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This volume covers comprehensive methods on ways to assess structural and ultrastructural changes in the mitochondria, cytoskeleton, and microglia using state-of-the-art microscopy techniques including super-resolution imaging, electron microscopy, and ultra-high field MRI. The chapters in this book cover topics such as analysis of neurodegeneration in the post-mortem characterization of preclinical animal models, in vivo modeling in cell death in different model systems and brain organoids, single cell clonal analysis using Mosaic Analysis with Double Markers in genetic mouse models, and genome and proteomic methods for analysis of mRNA dynamics and quantitation of targeted peptides. 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. Cutting-edge and thorough, Neuronal Cell Death: Methods and Protocols is a valuable resource for any scientist and researcher interested in learning more about this developing field.