We thank the entire Allen Institute for Cell Science team, who generated and characterized the gene-edited hiPS cell lines, developed image-based assays, and recorded the high replicate data sets suitable for modeling and without whom this work would not have been possible. We especially thank the Allen Institute for Cell Science Gene Editing, Assay Development, Microscopy, and Pipeline teams for providing cell lines and images of different transmitted-light imaging modalities, and particularly Kaytlyn Gerbin, Angel Nelson, and Haseeb Malik for performing the cardiomyocyte differentiation and culture, Winnie Leung, Joyce Tang, Melissa Hendershott and Nathalie Gaudreault for gathering the additional time series, CAAX-labeled, cardiomyocyte, HEK-293, and HT-1080 data. We would like to thank the Allen Institute for Cell Science Animated Cell team and Thao Do specifically for providing her expertise in figure preparation. We thank Daniel Fernandes for developing an early proof of concept 2D version of the model. We would like to thank members of the Allen Institute for Brain Science Synapse Biology department for preparing samples and providing images that were the basis for training the conjugate array tomography data. These contributions were absolutely critical for model development. Cardiomyocyte and hiPSC data in this publication were derived from cells in the Allen Cell Collection, a collection of fluorescently labeled hiPSCs derived from the parental WTC line provided by Bruce R. Conklin, at The Gladstone Institutes. We thank Google Accelerated Science for telling us about their studies of 2D deep learning in neurons before beginning this project. This work was supported by grants from NIH/NINDS (R01NS092474) and NIH/NIMH (R01MH104227). We thank Paul G. Allen, founder of the Allen Institute for Cell Science, for his vision, encouragement and support.