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The workflow integrates automated subthalamic nucleus (STN) segmentation from preoperative MRI using a two\u2010step convolutional neural network (CNN), classification of microelectrode recordings (MER) with a transformer encoder and spatial co\u2010alignment via a discrete optimisation procedure. Implemented as a 3D Slicer plugin, the pipeline enables real\u2010time visualisation and interactive use during surgery. In validation on retrospective data of 17 trajectories from 12 Parkinson's disease patients, co\u2010alignment reduced the mean lateral localisation error by 0.3\u2009mm relative to an intraoperative reference, indicating improved agreement between electrophysiological and anatomical targets. Automated STN segmentation achieved a Dice similarity of 0.62\u2009\u00b1\u20090.10, providing a robust starting point for manual refinement. This approach improves the understanding of electrode position within STN during surgery, incorporating preoperative and intraoperative data, offers clinicians a practical, real\u2010time tool to enhance targeting accuracy. By directly integrating imaging and MER evidence, the framework addresses persistent challenges in DBS and represents a step toward more personalised and precise neurosurgical interventions.<\/jats:p>","DOI":"10.1111\/ejn.70309","type":"journal-article","created":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T02:55:35Z","timestamp":1763607335000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Precise Electrode Co\u2010Alignment in Deep Brain Stimulation Fusing Neuroimaging and Electrophysiology"],"prefix":"10.1111","volume":"62","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1085-4312","authenticated-orcid":false,"given":"Igor","family":"Varga","sequence":"first","affiliation":[{"name":"Department of Cybernetics Faculty of Electrical Engineering, Czech Technical University  Prague 2 Czech Republic"},{"name":"Czech Centre for Phenogenomics BIOCEV\u2014Institute of Molecular Genetics  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Novak","sequence":"additional","affiliation":[{"name":"Department of Cybernetics Faculty of Electrical Engineering, Czech Technical University  Prague 2 Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dusan","family":"Urgosik","sequence":"additional","affiliation":[{"name":"Department of Neurology, First Faculty of Medicine Charles University and General University Hospital in Prague  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Kybic","sequence":"additional","affiliation":[{"name":"Department of Cybernetics Faculty of Electrical Engineering, Czech Technical University  Prague 2 Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filip","family":"Ruzicka","sequence":"additional","affiliation":[{"name":"Department of Neurology, First Faculty of Medicine Charles University and General University Hospital in Prague  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5656-5164","authenticated-orcid":false,"given":"Pavel","family":"Filip","sequence":"additional","affiliation":[{"name":"Department of Cybernetics Faculty of Electrical Engineering, Czech Technical University  Prague 2 Czech Republic"},{"name":"Department of Neurology, First Faculty of Medicine Charles University and General University Hospital in Prague  Prague Czech Republic"},{"name":"Center for Magnetic Resonance Research (CMRR) University of Minnesota  Minneapolis Minnesota USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Jech","sequence":"additional","affiliation":[{"name":"Department of Neurology, First Faculty of Medicine Charles University and General University Hospital in Prague  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Horn","sequence":"additional","affiliation":[{"name":"Institute for Network Stimulation, Clinic for Stereotaxy and Functional Neurosurgery University Hospital Cologne  Cologne Germany"},{"name":"Center for Brain Circuit Therapeutics Department of Neurology Brigham &amp; Women's Hospital, Harvard Medical School  Boston Massachusetts USA"},{"name":"MGH Neurosurgery &amp; Center for Neurotechnology and Neurorecovery (CNTR) at MGH Neurology Massachusetts General Hospital, Harvard Medical School  Boston Massachusetts USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduard","family":"Bakstein","sequence":"additional","affiliation":[{"name":"Department of Cybernetics Faculty of Electrical Engineering, Czech Technical University  Prague 2 Czech Republic"},{"name":"National Institute of Mental Health  Klecany Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,11,19]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12021-011-9109-y"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/hbm.26097"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.1088\/1741-2552\/abcb15"},{"issue":"9","key":"e_1_2_12_5_1","first-page":"1516","article-title":"Is the Subthalamic Nucleus Hypointense on T2\u2010Weighted Images? 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