{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T03:33:59Z","timestamp":1784864039290,"version":"3.55.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2022,8,16]],"date-time":"2022-08-16T00:00:00Z","timestamp":1660608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U2C-CA233262"],"award-info":[{"award-number":["U2C-CA233262"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U2C-CA233280"],"award-info":[{"award-number":["U2C-CA233280"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ludwig Cancer Center"},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-027106"],"award-info":[{"award-number":["INV-027106"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Stitching microscope images into a mosaic is an essential step in the analysis and visualization of large biological specimens, particularly human and animal tissues. Recent approaches to highly multiplexed imaging generate high-plex data from sequential rounds of lower-plex imaging. These multiplexed imaging methods promise to yield precise molecular single-cell data and information on cellular neighborhoods and tissue architecture. However, attaining mosaic images with single-cell accuracy requires robust image stitching and image registration capabilities that are not met by existing methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We describe the development and testing of ASHLAR, a Python tool for coordinated stitching and registration of 103 or more individual multiplexed images to generate accurate whole-slide mosaics. ASHLAR reads image formats from most commercial microscopes and slide scanners, and we show that it performs better than existing open-source and commercial software. ASHLAR outputs standard OME-TIFF images that are ready for analysis by other open-source tools and recently developed image analysis pipelines.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ASHLAR is written in Python and is available under the MIT license at https:\/\/github.com\/labsyspharm\/ashlar. The newly published data underlying this article are available in Sage Synapse at https:\/\/dx.doi.org\/10.7303\/syn25826362; the availability of other previously published data re-analyzed in this article is described in Supplementary Table S4. An informational website with user guides and test data is available at https:\/\/labsyspharm.github.io\/ashlar\/.<\/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\/btac544","type":"journal-article","created":{"date-parts":[[2022,8,16]],"date-time":"2022-08-16T09:57:52Z","timestamp":1660643872000},"page":"4613-4621","source":"Crossref","is-referenced-by-count":131,"title":["Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0811-637X","authenticated-orcid":false,"given":"Jeremy L","family":"Muhlich","sequence":"first","affiliation":[{"name":"Human Tumor Atlas Network, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7228-4696","authenticated-orcid":false,"given":"Yu-An","family":"Chen","sequence":"additional","affiliation":[{"name":"Human Tumor Atlas Network, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clarence","family":"Yapp","sequence":"additional","affiliation":[{"name":"Human Tumor Atlas Network, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7446-2353","authenticated-orcid":false,"given":"Douglas","family":"Russell","sequence":"additional","affiliation":[{"name":"Human Tumor Atlas Network, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7528-9668","authenticated-orcid":false,"given":"Sandro","family":"Santagata","sequence":"additional","affiliation":[{"name":"Human Tumor Atlas Network, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Department of Pathology, Brigham and Women\u2019s Hospital , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter K","family":"Sorger","sequence":"additional","affiliation":[{"name":"Human Tumor Atlas Network, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Department of Systems Biology, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,8,16]]},"reference":[{"key":"2023041408225477800_","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023041408225477800_","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nm.3488","article-title":"Multiplexed ion beam imaging of human breast tumors","volume":"20","author":"Angelo","year":"2014","journal-title":"Nat. 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