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Cutting edge deep learning techniques allow for image segmentation with great speed and accuracy. However, application to problems in materials science is often difficult since these complex models may have difficultly learning meaningful image features that would enable extension to new datasets. In situ electron microscopy provides a clear platform for utilizing automated image analysis. In this work, we consider the case of studying coarsening dynamics in supported nanoparticles, which is important for understanding, for example, the degradation of industrial catalysts. By systematically studying dataset preparation, neural network architecture, and accuracy evaluation, we describe important considerations in applying deep learning to physical applications, where generalizable and convincing models are required. With a focus on unique challenges that arise in high-resolution images, we propose methods for optimizing performance of image segmentation using convolutional neural networks, critically examining the application of complex deep learning models in favor of motivating intentional process design.