Robust 3D cell segmentation by local region growing in convex volumes

Clustering of cells is based on their expression profiles (either volume, average expression, standard deviation, sum, median or Pearson correlation coefficient). As an example, the hierarchical clustergram of median expression values was computed on 8343 cells in the germinal layers of monkey developing cerebral cortex stained for Pax6 (red), Tbr2 (blue), Ki67 (green), and nuclear staining DAPI. Cells where clustered with the standard k-means algorithm, whereby the number of clusters k=6 was determined empirically.