Whole-organ and whole-body 3D atlases enable cellome-wide profiling
Summary
Recent advancements in tissue clearing and light-sheet fluorescence microscopy have enabled whole-organ/body-scale analysis at single-cell resolution. However, comprehensive bioinformatics resources like digitized whole-cellome maps, analogous to whole-genome sequencing, remain limited. Here, we present the CUBIC Organ/Body Atlas, a set of three-dimensional single-cell-resolution references for eleven adult mouse organs and a neonatal whole-mouse body. To generate this atlas, we optimized
Content
# Whole-organ and whole-body 3D atlases enable cellome-wide profiling
*Published: 2026 Mar 19*
Recent advancements in tissue clearing and light-sheet fluorescence microscopy
have enabled whole-organ/body-scale analysis at single-cell resolution. However,
comprehensive bioinformatics resources like digitized whole-cellome maps,
analogous to whole-genome sequencing, remain limited. Here, we present the CUBIC
Organ/Body Atlas, a set of three-dimensional single-cell-resolution references
for eleven adult mouse organs and a neonatal whole-mouse body. To generate this
atlas, we optimized tissue clearing protocols and developed exMOVIE, an imaging
system achieving sufficient working distance and axial resolution for
organ-/body-wide three-dimensional imaging and subsequent cell nuclei detection.
The atlas facilitates comparative analysis among multiple samples at single-cell
resolution, allowing for applications in organ development studies, disease
state analysis, and whole-body immune cell profiling with three-dimensional
immunostaining. Thus, the CUBIC Organ/Body Atlas contributes to establishing a
common cellomics workflow, advancing our systems-level understanding of
organisms in physiological, developmental, and pathological processes.
DOI: 10.1016/j.cell.2025.12.057