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Here, we introduce an image processing pipeline for high-resolution, compartment-based analysis of protein localization, using the native three-dimensional architecture of the human anterior lens epithelium and capsule complex as a robust ex vivo proof-of-principle platform for precise cell segmentation and quantitative analysis. This platform integrates whole-mount immunostaining, 3D confocal imaging, computational tissue flattening, digital segmentation, and spatial regression to quantitatively map subcellular protein distributions at the tissue scale. To demonstrate the utility of this approach, we examined the spatial distribution of \u03b1B-crystallin (CRYAB), a stress-associated small heat shock protein, and \u03b2B2-crystallin (CRYBB2), a predominantly structural lens protein, in specimens obtained during cataract surgery. We observed a marked accumulation of CRYAB in epithelial cells at the capsule edge following both laser and manual capsulorhexis, indicating a localized stress response to surgical intervention. In contrast, CRYBB2 distribution remained unaffected. Furthermore, both proteins exhibited consistent cytoplasmic localization, while only CRYBB2 occasionally showed exclusive nuclear accumulation. This pipeline offers a scalable framework for quantitatively resolving protein localization in native epithelial architectures, using CRYAB and CRYBB2 as examples of how stress-associated changes can be spatially mapped in situ within the human lens.<\/jats:p>","DOI":"10.1038\/s41598-025-17896-0","type":"journal-article","created":{"date-parts":[[2025,10,3]],"date-time":"2025-10-03T10:30:35Z","timestamp":1759487435000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Quantitative spatial analysis of crystallin proteins in human lens epithelial cells"],"prefix":"10.1038","volume":"15","author":[{"given":"Alessandro","family":"Cristoforetti","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giorgio","family":"Baldessari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lizaveta","family":"Chychko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ignacio Babiloni","family":"Chust","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuele","family":"Sartori","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sonja","family":"Schickhardt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Flavia","family":"Ravelli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia","family":"Bertoluzza","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias","family":"Carl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saadettin","family":"Sel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerd U.","family":"Auffarth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucia","family":"Poggi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,10,3]]},"reference":[{"key":"17896_CR1","doi-asserted-by":"publisher","first-page":"102407","DOI":"10.1016\/j.arr.2024.102407","volume":"99","author":"A Cvekl","year":"2024","unstructured":"Cvekl, A. & Vijg, J. 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