{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T00:26:58Z","timestamp":1793924818398,"version":"4.8.0"},"reference-count":44,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T00:00:00Z","timestamp":1793491200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T00:00:00Z","timestamp":1793491200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T00:00:00Z","timestamp":1792281600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003542","name":"Ministry of Science Research and the Arts Baden-W\u00fcrttemberg","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003542","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Magnetic Resonance"],"published-print":{"date-parts":[[2026,11]]},"DOI":"10.1016\/j.jmr.2026.108186","type":"journal-article","created":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T06:32:03Z","timestamp":1792391523000},"page":"108186","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Large-domain histology-based diffusion MRI simulation via independent local simulations"],"prefix":"10.1016","volume":"392","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-0744-150X","authenticated-orcid":false,"given":"Iris A.","family":"Kohler","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6439-8124","authenticated-orcid":false,"given":"Tristan A.","family":"Kuder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"G\u00f6dicke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4128-9440","authenticated-orcid":false,"given":"Mark E.","family":"Ladd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4001-1164","authenticated-orcid":false,"given":"J\u00fcrgen","family":"Hesser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmr.2026.108186_b1","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1002\/jmri.29144","article-title":"Advanced diffusion-weighted MRI for cancer microstructure assessment in body imaging, and its relationship with histology","volume":"60","author":"Fokkinga","year":"2023","journal-title":"J. Magn. Reson. Imaging"},{"key":"10.1016\/j.jmr.2026.108186_b2","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1053\/j.sult.2021.07.006","article-title":"Diffusion-weighted imaging: Recent advances and applications","volume":"42","author":"Martinez-Heras","year":"2021","journal-title":"Semin. Ultrasound, CT MRI"},{"key":"10.1016\/j.jmr.2026.108186_b3","doi-asserted-by":"crossref","DOI":"10.1016\/j.jneumeth.2020.108951","article-title":"The sensitivity of diffusion MRI to microstructural properties and experimental factors","volume":"347","author":"Afzali","year":"2021","journal-title":"J. Neurosci. Methods"},{"key":"10.1016\/j.jmr.2026.108186_b4","doi-asserted-by":"crossref","DOI":"10.1016\/j.jneumeth.2020.108861","article-title":"Challenges for biophysical modeling of microstructure","volume":"344","author":"Jelescu","year":"2020","journal-title":"J. Neurosci. Methods"},{"key":"10.1016\/j.jmr.2026.108186_b5","doi-asserted-by":"crossref","first-page":"e101","DOI":"10.1002\/jmri.26518","article-title":"Quantitative imaging biomarkers alliance (QIBA) recommendations for improved precision of DWI and DCE-MRI derived biomarkers in multicenter oncology trials","volume":"49","author":"Shukla-Dave","year":"2019","journal-title":"J. Magn. Reson. Imaging"},{"key":"10.1016\/j.jmr.2026.108186_b6","article-title":"Multi-modal image registration: matching MRI with histology","volume":"vol. 7626","author":"Alic","year":"2010"},{"key":"10.1016\/j.jmr.2026.108186_b7","doi-asserted-by":"crossref","DOI":"10.1016\/j.ejrad.2021.109964","article-title":"Correlation of in-vivo imaging with histopathology: A review","volume":"144","author":"Sen","year":"2021","journal-title":"Eur. J. Radiol."},{"key":"10.1016\/j.jmr.2026.108186_b8","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/mrm.10078","article-title":"Biexponential diffusion attenuation in the rat spinal cord: Computer simulations based on anatomic images of axonal architecture","volume":"47","author":"Chin","year":"2002","journal-title":"Magn. Reson. Med."},{"key":"10.1016\/j.jmr.2026.108186_b9","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1002\/mrm.20223","article-title":"Assessment of axonal fiber tract architecture in excised rat spinal cord by localized NMR q-space imaging: Simulations and experimental studies","volume":"52","author":"Chin","year":"2004","journal-title":"Magn. Reson. Med."},{"key":"10.1016\/j.jmr.2026.108186_b10","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.neuroimage.2014.09.006","article-title":"Mapping mean axon diameter and axonal volume fraction by MRI using temporal diffusion spectroscopy","volume":"103","author":"Xu","year":"2014","journal-title":"NeuroImage"},{"key":"10.1016\/j.jmr.2026.108186_b11","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1007\/s00429-019-01844-6","article-title":"Along-axon diameter variation and axonal orientation dispersion revealed with 3D electron microscopy: implications for quantifying brain white matter microstructure with histology and diffusion MRI","volume":"224","author":"Lee","year":"2019","journal-title":"Brain Struct. Funct."