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Stuart joined Janelia in 2012 in a collaboration between Janelia's EM connectomics labs and the developers of ilastik, a popular open source image analysis and segmentation application which empowers biologists with machine-learning-based image processing methods in a user-friendly package. He worked as lead developer for that project, implementing the core of version 1.0 and extending it for large-scale EM applications. In 2017, he joined the FlyEM Team Project as software engineer, focusing on data engineering and segmentation analysis. In 2021, he assumed leadership of FlyEM and serves as Project Scientist. FlyEM is currently generating the connectome of the full drosophila central nervous system, slated for release in late 2023.