My lab develops computational methods and tools to automatically reconstruct and analyze microscopy datasets of cells and tissues. At a resolution of a few nanometers per pixel, Janelia's electron microscopes acquire incredibly rich images of complete cells and tissues. In the past, we have used these data to reconstruct neural circuits and synaptic contacts in the brain of Drosophila melanogaster. But they also enable us to reconstruct the full ensemble of cellular organelles, the cytoskeleton, and other macromolecular structures in the cell and tissues. We expand upon the state of the art in machine learning and scalable data processing to handle, visualize, and share these fascinating yet incredibly large and heterogeneous datasets. As open science enthusiasts, we develop all our tools as open-source software and contribute to the rapidly evolving ecosystem of open source and open data projects interested in bio-image analysis.