Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning
Fig 3
Distinct phenotypic responses in dense neuronal cultures.
A) Representative images of neurons from control groups. B) Two dimensional principal component projection of 3D multichannel image feature space for each plate. Each point represents one 3D multichannel image. Only plate 1 contained the 30 nM concentration of the inhibitors of the anti-apoptotic proteins while plates 2 and 3 contain more concentrations for the STS and ActD controls (tan-brown dots, respectively) making the distributions appear more different than they actually are. C) Automated clustering using affinity propagation. The pie charts mark the cluster centroids and show the distribution of different treatments within each cluster. The sizes of the pie charts represent the number of data points within each cluster, cluster numbers are given above the pie charts. D) Heatmap of the distribution of phenotypes in response to the different treatments across clusters for each plate provide interpretative data complementary to but different from the pie charts in B) that show the distributions within clusters. ActD–Actinomycin D, STS–Staurosporine; for B & C: the colors correspond to the different treatment groups as indicated in the legend for concentrations in nM.