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Summary How individual cells form precise connections with partners in a complicated environment has been a longstanding question. However, most cell matching studies have used qualitative approaches, which may miss subtle but significant morphological changes. Here, we describe the use of embryonic Drosophila heart formation as a simplified system to quantitatively study cell matching. We provide a step-by-step protocol for large-scale embryo preparation and immunostaining and imaging details. We also describe steps for quantifying cellular mismatch from the batch images. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2018 and 2020 ).