},{"key":"10.1016\/j.jmr.2026.108186_b12","series-title":"Medical Image Computing and Computer-Assisted Intervention \u2013 MICCAI 2010","first-page":"404","article-title":"High-fidelity meshes from tissue samples for diffusion MRI simulations","author":"Panagiotaki","year":"2010"},{"key":"10.1016\/j.jmr.2026.108186_b13","doi-asserted-by":"crossref","DOI":"10.1038\/s42003-025-09096-3","article-title":"Histology-informed microstructural diffusion simulations for MRI cancer characterisation\u2014the Histo-\u03bcSim framework","volume":"8","author":"Grigoriou","year":"2025","journal-title":"Commun. Biology"},{"key":"10.1016\/j.jmr.2026.108186_b14","doi-asserted-by":"crossref","unstructured":"P.A. Cook, Y. Bai, S. Nedjati-Gilani, K.K. Seunarine, M.G. Hall, G.J. Parker, D.C. Alexander, Camino: Open-source diffusion-MRI reconstruction and processing, in: Proceedings of the 14th Scientific Meeting of the International Society for Magnetic Resonance in Medicine, ISMRM, Seattle, WA, USA, 2006, p. 2759.","DOI":"10.54294\/fgfrtv"},{"key":"10.1016\/j.jmr.2026.108186_b15","doi-asserted-by":"crossref","DOI":"10.21105\/joss.02527","article-title":"Disimpy: A massively parallel Monte Carlo simulator for generating diffusion-weighted mri data in python","volume":"5","author":"Kerkel\u00e4","year":"2020","journal-title":"J. Open Source Softw."},{"key":"10.1016\/j.jmr.2026.108186_b16","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuroimage.2019.116120","article-title":"SpinDoctor: A MATLAB toolbox for diffusion MRI simulation","volume":"202","author":"Li","year":"2019","journal-title":"NeuroImage"},{"key":"10.1016\/j.jmr.2026.108186_b17","doi-asserted-by":"crossref","DOI":"10.1016\/j.mri.2025.110428","article-title":"MATI: A GPU-accelerated toolbox for microstructural diffusion MRI simulation and data fitting with a graphical user interface","volume":"122","author":"Xu","year":"2025","journal-title":"Magn. Reson. Imaging"},{"key":"10.1016\/j.jmr.2026.108186_b18","doi-asserted-by":"crossref","DOI":"10.3389\/fninf.2020.00008","article-title":"Robust Monte-Carlo simulations in Diffusion-MRI: Effect of the substrate complexity and parameter choice on the reproducibility of results","volume":"14","author":"Rafael-Patino","year":"2020","journal-title":"Front. Neuroinform."},{"key":"10.1016\/j.jmr.2026.108186_b19","doi-asserted-by":"crossref","DOI":"10.1016\/j.medengphy.2023.104013","article-title":"Monte Carlo simulation of water diffusion through cardiac tissue models","volume":"120","author":"Jing","year":"2023","journal-title":"Med. Eng. Phys."},{"key":"10.1016\/j.jmr.2026.108186_b20","doi-asserted-by":"crossref","DOI":"10.1016\/j.dib.2021.107429","article-title":"The diffusion-simulated connectivity (DiSCo) dataset","volume":"38","author":"Rafael-Patino","year":"2021","journal-title":"Data Brief"},{"key":"10.1016\/j.jmr.2026.108186_b21","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1002\/mrm.27561","article-title":"Novel insights into in-vivo diffusion tensor cardiovascular magnetic resonance using computational modeling and a histology-based virtual microstructure","volume":"81","author":"Rose","year":"2019","journal-title":"Magn. Reson. Med."},{"key":"10.1016\/j.jmr.2026.108186_b22","series-title":"Realistic voxel sizes and reduced signal variation in Monte Carlo simulation for diffusion MR data synthesis","author":"Hall","year":"2017"},{"key":"10.1016\/j.jmr.2026.108186_b23","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0076626","article-title":"Diffusion Microscopist Simulator: A general Monte Carlo simulation system for diffusion magnetic resonance imaging","volume":"8","author":"Yeh","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jmr.2026.108186_b24","doi-asserted-by":"crossref","DOI":"10.1016\/j.jneumeth.2020.109018","article-title":"Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in three-dimensional cell segmentations of microscopy images","volume":"350","author":"Lee","year":"2021","journal-title":"J. Neurosci. Methods"},{"key":"10.1016\/j.jmr.2026.108186_b25","doi-asserted-by":"crossref","DOI":"10.1162\/imag_a_00533","article-title":"SpinWalk: A Monte Carlo simulator for MR-signal formation in inhomogeneous tissue","volume":"3","author":"Aghaeifar","year":"2025","journal-title":"Imaging Neurosci."},{"key":"10.1016\/j.jmr.2026.108186_b26","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1109\/TMI.2017.2679809","article-title":"Monte Carlo simulations of diffusion weighted MRI in myocardium: Validation and sensitivity analysis","volume":"36","author":"Bates","year":"2017","journal-title":"IEEE Trans. Med. Imaging"},{"key":"10.1016\/j.jmr.2026.108186_b27","doi-asserted-by":"crossref","DOI":"10.1016\/j.media.2021.102325","article-title":"Connecting macroscopic diffusion metrics of cardiac diffusion tensor imaging and microscopic myocardial structures based on simulation","volume":"77","author":"Wang","year":"2022","journal-title":"Med. Image Anal."},{"key":"10.1016\/j.jmr.2026.108186_b28","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1006\/jmrb.1995.1141","article-title":"Diffusive edge enhancement in imaging","volume":"109","author":"de Swiet","year":"1995","journal-title":"J. Magn. Reson. B"},{"key":"10.1016\/j.jmr.2026.108186_b29","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1002\/mrm.10536","article-title":"An image-based finite difference model for simulating restricted diffusion","volume":"50","author":"Hwang","year":"2003","journal-title":"Magn. Reson. Med."