"Virtual Mouse" Takes a Step Closer: Two New Platforms Map Whole-Body Biology at Unprecedented Scale
Two independent research teams have published powerful new methods for mapping molecular and cellular activity across entire mouse bodies, providing transformative tools for studying systemic biological processes and disease.
University of Chicago Platform (Array-seq)
Researchers at the University of Chicago's Pritzker School of Molecular Engineering (UChicago PME), led by Associate Professor Nicolas Chevrier, developed a system to map gene expression across entire mouse body sections. The work, led by staff scientist Maggie Clevenger, involved both industrial and academic collaborators.
The technique accurately mapped all organs, tissue regions, and approximately 75% of known cell types in the mouse body. The findings were published in Cell.
The method uses spatial transcriptomics, which combines high-resolution microscopy and genetic sequencing to measure gene expression across tissue. In 2025, the team developed Array-seq. To adapt it for whole-mouse analysis, the researchers created methods to generate thin slices of frozen mouse bodies, transfer them onto Array-seq slides, and preserve RNA integrity. This work involved collaboration with Professor Tadafumi Kawamoto of Tsurumi University, producing cross-sections comparable to the thickness of an average cell.
Following spatial transcriptomics, the team created a new computational model for cellular information annotation of the entire mouse, in collaboration with Ashwini Patil of Combinatics. Additionally, in collaboration with Professor Feng Bao of Fudan University, a machine learning model was created to label organs, tissues, and cell types on hematoxylin and eosin-stained tissue sections.
The technologies were tested by measuring inflammation in a mouse model of sepsis. The team quantified the impact of systemic inflammation on every cell type and major organ tissue.
"This tool allows for generating datasets at a previously unavailable scale and lays a foundation for a 'virtual mouse' that could test therapies and facilitate understanding of body-wide biological processes."
Chevrier stated that applications may include studying how genes affect various areas of the body or assessing the effects of new drugs. The subsequent goal involves modeling the entire mouse body, which could contribute to creating a "virtual mouse" model for research.
Helmholtz Munich Platform (MouseMapper)
Researchers at Helmholtz Munich, Ludwig Maximilians University Munich (LMU), and collaborating institutions developed MouseMapper, an AI framework that maps disease-related changes across the entire mouse body at cellular resolution.
The platform automatically segments 31 organs and tissue types while mapping nerves and immune cells, enabling whole-body analysis in intact mice.
Using MouseMapper, the researchers investigated obesity in mice fed a high-fat diet. They observed structural changes in sensory nerves of the trigeminal nerve, with fewer endings and branches in obese mice. Behavioral experiments indicated reduced sensory responses. Spatial proteomics identified molecular alterations in the trigeminal ganglion associated with nerve remodeling and inflammation. Similar molecular signatures were found in human trigeminal tissue from individuals with obesity, suggesting cross-species conservation.
The study was published in Nature. The researchers made whole-body datasets publicly available for other researchers to use.