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Myofiber features are often determined using immunofluorescence on a local sampling, typically obtained from a median region. This median region is assumed to represent the entire muscle. However, it remains largely unknown to what extent this local sampling represents the entire muscle. We present a pipeline to study the architecture of muscle fiber features over the entire muscle, including sectioning, staining, imaging to image quantification and data\u2010driven analysis with Myofiber type were identified by the expression of myosin heavy chain (MyHC) isoforms, representing contraction properties. We reconstructed muscle architecture from consecutive cross\u2010sections stained for laminin and MyHC isoforms. Examining the entire muscle using consecutive cross\u2010sections is extremely laborious, we provide consideration to reduce the dataset without loosing spatial information. Data\u2010driven analysis with over 150,000 myofibers showed spatial variations in myofiber geometric features, myofiber type, and the distribution of neuromuscular junctions over the entire muscle. We present a workflow to study histological changes over the entire muscle using high\u2010throughput imaging, image quantification, and data\u2010driven analysis. Our results suggest that asymmetric spatial distribution of these features over the entire muscle could impact muscle function. Therefore, instead of a single sampling from a median region, representative regions covering the entire muscle should be investigated in future studies.<\/jats:p>","DOI":"10.1002\/cyto.a.24465","type":"journal-article","created":{"date-parts":[[2021,6,5]],"date-time":"2021-06-05T10:05:09Z","timestamp":1622887509000},"page":"1240-1249","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Discovering fiber type architecture over the entire muscle using data\u2010driven analysis"],"prefix":"10.1002","volume":"99","author":[{"given":"Davide","family":"Bindellini","sequence":"first","affiliation":[{"name":"Department of Human Genetics Leiden University Medical Centre  Leiden The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lennard M.","family":"Voortman","sequence":"additional","affiliation":[{"name":"Department of Chemical Cell Biology Leiden University Medical Centre  Leiden The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cyriel S.","family":"Olie","sequence":"additional","affiliation":[{"name":"Department of Human Genetics Leiden University Medical Centre  Leiden The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maaike","family":"van Putten","sequence":"additional","affiliation":[{"name":"Department of Human Genetics Leiden University Medical Centre  Leiden The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erik","family":"van den Akker","sequence":"additional","affiliation":[{"name":"Biomedical Data Science Leiden University Medical Centre  Leiden The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3152-1952","authenticated-orcid":false,"given":"Vered","family":"Raz","sequence":"additional","affiliation":[{"name":"Department of Human Genetics Leiden University Medical Centre  Leiden The 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