{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:38:25Z","timestamp":1783489105655,"version":"3.55.0"},"reference-count":38,"publisher":"The Endocrine Society","issue":"2","license":[{"start":{"date-parts":[[2022,12,3]],"date-time":"2022-12-03T00:00:00Z","timestamp":1670025600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"crossref","award":["2014-2020.4.01.15-0012"],"award-info":[{"award-number":["2014-2020.4.01.15-0012"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002301","name":"Estonian Research Council","doi-asserted-by":"crossref","award":["PRG1259"],"award-info":[{"award-number":["PRG1259"]}],"id":[{"id":"10.13039\/501100002301","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002301","name":"Estonian Research Council","doi-asserted-by":"crossref","award":["PRG1604 to O.M. and D.M."],"award-info":[{"award-number":["PRG1604 to O.M. and D.M."]}],"id":[{"id":"10.13039\/501100002301","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002301","name":"Estonian Research Council","doi-asserted-by":"crossref","award":["952060"],"award-info":[{"award-number":["952060"]}],"id":[{"id":"10.13039\/501100002301","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100006306","name":"Sigrid Jus\u00e9lius Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100006306","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010125","name":"Jalmari and Rauha Ahokas Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100010125","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Spermatogenesis is a complex differentiation process that takes place in the seminiferous tubules. A specific organization of spermatogenic cells within the seminiferous epithelium enables a synchronous progress of germ cells at certain steps of differentiation on the spermatogenic pathway. This can be observed in testis cross-sections where seminiferous tubules can be classified into distinct stages of constant cellular composition (12 stages in the mouse). For a detailed analysis of spermatogenesis, these stages have to be individually observed from testis cross-sections. However, the recognition of stages requires special training and expertise. Furthermore, the manual scoring is laborious considering the high number of tubule cross-sections that have to be analyzed. To facilitate the analysis of spermatogenesis, we have developed a convolutional deep neural network-based approach named \u201cSTAGETOOL.\u201d STAGETOOL analyses histological images of 4\u2032,6-diamidine-2\u2032-phenylindole dihydrochloride (DAPI)-stained mouse testis cross-sections at \u00d7400 magnification, and very accurately classifies tubule cross-sections into 5 stage classes and cells into 9 categories. STAGETOOL classification accuracy for stage classes of seminiferous tubules of a whole-testis cross-section is 99.1%. For cellular level analysis the F1 score for 9 seminiferous epithelial cell types ranges from 0.80 to 0.98. Furthermore, we show that STAGETOOL can be applied for the analysis of knockout mouse models with spermatogenic defects, as well as for automated profiling of protein expression patterns. STAGETOOL is the first fluorescent labeling\u2013based automated method for mouse testis histological analysis that enables both stage and cell-type recognition. While STAGETOOL qualitatively parallels an experienced human histologist, it outperforms humans time-wise, therefore representing a major advancement in male reproductive biology research.<\/jats:p>","DOI":"10.1210\/endocr\/bqac202","type":"journal-article","created":{"date-parts":[[2022,12,3]],"date-time":"2022-12-03T08:43:08Z","timestamp":1670056988000},"source":"Crossref","is-referenced-by-count":6,"title":["STAGETOOL, a Novel Automated Approach for Mouse Testis Histological Analysis"],"prefix":"10.1210","volume":"164","author":[{"given":"Oliver","family":"Meikar","sequence":"first","affiliation":[{"name":"Institute of Biomedicine and Translational Medicine, University of Tartu , 50411 Tartu , Estonia"},{"name":"Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku , 20520 Turku , Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Majoral","sequence":"additional","affiliation":[{"name":"Computational 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