Fig. 5

SLICER applied to mouse neural stem cells. a Cellular trajectory inferred by SLICER. Color corresponds to inferred geodesic distance from the start cell (“differentiation progress”). The lines indicate edges used in the shortest paths to each point. b Clustering using the connected components in the low-dimensional k-nearest neighbor graph before trajectory construction identifies four cell types. SLICER provides the option to select which cell types to include when building a trajectory. Panels c through g show the expression levels of marker genes for different cell types: c active neural stem cells, d quiescent neural stem cells, e neuroblasts, f oligodendrocytes, and g neuroblasts. h Geodesic entropy plot for the trajectory shown in panel a. The dotted line represents an entropy value of 1, the threshold for branch detection. i Cells colored according to the branches that SLICER assigned using geodesic entropy. The interpretations indicated in the legend were deduced based on marker genes such as those shown in panels c–g after branch assignment