Yiing Lin

Mar 1, 2024 | nature.com | Sanjay Jain |Liming Pei |Jeffrey M. Spraggins |Joana Gonçalves |John Hickey |Neil L. Kelleher | +9 more

Correction to: Nature Cell Biology https://doi.org/10.1038/s41556-023-01194-w. Published online 19 July 2023. In the version of this article originally published, the name of Tianyang Xu was misspelled as Tiangyang Xu. The name has been corrected in the HTML and PDF versions of the article. About this articleJain, S., Pei, L., Spraggins, J.M. et al. Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol (2024).

Jul 19, 2023 | nature.com | John Hickey |Winston R. Becker |Chenchen Zhu |Derek Chen |Daniel Cotter |Annika K Weimer | +10 more

AbstractThe intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health1. The intesting has a length of over nine metres, along which there are differences in structure and function2. The localization of individual cell types, cell type development trajectories and detailed cell transcriptional programs probably drive these differences in function.

Jul 19, 2023 | nature.com | Sanjay Jain |Liming Pei |Jeffrey M. Spraggins |Joana Gonçalves |John Hickey |Neil L. Kelleher | +9 more

Data types, organs and technologiesSince the second quarter of 2023, HuBMAP datasets using 18 different analytical technologies or assay types have been publicly available (Figs. 1a and 2). These encompass 1,672 publicly available datasets from regions with no histopathologic abnormality from 14 organs across 180 donors. Protocols were optimized to minimize the ischaemia time of healthy donors. All published data are freely available via the HuBMAP portal (https://portal.hubmapconsortium.org).

Jul 19, 2023 | nature.com | Yashvardhan Jain |Leah L. Godwin |Yingnan Ju |Ellen Quardokus |Andreas Bueckle |Yiing Lin | +4 more

Data preparationFor the “HuBMAP – Hacking the Kidney” Kaggle competition, a dataset was compiled comprising 30 Periodic acid-Schiff (PAS) stain whole slide images (WSIs) with 7102 segmented renal glomeruli (see Supplementary Table 3 and “Methods”). To determine if algorithms generalize to other FTU types, a second dataset was compiled comprising seven colon hematoxylin and eosin (H&E) stain WSIs with 395 segmented colonic crypts (see Supplementary Table 4 and “Methods”).