Yingnan Ju

Jul 19, 2023 | nature.com | Yingnan Ju |Elizabeth Zephyrine McDonough |Katy Börner

AbstractMapping the human body at single cell resolution in three dimensions (3D) is important for understanding cellular interactions in context of tissue and organ organization. 2D spatial cell analysis in a single tissue section may be limited by cell numbers and histology. Here we show a workflow for 3D reconstruction of multiplexed sequential tissue sections: MATRICS-A (Multiplexed Image Three-D Reconstruction and Integrated Cell Spatial - Analysis).

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”).