{"entity": "researcher", "timestamp": "2026-04-16T17:37:28.751Z", "family": "Girelli", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4264-6494", "affiliations": ["Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.", "Science for Life Laboratory, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7"}}, "publications": [{"entity": "publication", "iuid": "8878962be50c44d791a0589626c424a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8878962be50c44d791a0589626c424a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8878962be50c44d791a0589626c424a7"}}, "title": "Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.", "authors": [{"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Girelli", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4264-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7.json"}}, {"family": "Wang", "given": "Su", "initials": "S"}, {"family": "Castillo", "given": "David", "initials": "D", "orcid": "0000-0003-0478-0828", "researcher": {"href": "https://publications.scilifelab.se/researcher/2430e6a8b8b341f18566cca62c27cc6d.json"}}, {"family": "Mattsson Langseth", "given": "Christoffer", "initials": "C"}, {"family": "Verron", "given": "Quentin", "initials": "Q"}, {"family": "Nguyen", "given": "Huy Q", "initials": "HQ"}, {"family": "Chattoraj", "given": "Shyamtanu", "initials": "S"}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Marti-Renom", "given": "Marc A", "initials": "MA"}, {"family": "Wu", "given": "Chao-Ting", "initials": "C"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2024-06-06", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": null, "issue": null, "pages": null}, "abstract": "Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with \u00d720 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications.", "doi": "10.1038/s41592-024-02294-7", "pmid": "38844629", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development", "Spatial Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-024-02294-7"}], "notes": [], "created": "2024-06-10T07:36:02.247Z", "modified": "2024-11-25T17:49:12.405Z"}, {"entity": "publication", "iuid": "d71873c329c7421db086762eddcf7cb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d71873c329c7421db086762eddcf7cb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d71873c329c7421db086762eddcf7cb7"}}, "title": "GPSeq reveals the radial organization of chromatin in the cell nucleus.", "authors": [{"family": "Girelli", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4264-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7.json"}}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Kallas", "given": "Tomasz", "initials": "T"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Spanjaard", "given": "Bastiaan", "initials": "B"}, {"family": "Mota", "given": "Ana", "initials": "A"}, {"family": "Kolbeinsdottir", "given": "Solrun", "initials": "S"}, {"family": "Gelali", "given": "Eleni", "initials": "E", "orcid": "0000-0003-0067-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a4d90932dd45509d71a672ec5a12af.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "38", "issue": "10", "pages": "1184-1193", "issn-l": "1087-0156"}, "abstract": "With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina toward the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100-kb resolution, which revealed radial patterns of genomic and epigenomic features and gene expression, as well as A and B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of whole-genome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations and found that they have distinctive radial arrangements in A and B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.", "doi": "10.1038/s41587-020-0519-y", "pmid": "32451505", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0519-y"}, {"db": "pmc", "key": "PMC7610410"}, {"db": "mid", "key": "EMS118404"}], "notes": [], "created": "2020-05-26T07:12:39.312Z", "modified": "2021-11-10T12:46:51.496Z"}]}