CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images.

Summary: The implementation of computational tools for analysis of microscopy images has been one of the most important technological innovations in biology, providing researchers unmatched capabilities to comprehend cell shape and connectivity. While numerous tools exist for image annotation and segmentation, there is a noticeable gap when it comes to morphometric analysis of microscopy images. Most existing tools often measure features solely on 2D serial images, which can be difficult to extrapolate to 3D.

3D reconstruction of the cerebellar germinal layer reveals tunneling connections between developing granule cells.

The difficulty of retrieving high-resolution, in vivo evidence of the proliferative and migratory processes occurring in neural germinal zones has limited our understanding of neurodevelopmental mechanisms. Here, we used a connectomic approach using a high-resolution, serial-sectioning scanning electron microscopy volume to investigate the laminar cytoarchitecture of the transient external granular layer (EGL) of the developing cerebellum, where granule cells coordinate a series of mitotic and migratory events. By integrating image segmentation, three-dimensional reconstruction, and deep-learning approaches, we found and characterized anatomically complex intercellular connections bridging pairs of cerebellar granule cells throughout the EGL.