The Bruggeman lab

Our segmentation and lineage tracking algorithms are reaching their final development phase!

Anne Schwabe (now at Bionanosciences, Delft, NL) and Johan van Heerden have been working hard on writing algorithms for cell segmentation and lineage tracking, given movies of growing bacteria with fluorescent gene-activity reporters, obtained with fluorescence microscopy. We are now reaching the final test phase of the algorithms and here you find an example of the segmentation algorithm. Note that I reduced the resolution of this movie greatly, the red line is drawn by the segmentation algorithm,
E coli growth on pyruvate. While the segmentation algorithm is finding the contours of cells it is also tracking cells. So, we track their positions, mothers, sizes, elongation rates, interdivision times, and other features. This gives us a quantitative description of the entire movie, after we which we can analyse the statistics and compare those to theories and hypotheses.