Lymphatic, nervous, and tumoral tissues, among others, exhibit physiology that emerges from three-dimensional interactions between genetically unique cells. Technologies capable of volumetrically imaging transcriptomes, genotypes, and morphologies in a single de novo measurement can provide a critical lens into the biological complexity of living systems. We present experimental and computational work to develop DNA microscopy: a modality of imaging that captures physical images of specimen genetic content using a massive distributed network of DNA molecules inside it. We demonstrate DNA microscopy in two-dimensional cell cultures and genome-wide in intact zebrafish embryos.