@article{Adams:2026:10.1016/j.crmeth.2026.101334,
author = {Adams, G and Tissot, FS and Liu, C and Mai, C and Brunsdon, C and Duffy, KR and Lo, Celso C},
doi = {10.1016/j.crmeth.2026.101334},
journal = {Cell Rep Methods},
title = {Practical AI-based cell extraction and spatial statistics for large 3D bone marrow tissue images.},
url = {http://dx.doi.org/10.1016/j.crmeth.2026.101334},
year = {2026}
}

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TY  - JOUR
AB  - Although the molecular regulation of hematopoiesis is well characterized, the spatial organization of hematopoietic cells within bone marrow (BM) remains unclear. Advances in microscopy have produced increasingly detailed images of murine BM, yet accurate and scalable methods to extract and analyze these complex datasets are limited. We present PACESS, a computational workflow for BM analysis that combines convolutional neural networks for 2D cell detection and classification with an automated method to extrapolate into 3D, spatial statistical analyses to define tissue regions based on local cell-type densities, and logistic regression to assess whether the relative abundances of cell types reflect reciprocal dependencies. Using PACESS, we investigate the spatial organization of T cells, megakaryocytes, and leukemic cells, revealing that distinct leukemic clusters generate diverse, previously unrecognized neighborhoods within the same BM cavity. PACESS, thus, provides a powerful tool to dissect BM architecture.
AU  - Adams,G
AU  - Tissot,FS
AU  - Liu,C
AU  - Mai,C
AU  - Brunsdon,C
AU  - Duffy,KR
AU  - Lo,Celso C
DO  - 10.1016/j.crmeth.2026.101334
PY  - 2026///
TI  - Practical AI-based cell extraction and spatial statistics for large 3D bone marrow tissue images.
T2  - Cell Rep Methods
UR  - http://dx.doi.org/10.1016/j.crmeth.2026.101334
UR  - https://www.ncbi.nlm.nih.gov/pubmed/41831446
ER  - 

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