GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE318nnn/GSE318959/primaryOK200OtherHomo sapiensOtherhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE318959GEOGSEfalseModeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysisTertiary lymphoid structures (TLSs) are sites of immune organization in peripheral tissues that arise from chronic inflammation. They play important roles in infection control and cancer but the mechanisms controlling their formation and function remain only partly understood. Here, we combine high-plex imaging, serial-section 3D reconstruction, and optimal trajectory analysis modeling to reconstruct TLSs in human lung infected with Mycobacterium tuberculosis. We find that TLSs are the extended and irregular , spatially heterogeneous structures shape of TLS whose state of maturation, as judged by germinal center (GC) organization, is poorly captured by 2D histopathology or spatial profilingprofiling, making assuagements of developmental stage (early, primary, or secondary) highly error prone. . Using 3D data, we show that TLSs having GCs are diverse in cellular composition, size, and morphology. Organizing this complexityModeling development in 3D using optimal transport (trajectory) analysis reveals multiple pathways of TLS development formation differing that differ in the timing and coordination of follicular dendritic cell network formation, and GC germinal center consolidation, and positioning within the tissue. These findings highlight the importance of volumetric analysis in understanding immune organization and provide new insights into TLS biology.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 sapiens