{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T18:08:55Z","timestamp":1790014135663,"version":"4.0.1"},"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002649","name":"Yeungnam University","doi-asserted-by":"publisher","award":["2023"],"award-info":[{"award-number":["2023"]}],"id":[{"id":"10.13039\/501100002649","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>Cross\u2011sectional area (CSA) of skeletal myofibers is a primary morphometric indicator of atrophy and regeneration, yet it is most commonly quantified on cryosections after immunofluorescent labeling of basal lamina proteins, which requires specialized reagents and equipment and limits reuse of routine histology slides. Here we present a practical, fully web\u2011based workflow that leverages Cellpose\u2011SAM on a public browser interface to segment myofibers directly from formalin-fixed paraffin-embedded (FFPE) skeletal muscle sections stained with hematoxylin and eosin (H&amp;E) or toluidine blue (TB), followed by downstream region\u2011of\u2011interest (ROI) curation and batch morphometry in Fiji\/ImageJ. We validated this approach across whole muscles and tissue preparations in mice. In exemplar experiments on both FFPE and frozen sections of mouse soleus, CSA distributions from H&amp;E and TB showed no significant differences. A sciatic nerve crush injury model exhibited a significant reduction in mean and median CSA in mouse soleus sections with a characteristic left-shift in distribution relative to sham controls, consistent with rapid denervation atrophy. This accessible pipeline lowers experimental barriers, enables analysis of archived H&amp;E or TB slides, and supports reproducible, high-throughput morphometry for neuromuscular research.<\/jats:p>","DOI":"10.1371\/journal.pone.0358476","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T17:26:30Z","timestamp":1790011590000},"page":"e0358476","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Web-based Cellpose\u2011SAM segmentation enables quantification of cross-sectional area in formalin-fixed paraffin-embedded skeletal muscle sections stained with hematoxylin and eosin"],"prefix":"10.1371","volume":"21","author":[{"given":"Jin-Hyang","family":"Park","sequence":"first","affiliation":[{"name":"College of Medicine Yeungnam University","place":["Daegu, Republic of Korea"],"department":["Department of Biochemistry and Molecular Biology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hye-Jin","family":"Yoon","sequence":"additional","affiliation":[{"name":"College of Medicine Yeungnam University","place":["Daegu, Republic of Korea"],"department":["Department of Biochemistry and Molecular Biology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soo-Ji","family":"Kim","sequence":"additional","affiliation":[{"name":"College of Medicine Yeungnam University","place":["Daegu, Republic of Korea"],"department":["Department of Biochemistry and Molecular Biology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jae-Ryong","family":"Kim","sequence":"additional","affiliation":[{"name":"College of Medicine Yeungnam University","place":["Daegu, Republic of Korea"],"department":["Department of Biochemistry and Molecular 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the rat sciatic nerve","volume":"90","author":"MM Inserra","year":"1992","journal-title":"Plastic and Reconstructive Surgery"},{"issue":"3","key":"pone.0358476.ref014","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1523\/JNEUROSCI.08-03-01026.1988","article-title":"Preferential reinnervation of motor nerves by regenerating motor axons","volume":"8","author":"T Brushart","year":"1988","journal-title":"J Neurosci"},{"key":"pone.0358476.ref015","first-page":"13","article-title":"Muscle Biopsy: A Practical Approach","author":"V Dubowitz","year":"2013"},{"key":"pone.0358476.ref016","first-page":"127","article-title":"Regeneration of skeletal muscle after injury","volume":"99","author":"SM Hughes","year":"2019","journal-title":"Physiological Reviews"},{"key":"pone.0358476.ref017","article-title":"Hematoxylin and Eosin Staining of Tissue and Cell Sections","author":"AH Fischer","year":"2008","journal-title":"Cold Spring Harbor 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Maier-Hein","year":"2024","journal-title":"Nat Methods"},{"issue":"7","key":"pone.0358476.ref025","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nat Methods"},{"issue":"22","key":"pone.0358476.ref026","doi-asserted-by":"crossref","first-page":"3532","DOI":"10.1093\/bioinformatics\/btw413","article-title":"MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ","volume":"32","author":"D Legland","year":"2016","journal-title":"Bioinformatics"},{"key":"pone.0358476.ref027","first-page":"79","article-title":"An investigation of fibre type composition of equine skeletal muscle","volume":"132","author":"NC Stickland","year":"1983","journal-title":"Journal of 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