1. MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution
- Author
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Till Fabian Mertens, Alina Tabea Liebheit, Johanna Ehl, Ralf Köhler, Asylkhan Rakhymzhan, Andrew Woehler, Lukas Katthän, Gernot Ebel, Wjatscheslaw Liublin, Ana Kasapi, Antigoni Triantafyllopoulou, Tim Julius Schulz, Raluca Aura Niesner, and Anja Erika Hauser
- Subjects
Science - 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 CX3CR1+ 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.
- Published
- 2024
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