VesiclePy is a deep learning toolkit for vesicle analysis in serial electron microscopy data (with a special focus on large vesicles outside of synapse), providing tools for segmentation, classification, spatial and statistical analysis of vesicles, along with web-based proofreading tools and visualization capabilities, as well as neuron classification with vesicle and morphology information. see README.md files, both the main one and those in subfolders, for usage instructions. documentation also available in code itself.