Fig. 4: Representation learning framework reveals interpretable spatial patterns for other punctate structures from the WTC-11 hiPS cell single-cell image dataset v1.
From: Interpretable representation learning for 3D multi-piece intracellular structures using point clouds
a, Dataset of punctate structures in hiPS cells from the WTC-11 hiPS cell single-cell image dataset v1 including nuclear pores, nuclear speckles, cohesins, histones, centrioles, peroxisomes and endosomes1. Shown are examples of images and sampled point cloud center slices of the mEGFP-tagged protein. b, Benchmarking unsupervised representations across classical and rotation-invariant image and point cloud models across efficiency metrics (model size (n = 1), inference time (n = 40) and emissions (n = 40)), generative metrics (reconstruction (n = 7,620) and evolution energy (n = 180)) and representation expressivity metrics (compactness (n = 5), classification (n = 5), rotation invariance error (n = 16,004) and average interpolate distance (n = 180)). Classification tasks included classifying seven different structures, and six different interphase/mitotic stages (Supplementary Note 1.2). Left, polar plot showing the performance across models where metrics are z-scored and scaled such that larger is better. Right, bar plots showing raw metric values across models for each metric. Error bars are the s.d. The best model for each metric is indicated. c, Real examples for each map point of PC1 computed using PCA fit to representations of each structure separately using the rotation-invariant point cloud model. Only cells in interphase were included. Shown are XY and XZ views. The structure channel is shown as center slices across the nuclear centroid for nuclear pores, cohesins and histones, or as maximum projections for nuclear speckles, centrioles, endosomes and peroxisomes. d, Latent walk for PC1. Shown are normalized PCs (s.d./σ) sampled at three map points (−2σ to 2σ in steps of σ). Reconstructions shown are cut at the midplane. Membrane centroids are marked for centrioles. Only cells in interphase were considered for this analysis. Centriole reconstructions were rotated to be aligned to the x axis.
