Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images
Fig 9
Comparison of in-vitro tube formation assay structures with eight different phenotypes.
A. The eight phenotypes resulted from WT and the knockdown of three CCM proteins, all with and without treatment by the ROCK inhibitor. Knockdown of the CCM proteins is associated with the disruption of the otherwise connected mesh. ROCK inhibitor leads to a more connected but still noticeably disorganized network. The scale bar is 200 μm. B. The first two principal components of each image’s boundary type histogram. Images of a similar type and appearance tend to have similar histograms. Here, the markers indicate the corresponding images in A. C. Two images from WTH1152 and CCM1H1152 that appear visually similar but have significantly different boundary type counts. Boundaries that are responsible for the difference are highlighted in blue and cyan. The scale bar is 200 μm. D. The difference in the normalized counts of boundaries of 12 types between CCM1H1152 and WTH1152 images shown in C. Boundary types 2 and 3 (indicated with blue and orange arrows in D and highlighted with the corresponding colors in C) represent small, isolated objects and small holes in wider locations in the network and appear significantly more often in CCM1H1152 formations as compared to otherwise similar WTH1152 structures. In contrast, WTH1152 structures tend to have more boundaries of type 10 (indicated with green arrow in D and highlighted with the same color in C), which represent medium sized holes with frequent bumps and protrusions extending into the hole.