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To extend this method, we developed an integrative imaging and processing pipeline which adds 3D context and screening capabilities by microCT (\u00b5CT) imaging of the entire paraffin block and adds ultrastructural information by correlative same-slide scanning electron microscopy (SEM). The different modalities are integrated by elastic registration to provide hybrid image datasets. Without compromising standard light microscopic readout, we overcome the limitations of conventional histology by combining and integrating several imaging modalities. The biochemical information contained in histological and immunohistological tissue staining is embedded into the 3D tissue configuration and is amplified by adding ultrastructural visualization of features of interest. By combining \u00b5CT and conventional histological processing, specimens can be screened, and specifically preselected areas of interest can be targeted in the subsequent sectioning process. While most of the \u00b5CT data shown in the manuscript was acquired at a Synchrotron, we further demonstrate that our workflow can also be applied using X-ray microscopy.<\/jats:p>","DOI":"10.1038\/s41598-025-02770-w","type":"journal-article","created":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T10:58:35Z","timestamp":1748429915000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Integrated 3D imaging of FFPE lung tissue combining microCT, light and electron microscopy allows for contextualized ultrastructural and histological analysis"],"prefix":"10.1038","volume":"15","author":[{"given":"Johanna","family":"Reiser","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonas","family":"Albers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angelika","family":"Svetlove","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mara","family":"Mertiny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felix K. 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All described studies on humans or human tissue were conducted with the approval of the responsible ethics committee, in accordance with national law and in accordance with the Declaration of Helsinki of 1975 (in the current, revised version). Analysis was performed on lung tissue specimens from 17 patients with an age of 75.1\u00b112.6 years that had passed away due to a COVID-19 infection. No minors were enrolled in the study. All patients gave their written consent. Animal material: No animal was sacrificed for the specific purpose of this study, as the thoracic visceral organ block is an animal by-product of commercial meat processing. The preparations were carried out under regular veterinary supervision of an approved meat processing plant and were treated with the same hygiene measures as for fresh meat. In accordance with Article 23 of Regulation (EC) 1069\/2009, registration for the storage, handling, transportation and disposal of animal by-products for research purposes in category 3 was registered to the competent veterinary regulatory authority under registration number DE08221103321.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"All authors have approved the final version of the manuscript and gave their consent for publication.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}}],"article-number":"18656"}}