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One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Code: https:\/\/github.com\/BioimageInformaticsTampere\/RegBenchmark. Whole slide image datasets: http:\/\/urn.fi\/urn: nbn: fi: csc-kata20170705131652639702.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty210","type":"journal-article","created":{"date-parts":[[2018,4,18]],"date-time":"2018-04-18T12:43:23Z","timestamp":1524055403000},"page":"3013-3021","source":"Crossref","is-referenced-by-count":43,"title":["Comparative analysis of tissue reconstruction algorithms for 3D histology"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9470-4783","authenticated-orcid":false,"given":"Kimmo","family":"Kartasalo","sequence":"first","affiliation":[{"name":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland"},{"name":"Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland"},{"name":"BioMediTech Institute, Tampere, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leena","family":"Latonen","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland"},{"name":"BioMediTech Institute, Tampere, Finland"},{"name":"Fimlab Laboratories, Tampere University Hospital, Tampere, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jorma","family":"Vihinen","sequence":"additional","affiliation":[{"name":"Faculty of Engineering Sciences, Tampere University of Technology, Tampere, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tapio","family":"Visakorpi","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland"},{"name":"BioMediTech Institute, Tampere, Finland"},{"name":"Fimlab Laboratories, Tampere University Hospital, Tampere, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matti","family":"Nykter","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland"},{"name":"Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland"},{"name":"BioMediTech Institute, Tampere, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9086-9591","authenticated-orcid":false,"given":"Pekka","family":"Ruusuvuori","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland"},{"name":"BioMediTech Institute, Tampere, Finland"},{"name":"Faculty of Computing and Electrical Engineering, Tampere University of Technology, Tampere 33101, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,4,19]]},"reference":[{"key":"2023061313385393200_bty210-B1","doi-asserted-by":"crossref","first-page":"1472","DOI":"10.1126\/science.1235381","article-title":"BigBrain: an ultrahigh-resolution 3D human brain model","volume":"340","author":"Amunts","year":"2013","journal-title":"Science"},{"key":"2023061313385393200_bty210-B2","first-page":"85","author":"Arganda-Carreras","year":"2006"},{"key":"2023061313385393200_bty210-B3","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1002\/jemt.20829","article-title":"3D reconstruction of histological sections: application to mammary gland tissue","volume":"73","author":"Arganda-Carreras","year":"2010","journal-title":"Microsci. 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