03341nas a2200745   4500000000100000000000100001008004100002260001200043653002500055653002100080653003100101653001800132653001300150100001600163700002400179700001600203700001500219700002300234700002400257700001700281700002300298700001700321700001900338700001400357700002100371700001700392700001700409700002500426700002100451700002100472700002000493700002400513700002100537700002100558700002700579700002100606700002000627700002200647700001900669700001900688700002300707700001700730700001600747700001100763700002000774700001600794700002700810700002300837700001600860700002100876700002400897700002100921700002500942700002200967700002100989700002001010700001501030700002301045245007301068856005501141300001201196490000801208520136501216022001402581       2024                            d  c2024-1110aComputational models10aData integration10aLymphocyte differentiation10aLymphopoiesis10aSoftware1 aNadav Yayon1 aVeronika R. Kedlian1 aLena Boehme1 aChenqu Suo1 aBrianna T. Wachter1 aRebecca T. Beuschel1 aOren Amsalem1 aKrzysztof Polanski1 aSimon Koplev1 aElizabeth Tuck1 aEmma Dann1 aJolien Van Hulle1 aShani Perera1 aTom Putteman1 aAlexander V. Predeus1 aMonika Dabrowska1 aLaura Richardson1 aCatherine Tudor1 aAlexandra Y. Kreins1 aJustin Engelbert1 aEmily Stephenson1 aVitalii Kleshchevnikov1 aFabrizio De Rita1 aDavid Crossland1 aMarita Bosticardo1 aFrancesca Pala1 aElena Prigmore1 aNana-Jane Chipampe1 aMartin Prete1 aLijiang Fei1 aKen To1 aRoger A. Barker1 aXiaoling He1 aFilip Van Nieuwerburgh1 aOmer Ali Bayraktar1 aMinal Patel1 aE. Graham Davies1 aMuzlifah A. Haniffa1 aVirginie Uhlmann1 aLuigi D. Notarangelo1 aRonald N. Germain1 aAndrea J. Radtke1 aJohn C. Marioni1 aTom Taghon1 aSarah A. Teichmann00aA spatial human thymus cell atlas mapped to a continuous tissue axis  uhttps://www.nature.com/articles/s41586-024-07944-6  a708-7180 v6353 aT cells develop from circulating precursor cells, which enter the thymus and migrate through specialized subcompartments that support their maturation and selection1. In humans, this process starts in early fetal development and is highly active until thymic involution in adolescence. To map the microanatomical underpinnings of this process in pre- and early postnatal stages, we established a quantitative morphological framework for the thymus—the Cortico-Medullary Axis—and used it to perform a spatially resolved analysis. Here, by applying this framework to a curated multimodal single-cell atlas, spatial transcriptomics and high-resolution multiplex imaging data, we demonstrate establishment of the lobular cytokine network, canonical thymocyte trajectories and thymic epithelial cell distributions by the beginning of the the second trimester of fetal development. We pinpoint tissue niches of thymic epithelial cell progenitors and distinct subtypes associated with Hassall’s corpuscles and identify divergence in the timing of medullary entry between CD4 and CD8 T cell lineages. These findings provide a basis for a detailed understanding of T lymphocyte development and are complemented with a holistic toolkit for cross-platform imaging data analysis, annotation and OrganAxis construction (TissueTag), which can be applied to any tissue.  a1476-4687