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Here, we describe new neural network models for the automated classification of cell types and tubule stages from whole-slide brightfield images of mouse testis. The cell type classifier recognizes 14 cell types, including multiple steps of meiosis I prophase, with an external validation accuracy of 96%. The tubule stage classifier distinguishes all 12 canonical tubule stages with external validation accuracy of 63%, which increases to 96% when allowing for \u00b11 stage tolerance. We addressed generalizability of SATINN, through extensive training diversification and testing on external (non-training population) wildtype and mutant datasets. This allowed us to use SATINN to successfully process data generated in multiple laboratories. We used SATINN to analyze testis images from eight different mutant lines, generated from three different labs with a range of tissue processing protocols. Finally, we show that it is possible to use SATINN output to cluster histology images in latent space, which, when applied to the eight mutant lines, reveals known relationships in their pathology. This work represents significant progress towards a tool for robust, automated testis histopathology that can be used by multiple labs.<\/jats:p>","DOI":"10.1093\/biolre\/ioaf033","type":"journal-article","created":{"date-parts":[[2025,2,16]],"date-time":"2025-02-16T23:13:27Z","timestamp":1739747607000},"page":"996-1014","source":"Crossref","is-referenced-by-count":1,"title":["SATINN v2: automated image analysis for mouse testis histology with multi-laboratory data integration"],"prefix":"10.1093","volume":"112","author":[{"given":"Ran","family":"Yang","sequence":"first","affiliation":[{"name":"Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University , Portland, OR ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fritzie T","family":"Celino-Brady","sequence":"additional","affiliation":[{"name":"Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University , Portland, OR ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica E M","family":"Dunleavy","sequence":"additional","affiliation":[{"name":"School of Biosciences and Bio21 Molecular Science and Biotechnology Institute, Faculty of Science, The University of Melbourne , Melbourne, VIC ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katinka A","family":"Vigh-Conrad","sequence":"additional","affiliation":[{"name":"Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University , Portland, OR ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georgia R","family":"Atkins","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine , Pittsburgh, PA ,","place":["United States"]},{"name":"Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine , Pittsburgh, PA ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rachel L","family":"Hvasta","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine , Pittsburgh, PA ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher R X","family":"Pombar","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine , Pittsburgh, PA ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander N","family":"Yatsenko","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine , Pittsburgh, PA ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyle E","family":"Orwig","sequence":"additional","affiliation":[{"name":"Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine , Pittsburgh, PA ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Moira K","family":"O\u2019Bryan","sequence":"additional","affiliation":[{"name":"School of Biosciences and Bio21 Molecular Science and Biotechnology Institute, Faculty of Science, The University of Melbourne , Melbourne, VIC ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana C","family":"Lima","sequence":"additional","affiliation":[{"name":"Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University , Portland, OR ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Donald F","family":"Conrad","sequence":"additional","affiliation":[{"name":"Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University , Portland, OR ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,2,17]]},"reference":[{"key":"2026032300570849800_ref1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1152\/physrev.00013.2015","article-title":"Spermatogenesis: the commitment to meiosis","volume":"96","author":"Griswold","year":"2016","journal-title":"Physiol Rev"},{"key":"2026032300570849800_ref2","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.scr.2018.04.009","article-title":"Spermatogonial stem cells and spermatogenesis in mice, monkeys and 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