Automated Analysis of Neuronal Morphology through an Unsupervised Classification Model of Neurites

Brain function emerges from a highly complex network of specialized cells that are interlinked by billions of synapses. The synaptic connectivity between neurons is established between the elongated processes of their axons and dendrites or, together, neurites. To establish these billions of often far-reaching connections, cellular neurites have to grow in highly specialized, cell-type dependent patterns covering often mm distances and connecting with thousands of other neurons. The outgrowth and branching of neurites are tightly controlled during development and are a commonly used functional readout of imaging in the neurosciences. Manual analysis of neuronal morphology from microscopy images, however, is very time intensive and error prone. Especially fully automated segmentation and classification of all neurites remain unavailable in open-source software. Here we present a standalone, GUI-based software for batch-quantification of neuronal morphology in fluorescence micrographs with minimal requirements for user interaction. Neurons are segmented using a Hessian-based algorithm to detect thin neurite structures combined with intensity- and shape-based detection of the cell body. To measure the number of branches in a neuron accurately, rather than just determining branch points, neurites are classified into axon, dendrites and their branches of increasing order by their length using a geodesic distance transform of the cell skeleton. The software was benchmarked against a large, published dataset and reproduced the phenotype observed after manual annotation before. Our tool promises greatly accelerated and improved morphometric studies of neuronal morphology by allowing for consistent and automated analysis of large datasets.