},{"key":"10.1016\/j.jmr.2026.108186_b30","series-title":"2024 IEEE International Symposium on Biomedical Imaging","first-page":"1","article-title":"Comparing Steam and PGSE diffusion MRI signal of rat lymph nodes using in-silico simulations","author":"Gardier","year":"2024"},{"key":"10.1016\/j.jmr.2026.108186_b31","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1002\/mp.14689","article-title":"Improving the characterization of meningioma microstructure in proton therapy from conventional apparent diffusion coefficient measurements using Monte Carlo simulations of diffusion MRI","volume":"48","author":"Buizza","year":"2021","journal-title":"Med. Phys."},{"key":"10.1016\/j.jmr.2026.108186_b32","doi-asserted-by":"crossref","DOI":"10.1016\/j.media.2022.102592","article-title":"Three-dimensional micro-structurally informed in silico myocardium\u2014towards virtual imaging trials in cardiac diffusion weighted MRI","volume":"82","author":"Lashgari","year":"2022","journal-title":"Med. Image Anal."},{"key":"10.1016\/j.jmr.2026.108186_b33","doi-asserted-by":"crossref","DOI":"10.3389\/fninf.2023.1208073","article-title":"CACTUS: a computational framework for generating realistic white matter microstructure substrates","volume":"17","author":"Villarreal-Haro","year":"2023","journal-title":"Front. Neuroinformatics"},{"key":"10.1016\/j.jmr.2026.108186_b34","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.neuroimage.2019.02.055","article-title":"MEDUSA: A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres","volume":"193","author":"Ginsburger","year":"2019","journal-title":"NeuroImage"},{"key":"10.1016\/j.jmr.2026.108186_b35","doi-asserted-by":"crossref","DOI":"10.1186\/s12943-025-02240-x","article-title":"From morphology to single-cell molecules: high-resolution 3D histology in biomedicine","volume":"24","author":"Xu","year":"2025","journal-title":"Mol. Cancer"},{"key":"10.1016\/j.jmr.2026.108186_b36","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-17204-5","article-title":"QuPath: Open source software for digital pathology image analysis","volume":"7","author":"Bankhead","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jmr.2026.108186_b37","author":"Erickson"},{"key":"10.1016\/j.jmr.2026.108186_b38","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.1002\/mrm.29720","article-title":"Cellular Exchange Imaging (CEXI): Evaluation of a diffusion model including water exchange in cells using numerical phantoms of permeable spheres","volume":"90","author":"Gardier","year":"2023","journal-title":"Magn. Reson. Med."},{"key":"10.1016\/j.jmr.2026.108186_b39","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1002\/mrm.29174","article-title":"Diffusion MRI signal cumulants and hepatocyte microstructure at fixed diffusion time: Insights from simulations, 9.4T imaging, and histology","volume":"88","author":"Grussu","year":"2022","journal-title":"Magn. Reson. Med."},{"key":"10.1016\/j.jmr.2026.108186_b40","first-page":"265","article-title":"Cell detection with star-convex polygons","volume":"vol. 11071 LNCS","author":"Schmidt","year":"2018"},{"key":"10.1016\/j.jmr.2026.108186_b41","series-title":"CGAL User and Reference Manual","author":"The CGAL Project","year":"2024"},{"key":"10.1016\/j.jmr.2026.108186_b42","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1017\/S0962492900002427","article-title":"Domain decomposition algorithms","volume":"3","author":"Chan","year":"1994","journal-title":"Acta Numer."},{"key":"10.1016\/j.jmr.2026.108186_b43","doi-asserted-by":"crossref","first-page":"N35","DOI":"10.1088\/0031-9155\/57\/4\/N35","article-title":"A finite difference method with periodic boundary conditions for simulations of diffusion-weighted magnetic resonance experiments in tissue","volume":"57","author":"Russell","year":"2012","journal-title":"Phys. Med. Biol."},{"key":"10.1016\/j.jmr.2026.108186_b44","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.jcp.2014.01.009","article-title":"A finite elements method to solve the Bloch-Torrey equation applied to diffusion magnetic resonance imaging","volume":"263","author":"Nguyen","year":"2014","journal-title":"J. Comput. Phys."}],"container-title":["Journal of Magnetic Resonance"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S109078072600176X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S109078072600176X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T23:54:17Z","timestamp":1793922857000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S109078072600176X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,11]]},"references-count":44,"alternative-id":["S109078072600176X"],"URL":"https:\/\/doi.org\/10.1016\/j.jmr.2026.108186","relation":{},"ISSN":["1090-7807"],"issn-type":[{"value":"1090-7807","type":"print"}],"subject":[],"published":{"date-parts":[[2026,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Large-domain histology-based diffusion MRI simulation via independent local simulations","name":"articletitle","label":"Article Title"},{"value":"Journal of Magnetic Resonance","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmr.2026.108186","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"108186"}}