This second edition volume expands on the previous edition with new methods and refinements ranging from tissue clearing and three-dimensional imaging, to explant culture systems, lineage tracing, high-resolution transcriptomics, metabolism, and chromatin structure analysis. The chapters in this book are organized by molecular depth, progressing from foundational methods to approaches that probe cellular and nuclear mechanisms. The protocols presented here reveal how cellular behaviors and molecular pathways are coordinated to shape the embryo. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mouse Embryogenesis: Methods and Protocols, Second Edition is a valuable resource for both expert and novice researchers who are looking to learn more about this advancing field. The methods discussed in this volume will inspire new questions and experimental strategies to further advance our understanding of mammalian development.