Clustering for Microscopy Images


In contrast to nearly all other tissues, the anatomy of cell differentiation in the bone marrow remains unknown. This is owing to a lack of strategies for examining myelopoiesis—the differentiation of myeloid progenitors into a large variety of innate immune cells—in situ in the bone marrow. Such strategies are required to understand differentiation and lineage-commitment decisions, and to define how spatial organizing cues inform tissue function. Here we develop approaches for imaging myelopoiesis in mice, and generate atlases showing the differentiation of granulocytes, monocytes and dendritic cells. We benchmarked various 3D clustering approaches including but not limited to K-means, DBSCAN, Density Peaks. Our results on the microscopy data indicate that local cues produced by distinct blood vessels are responsible for the spatial organization of definitive blood cell differentiation.


J. Zhang, Q. Wu, C. B. Johnson, G. Pham, J. M. Kinder, A. Olsson, A. Slaughter, M. May, B. Weinhaus, A. D'Alessandro, J. D. Engel, J. X. Jiang, J. M. Kofron, L. F. Huang, V. B. S. Prasath, S. S. Way, N. Salomonis, H. L. Grimes, D. Lucas. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature, 590, 457-462, February 2021. doi:10.1038/s41586-021-03201-2