Extended Data Fig. 8: FIB-SEM imaging and automated deep-learning-based segmentation of the 2nd dataset from obese liver and obese liver expressing Climp-63.
From: Regulation of liver subcellular architecture controls metabolic homeostasis
a, Single section SEM of liver from obese mouse liver at 8 nm pixel size. b, 3D-reconstruction of FIB-SEM images. c, Convolutional neural network-based automated segmentation of liver volumes. The dimensions of the volume are depicted in the figure. ER (endoplasmic reticulum, blue), Mito (mitochondria, purple), LD (lipid droplet, yellow), Nucleus (gray). d, Single section SEM of liver from obese mouse expressing Ad-Climp-63 in fed state at 8 nm pixel size. e, 3D reconstruction of FIB-SEM images derived from obese Climp-63 liver volume. f, Convolutional neural network-based automated segmentation of liver volumes. The dimensions of the volume are depicted in the figure. ER (endoplasmic reticulum, blue), Mito (mitochondria, purple), LD (lipid droplet, yellow). g, h, Reconstruction of 5 full or partial hepatocyte volumes from obese liver (g) and obese liver expressing Ad-Climp-63 (h). Volumes of the cells are depicted in the figure. i, Sub-segmentation and 3D reconstruction of ER sheets (red) and tubules (gray) from obese mouse dataset. j, Example volumes of ER sheets and k, ER tubules from this dataset. l, Percent of ER sheets (black) and tubules (gray) relative to total ER from indicated datasets. n = 5 cells per group. m, Ratio of ER sheets to tubule volume (**p = 0.003). n = 5 cells per group. n, Lipid droplet content from the indicated datasets. n = 5 cells per group. (*p = 0.0256). o, Analysis of mitochondria associated membranes (MAMs) from indicated FIB-SEM datasets. Analysis was done in 3 separate volumes of 2000x2000x400 voxels in each dataset (****p < 0.0001). p, q, Analysis of mitochondria sphericity and roundness from indicated FIB-SEM datasets. n = 127 (lean), n = 112 (obese), n = 217 (obese Climp-63) mitochondria. Analysis was done in the same volumes as Extended Data Fig. 8o, with the mitochondria volumes that are fully present in the ROI (*p = 0.003, ****p < 0.0001). All data (Extended Data Fig. 8l–n, p, q) are presented as mean values +/− SEM. Unpaired t-test was used for all the statistical analyses.
