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Analysis of Multidimensional Microscopy Data Using Cell-ACDC
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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.

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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.

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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.