{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T15:36:00Z","timestamp":1779204960962,"version":"3.51.4"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2024,8,17]],"date-time":"2024-08-17T00:00:00Z","timestamp":1723852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Sanofi Digital"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Spatial transcriptomics allow to quantify mRNA expression within the spatial context. Nonetheless, in-depth analysis of spatial transcriptomics data remains challenging and difficult to scale due to the number of methods and libraries required for that purpose.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present SpatialOne, an end-to-end pipeline designed to simplify the analysis of 10x Visium data by combining multiple state-of-the-art computational methods to segment, deconvolve, and quantify spatial information; this approach streamlines the analysis of reproducible spatial-data at scale.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SpatialOne source code and execution examples are available at https:\/\/github.com\/Sanofi-Public\/spatialone-pipeline, experimental data is available at https:\/\/zenodo.org\/records\/12605154. SpatialOne is distributed as a docker container image.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae509","type":"journal-article","created":{"date-parts":[[2024,8,15]],"date-time":"2024-08-15T14:49:42Z","timestamp":1723733382000},"source":"Crossref","is-referenced-by-count":3,"title":["SpatialOne: end-to-end analysis of visium data at scale"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-1380-6950","authenticated-orcid":false,"given":"Mena","family":"Kamel","sequence":"first","affiliation":[{"name":"Digital R&D, Sanofi , Paris 75017, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amrut","family":"Sarangi","sequence":"additional","affiliation":[{"name":"Digital R&D, Sanofi , Paris 75017, 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