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To address this, we conducted a systematic review and meta-analysis of spinal muscular atrophy (SMA) mouse studies, revealing 60% variability in reported MN loss, largely attributable to nonspecific spinal cord sampling. Using a whole-segment approach with tissue clearing, MN tracing, and multimodal imaging, we confirmed segment-dependent differences in MN counts. Common MN markers (SMI-32, Nissl) lacked specificity, whereas choline acetyltransferase (ChAT) provided robust labeling in murine and human spinal cords. Deep learning\u2013based whole-mount segmentation enabled unbiased MN quantification and validated manual counts. Integrating analysis with computational modeling established segment sampling as a key driver of variability and revealed degeneration patterns: widespread MN loss in amyotrophic lateral sclerosis (ALS), selective MN loss in severe SMA, and preservation in mild SMA models. These findings establish a framework for reproducible MN quantification.<\/jats:p>\n                <jats:sec>\n                  <jats:title>Highlights<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>Spinal cord segment-specific analysis reduces variability and allows accurate MN quantification<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>ChAT is the most reliable MN marker in murine and human spinal cords<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Deep learning\u2013based segmentation enables unbiased MN quantification in intact spinal cords<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>MN degeneration is widespread in ALS but restricted to pools innervating proximal muscles in severe SMA<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>","DOI":"10.64898\/2026.04.15.718647","type":"posted-content","created":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T18:00:13Z","timestamp":1776708013000},"source":"Crossref","is-referenced-by-count":1,"title":["A standardized framework resolves ambiguity in motor neuron loss across neurodegenerative diseases"],"prefix":"10.64898","author":[{"given":"Leonie","family":"Sowoidnich","sequence":"first","affiliation":[{"name":"Carl-Ludwig-Institute for Physiology, Leipzig University, 04103 Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron L.","family":"Norman","sequence":"additional","affiliation":[{"name":"Carl-Ludwig-Institute for Physiology, Leipzig University, 04103 Leipzig, 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