{"entity": "researcher", "timestamp": "2026-09-25T23:05:12.905Z", "family": "Bernhem", "given": "Kristoffer", "initials": "K", "orcid": "0000-0003-3669-9848", "affiliations": ["Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba3c7a36a8204919a67539b8631ca566.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba3c7a36a8204919a67539b8631ca566"}}, "publications": [{"entity": "publication", "iuid": "0b57b17638ab481c8bd33905c776998b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0b57b17638ab481c8bd33905c776998b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0b57b17638ab481c8bd33905c776998b"}}, "title": "Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy - identification and correction.", "authors": [{"family": "Adler", "given": "Jeremy", "initials": "J", "orcid": "0000-0003-1741-7876", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57f38a1cb13848cba5e762f68d648314.json"}}, {"family": "Bernhem", "given": "Kristoffer", "initials": "K", "orcid": "0000-0003-3669-9848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba3c7a36a8204919a67539b8631ca566.json"}}, {"family": "Parmryd", "given": "Ingela", "initials": "I", "orcid": "0000-0003-4834-3611", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1279c810d97d45c4a7c4ae460acb2840.json"}}], "type": "journal article", "published": "2024-06-29", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "791", "issn-l": "2399-3642"}, "abstract": "According to single-molecule localisation microscopy almost all plasma membrane proteins are clustered. We demonstrate that clusters can arise from variations in membrane topography where the local density of a randomly distributed membrane molecule to a degree matches the variations in the local amount of membrane. Further, we demonstrate that this false clustering can be differentiated from genuine clustering by using a membrane marker to report on local variations in the amount of membrane. In dual colour live cell single molecule localisation microscopy using the membrane probe DiI alongside either the transferrin receptor or the GPI-anchored protein CD59, we found that pair correlation analysis reported both proteins and DiI as being clustered, as did its derivative pair correlation-photoactivation localisation microscopy and nearest neighbour analyses. After converting the localisations into images and using the DiI image to factor out topography variations, no CD59 clusters were visible, suggesting that the clustering reported by the other methods is an artefact. However, the TfR clusters persisted after topography variations were factored out. We demonstrate that membrane topography variations can make membrane molecules appear clustered and present a straightforward remedy suitable as the first step in the cluster analysis pipeline.", "doi": "10.1038/s42003-024-06472-3", "pmid": "38951588", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11217499"}, {"db": "pii", "key": "10.1038/s42003-024-06472-3"}], "notes": [], "created": "2026-09-23T12:24:48.443Z", "modified": "2026-09-23T12:24:48.568Z"}, {"entity": "publication", "iuid": "58d11282d0e9462d8565a1a439be647e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/58d11282d0e9462d8565a1a439be647e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/58d11282d0e9462d8565a1a439be647e"}}, "title": "SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy.", "authors": [{"family": "Bernhem", "given": "Kristoffer", "initials": "K", "orcid": "0000-0003-3669-9848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba3c7a36a8204919a67539b8631ca566.json"}}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04321d9fb805493db538489927a42c8f.json"}}], "type": "journal article", "published": "2018-01-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "34", "issue": "1", "pages": "137-138", "issn-l": "1367-4803"}, "abstract": "SMLocalizer combines the availability of ImageJ with the power of GPU processing for fast and accurate analysis of single molecule localization microscopy data. Analysis of 2D and 3D data in multiple channels is supported.\n\nPlugin freely available for Fiji and ImageJ2.0 through https://sourceforge.net/projects/smlocalizer/. Plugin also available for continuous updates through ImageJ update system, add http://sites.imagej.net/Cellular-Biophysics-KTH/ as update site in ImageJ. Java and CUDA source code freely available on the web at https://github.com/KristofferBernhem/SMlocalizer.\n\nbrismar@kth.se.\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btx553", "pmid": "28968783", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5870682"}, {"db": "pii", "key": "4103397"}], "notes": [], "created": "2018-12-05T12:25:02.354Z", "modified": "2026-09-23T14:53:24.835Z"}, {"entity": "publication", "iuid": "5f2dde9c9b2a42ea9a2cc35bf973b0c2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5f2dde9c9b2a42ea9a2cc35bf973b0c2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5f2dde9c9b2a42ea9a2cc35bf973b0c2"}}, "title": "Multifocus structured illumination microscopy for fast volumetric super-resolution imaging.", "authors": [{"family": "Abrahamsson", "given": "Sara", "initials": "S"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Agostinho", "given": "Ana", "initials": "A", "orcid": "0000-0001-6270-7384", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/16a9e7e5cd0245db94d3b0fb0e1fd58a.json"}}, {"family": "Jans", "given": "Daniel C", "initials": "DC", "orcid": "0000-0002-6356-9742", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ff40f8719c944e6b0ff27ded3b05a27.json"}}, {"family": "Jost", "given": "Aurelie", "initials": "A"}, {"family": "M\u00fcller", "given": "Marcel", "initials": "M"}, {"family": "Nilsson", "given": "Linnea", "initials": "L", "orcid": "0000-0001-7887-7978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2270bd45d70049eabfee68d8df850fc6.json"}}, {"family": "Bernhem", "given": "Kristoffer", "initials": "K", "orcid": "0000-0003-3669-9848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba3c7a36a8204919a67539b8631ca566.json"}}, {"family": "Lambert", "given": "Talley J", "initials": "TJ"}, {"family": "Heintzmann", "given": "Rainer", "initials": "R"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04321d9fb805493db538489927a42c8f.json"}}], "type": "journal article", "published": "2017-09-01", "journal": {"title": "Biomed Opt Express", "issn": "2156-7085", "volume": "8", "issue": "9", "pages": "4135-4140", "issn-l": "2156-7085"}, "abstract": "We here report for the first time the synergistic implementation of structured illumination microscopy (SIM) and multifocus microscopy (MFM). This imaging modality is designed to alleviate the problem of insufficient volumetric acquisition speed in super-resolution biological imaging. SIM is a wide-field super-resolution technique that allows imaging with visible light beyond the classical diffraction limit. Employing multifocus diffractive optics we obtain simultaneous wide-field 3D imaging capability in the SIM acquisition sequence, improving volumetric acquisition speed by an order of magnitude. Imaging performance is demonstrated on biological specimens.", "doi": "10.1364/BOE.8.004135", "pmid": "28966852", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5611928"}, {"db": "pii", "key": "294866"}, {"db": "figshare", "key": "10.6084/m9.figshare.4928747"}], "notes": [], "created": "2018-12-05T12:09:26.279Z", "modified": "2026-09-23T14:53:58.516Z"}]}