clearing. Because the efficiency of delipidation and refractive-index matching varies considerably depending on the type of organ and in the whole-body case, the processing procedure was optimized for each organ, enabling uniform clearing and high-quality three-dimensional observation. For example, delipidation of the kidney required 10 days (twice the usual time) and clearing of the liver required the concentration of the refractive-index matching solution to be raised in steps. Clearing the entire body of neonatal mice took approximately one month. Yoshida noted, "Establishing the clearing protocol for neonatal mice was a real challenge."

After clearing, the samples are scanned and imaged with a thin sheet of light; however, conventional light-sheet microscopes cannot image large specimens at high resolution. The group therefore developed a light-sheet microscope with a deep observation range of 3 cm (or 6 cm when imaging from both the top and bottom) and a resolution capable of distinguishing individual cells. The positional information of each cell was comprehensively extracted from the resulting three-dimensional images. For example, it was found that the whole body of a neonatal mouse consists of an average of approximately 610 million cells in males and approximately 530 million cells in females, while the heart of an adult mouse contains 28.1 million cells and the lungs contain 120 million cells. Using the positional information of all these cells, a three-dimensional atlas was constructed comprising all the cells contained in every organ and in the whole body. Matsumoto noted, "Because the data volume was enormous—around 20 terabytes for a single liver—the challenge was how to collect data quickly while maintaining good resolution from deep to shallow regions."

The researchers further used this atlas to analyze changes in cell distribution across whole organs under varying conditions, including developmental stages, disease models, and drug administration. Specifically, they succeeded in capturing region-specific changes in cell numbers during kidney development, organ damage caused by drug administration, and systemic changes in the distribution of immune cells associated with inflammation, all in three dimensions and quantitatively.

The group also presented an application demonstrating whole-body-scale analysis of a specific cell type using the three-dimensional atlas. Focusing on macrophages, which are important to immunity, they combined three-dimensional immunostaining of their marker IBA1 with three-dimensional imaging to visualize the distribution of macrophages at whole-body scale. By mapping this data onto the three-dimensional atlas, they found that the number, density, and spatial distribution of macrophages differ from organ to organ. In certain organs such as the spleen, macrophages were found to accumulate locally. This suggests that macrophages may play different roles and functions in different organs, and further understanding of the physiological significance of macrophages is expected in future research.

The atlas is expected to serve as a foundational technology for quantitatively evaluating changes in cell distribution and cell numbers at whole-body scale. Moreover, by combining the three-dimensional atlas data acquired with existing gene expression data and two-dimensional spatial analysis data such as spatial transcriptomics, it will be possible to advance toward integrated analyses that merge morphological and molecular information. Such integrated analyses may lead to a deeper understanding of diseases and to the development of new indicators for pathological analysis. Ueda stated, "We are also considering future application to human organs."

Journal Information
Publication: Cell
Title: Whole-organ and whole-body 3D atlases enable cellome-wide profiling
DOI: 10.1016/j.cell.2025.12.057