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Updated: May 22, 2026
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Analysis of Multidimensional Microscopy Data Using Cell-ACDC
Published on: November 7, 2025
A deep-learning framework reveals whole-body perturbations at cell level.
Doris Kaltenecker1,2,3, Izabela Horvath4,5, Rami Al-Maskari4,5,6
1Institute for Diabetes and Cancer (IDC), Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany.
Nature
|May 20, 2026
Summary
Researchers developed MouseMapper, a deep learning tool for whole-body disease analysis in mice. This technology reveals systemic changes in nerves and immune cells, linking obesity to sensory deficits and identifying conserved molecular pathways.
Area of Science:
- Biomedical imaging
- Computational biology
- Systems biology
Background:
- Diseases like obesity cause widespread systemic effects impacting multiple organ systems.
- Existing tools lack the comprehensive, high-resolution analysis needed for whole-body disease pathology.
- A need exists for advanced methods to quantify multi-system changes across an entire organism.
Purpose of the Study:
- To introduce MouseMapper, a novel deep learning framework for multi-system disease analysis at the whole-body scale.
- To enable quantitative, high-resolution analysis of anatomical and cellular changes across 31 organs and tissues.
- To apply MouseMapper to study diet-induced obesity and its systemic consequences.
Main Methods:
- Development of foundation-model-based deep learning algorithms for automated segmentation and analysis.
- Quantitative whole-body analysis of neural and immune cell structures.
- Integration of imaging data with proteomic analysis for molecular insights.
Main Results:
- MouseMapper successfully segmented 31 organs and tissues, enabling whole-body quantitative analysis of nerves and immune cells.
- Diet-induced obesity led to structural alterations in trigeminal ganglia nerves, correlating with whisker sensory deficits.
- Proteomic analysis revealed conserved pathways (axon remodeling, complement) affected in both mice and humans.
- Generated 3D inflammation maps by characterizing immune cell composition across tissues.
Conclusions:
- MouseMapper provides a powerful and scalable approach for identifying and quantifying systemic pathologies.
- The framework demonstrates generalizability across different imaging resolutions and datasets.
- This study bridges molecular insights from animal models to human conditions, offering a new paradigm for disease research.
