MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution
2024 | journal article. A publication with affiliation to the University of Göttingen.
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MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution
Mertens, T. F.; Liebheit, A. T.; Ehl, J.; Köhler, R.; Rakhymzhan, A.; Woehler, A. & Katthän, L. et al. (2024)
Nature Communications, 15(1). DOI: https://doi.org/10.1038/s41467-024-45827-6
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Details
- Authors
- Mertens, Till Fabian; Liebheit, Alina Tabea; Ehl, Johanna; Köhler, Ralf; Rakhymzhan, Asylkhan; Woehler, Andrew; Katthän, Lukas; Ebel, Gernot; Liublin, Wjatscheslaw; Kasapi, Ana; Hauser, Anja Erika
- Abstract
- Abstract Analyzing immune cell interactions in the bone marrow is vital for understanding hematopoiesis and bone homeostasis. Three-dimensional analysis of the complete, intact bone marrow within the cortex of whole long bones remains a challenge, especially at subcellular resolution. We present a method that stabilizes the marrow and provides subcellular resolution of fluorescent signals throughout the murine femur, enabling identification and spatial characterization of hematopoietic and stromal cell subsets. By combining a pre-processing algorithm for stripe artifact removal with a machine-learning approach, we demonstrate reliable cell segmentation down to the deepest bone marrow regions. This reveals age-related changes in the marrow. It highlights the interaction between CX 3 CR1 + cells and the vascular system in homeostasis, in contrast to other myeloid cell types, and reveals their spatial characteristics after injury. The broad applicability of this method will contribute to a better understanding of bone marrow biology.
- Issue Date
- 2024
- Journal
- Nature Communications
- eISSN
- 2041-1723
- Language
- English
- Sponsor
- Deutsche Forschungsgemeinschaft https://doi.org/10.13039/501100001659
Einstein Stiftung Berlin https://doi.org/10.13039/501100006188