Context-explorer: Analysis of spatially organized protein expression in high-throughput screens
Fig 2
Classification of cells into colonies.
A) mPSCs restricted to grow on micropatterned ECM spots (left) can be classified into colonies via the DBSCAN algorithm (middle). Merged and partial colonies can be excluded by applying filters to the DBSCAN clustering results (right). Each data point represents a cell and colonies are encircled with green lines. Scale bar = 500 μm. B) Number of cells per colony in wells from a 96-well plate after running DBSCAN. C) Number of cells per colony in wells after excluding merged and partial colonies from the DBSCAN results. D) Number of colonies per well after running DBSCAN with and without filters, and from a visual inspection of the images. E) Colony identification for colonies of different sizes in the same well (left), colonies of non-circular geometries (middle), and colonies in wells without pre-patterned ECM spots (right). Scale bar = 500 μm.