Classify Cells Based on Their Shape

This example demonstrates how to segment and analyze cells to classify simple cells from pairs or clusters of cells. New contour properties in ComponentMeasurements are used and the contour is compared with the convex hull around cells. This comparison can show convexity defects used for classification of cell types.

Image from Liu, Y., Aubrey, W., Martin, K., Sparkes, A., Lu, C. and King, R.D., 2011. The analysis of yeast cell morphology features in exponential and stationary Phase. Journal of Biological Systems, 19(04), pp. 561–575.

Compute a segmentation mask and use it to measure the contours.

Build a small utility to get the ConvexHullMesh of the contours and compute the defects. Using PeakDetect, you can also find the junction points between two cells.

It is now possible to construct the lobed cells finder using contour convexity defects and FindPeaks.

Finally, you get the cell shape classifier based on convexity defects, which reports whether the cell is simple (no or one defect), a pair of cells (two defects) or complex (multiple defects).