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MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution

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Item Type:Article
Title:MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution
Creators Name:Mertens, T.F. and Liebheit, A.T. and Ehl, J. and Köhler, R. and Rakhymzhan, A. and Woehler, A. and Katthän, L. and Ebel, G. and Liublin, W. and Kasapi, A. and Triantafyllopoulou, A. and Schulz, T.J. and Niesner, R.A. and Hauser, A.E.
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.
Keywords:Imaging, Imaging the Immune System, Osteoimmunology, Animals, Mice
Source:Nature Communications
Publisher:Nature Publishing Group
Page Range:1764
Date:26 February 2024
Official Publication:https://doi.org/10.1038/s41467-024-45827-6
PubMed:View item in PubMed

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