{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T16:30:28Z","timestamp":1787675428166,"version":"build-2784847793"},"reference-count":16,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T00:00:00Z","timestamp":1783900800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T00:00:00Z","timestamp":1783900800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["FOR5427 SP1\u2010SH542\/2\u20101"],"award-info":[{"award-number":["FOR5427 SP1\u2010SH542\/2\u20101"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["FOR5427 SP4"],"award-info":[{"award-number":["FOR5427 SP4"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["539301313 EN984\/18\u20101"],"award-info":[{"award-number":["539301313 EN984\/18\u20101"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["574526432 EN984\/19\u20101"],"award-info":[{"award-number":["574526432 EN984\/19\u20101"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["449437943 TR332 A3"],"award-info":[{"award-number":["449437943 TR332 A3"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["Z1"],"award-info":[{"award-number":["Z1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["504501554 INST 20876\/486\u20101"],"award-info":[{"award-number":["504501554 INST 20876\/486\u20101"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["01EW2503 ERA\u2010NET NEURON"],"award-info":[{"award-number":["01EW2503 ERA\u2010NET NEURON"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["549898653 SFB1752 B05"],"award-info":[{"award-number":["549898653 SFB1752 B05"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Microscopy"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Deep Visual Proteomics (DVP) combines high\u2010resolution microscopy, computational instance segmentation, laser capture microdissection (LMD), and ultrasensitive mass spectrometry to enable spatially resolved molecular analysis of defined cellular populations. Within this workflow, LMD plays a central role by physically isolating microscopy\u2010defined regions of interest for downstream proteomic profiling. However, accurate image\u2010to\u2010stage transfer remains challenging due to limitations in imaging resolution, tissue preparation variability, laser cutting parameters, and partially manual alignment procedures. Here, we present an open\u2010source semi\u2010automated image\u2010to\u2010LMD interoperability framework for DVP that integrates fiducial marker detection, coordinate transformation, and segmentation\u2010driven contour export for reproducible microdissection. Using neutrophil isolation from murine urinary bladder tissue as a representative use case, we demonstrate robust alignment of computationally defined cellular boundaries with LMD\u2010guided excision. By improving interoperability, transparency, and workflow standardisation, this framework strengthens the integration of microscopy and spatial proteomics and supports reproducible analysis of spatially defined immune cell populations.<\/jats:p>","DOI":"10.1111\/jmi.70145","type":"journal-article","created":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T14:57:24Z","timestamp":1783954644000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Bioimage analysis in deep visual proteomics: Advancing transparency, reproducibility, and FAIR principles"],"prefix":"10.1111","author":[{"given":"Devon","family":"Siemes","sequence":"first","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angelo","family":"Novak","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Thiebes","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"Widera","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Tautges","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Voss","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"Borgards","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominik","family":"Habermann","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianxu","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Biospectroscopy Leibniz\u2010Institut F\u00fcr Analytische Wissenschaften ISAS  Dortmund Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Shevchuk","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7301-353X","authenticated-orcid":false,"given":"Daniel R.","family":"Engel","sequence":"additional","affiliation":[{"name":"Department of Immunodynamics Institute of Experimental Immunology and Imaging University Hospital Essen  Essen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,13]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2024.110620"},{"key":"e_1_2_7_3_1","doi-asserted-by":"crossref","unstructured":"Makhmut A. Qin D. Fritzsche S. Nimo J. K\u00f6nig J. &Coscia F.(2023).A framework for ultra\u2010low\u2010input spatial tissue proteomics.Cell Systems 14 1002\u20131014 e1005.https:\/\/doi.org\/10.1016\/j.cels.2023.10.003","DOI":"10.1016\/j.cels.2023.10.003"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2024.100750"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010022\u201001302\u20105"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2025.101396"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010025\u201008885\u20104"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2024.12.023"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2016.18"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41597\u2010022\u201001710\u2010x"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1101\/2025.04.28.651001"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1002\/bies.202300114"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.64898\/2025.12.19.695433"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1101\/2025.07.13.662099"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.453"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010019\u20100686\u20102"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1101\/2023.06.01.542416"}],"container-title":["Journal of Microscopy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jmi.70145","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/jmi.70145","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jmi.70145","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T14:57:25Z","timestamp":1783954645000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/jmi.70145"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,13]]},"references-count":16,"alternative-id":["10.1111\/jmi.70145"],"URL":"https:\/\/doi.org\/10.1111\/jmi.70145","archive":["Portico"],"relation":{},"ISSN":["0022-2720","1365-2818"],"issn-type":[{"value":"0022-2720","type":"print"},{"value":"1365-2818","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,13]]},"assertion":[{"value":"2025-12-02","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-18","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-13","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"jmi.70145"}}