Extended Data Fig. 5. Individual cell segmentation and cell type identification in LUSC and LUAD SBEM volumes.
a, SBEM volume (75 μm*75 μm*12 μm) of OXPHOSLO LUSC tumor (left panel). Inter-cellular space between LUSC cells and neutrophils is colored as yellow and images were processed in Amira (central panel) with steps of binary smoothing, adaptive thresholding, Gaussian filter and variance to achieve individual cell segmentation. Individual cells were segmented from serial 2D SBEM images were reconstructed in 3D volume (right panel). Scale bar = 10 μm. b, Morphological features and special organelle structures were used to distinguish the cell types of LUSC, neutrophil (NTPH), LUAD and red blood cell (RBC) in OXPHOSLO LUSC SBEM volume. Scale bar = 3 μm. c, Representative 2D SBEM image of OXPHOSHI LUAD tumor. Scale bar = 15 μm. d, Morphological features and special organelle structures identified in the cell types of LUAD and macrophage from OXPHOSHI LUAD SBEM images. Scale bar = 3 μm. e, The landscape of SBEM imaged OXPHOSHI LUAD tumor volume after individual cell segmentation and cell-type classification (left panel). Quantification of different cell types (right panel). LUAD-red, macrophage-yellow, red blood cell (RBC)-purple.