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In this paper, a novel image-based computational model simulating blood flow through and around platelet aggregates is presented. The microstructure of aggregates was captured by two different modalities of microscopy images of\n                    <jats:italic>in vitro<\/jats:italic>\n                    whole blood perfusion experiments in microfluidic chambers coated with collagen. One set of images captured the geometry of the aggregate outline, while the other employed platelet labelling to infer the internal density. The platelet aggregates were modelled as a porous medium, the permeability of which was calculated with the Kozeny-Carman equation. The computational model was subsequently applied to study hemodynamics inside and around the platelet aggregates. The blood flow velocity, shear stress and kinetic force exerted on the aggregates were investigated and compared under 800\n                    <jats:italic>s<\/jats:italic>\n                    <jats:sup>\u22121<\/jats:sup>\n                    , 1600\n                    <jats:italic>s<\/jats:italic>\n                    <jats:sup>\u22121<\/jats:sup>\n                    and 4000\n                    <jats:italic>s<\/jats:italic>\n                    <jats:sup>\u22121<\/jats:sup>\n                    wall shear rates. The advection-diffusion balance of agonist transport inside the platelet aggregates was also evaluated by local P\u00e9clet number. The findings show that the transport of agonists is not only affected by the shear rate but also significantly influenced by the microstructure of the aggregates. Moreover, large kinetic forces were found at the transition zone from shell to core of the aggregates, which could contribute to identifying the boundary between the shell and the core. The shear rate and the rate of elongation flow were investigated as well. The results imply that the emerging shapes of aggregates are highly correlated to the shear rate and the rate of elongation. The framework provides a way to incorporate the internal microstructure of the aggregates into the computational model and yields a better understanding of the hemodynamics and physiology of platelet aggregates, hence laying the foundation for predicting aggregation and deformation under different flow conditions.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1010965","type":"journal-article","created":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T14:04:11Z","timestamp":1688997851000},"page":"e1010965","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Image-based flow simulation of platelet aggregates under different shear rates"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4189-5010","authenticated-orcid":true,"given":"Yue","family":"Hao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G\u00e1bor","family":"Z\u00e1vodszky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Tersteeg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mojtaba","family":"Barzegari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfons G.","family":"Hoekstra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,7,10]]},"reference":[{"issue":"3","key":"pcbi.1010965.ref001","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/S1473-0502(03)00044-2","article-title":"Platelets in hemostasis and thrombosis: role of integrins and their ligands","volume":"28","author":"H Ni","year":"2003","journal-title":"Transfusion and Apheresis Science"},{"issue":"6","key":"pcbi.1010965.ref002","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/nm.1955","article-title":"A shear gradient\u2013dependent platelet aggregation mechanism drives thrombus formation","volume":"15","author":"WS Nesbitt","year":"2009","journal-title":"Nature Medicine"},{"issue":"jbr150602","key":"pcbi.1010965.ref003","first-page":"437","article-title":"Platelets in hemostasis and thrombosis: Novel mechanisms of fibrinogen-independent platelet aggregation and fibronectinmediated protein wave of hemostasis","volume":"29","author":"Y Hou","year":"2015","journal-title":"The Journal of Biomedical Research"},{"issue":"12","key":"pcbi.1010965.ref004","doi-asserted-by":"crossref","first-page":"5087","DOI":"10.1182\/blood-2006-12-027698","article-title":"The growing complexity of platelet aggregation","volume":"109","author":"SP Jackson","year":"2007","journal-title":"Blood"},{"issue":"2","key":"pcbi.1010965.ref005","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1172\/JCI973","article-title":"Distinct mechanisms of platelet aggregation as a consequence of different shearing flow conditions","volume":"101","author":"S Goto","year":"1998","journal-title":"The Journal of Clinical Investigation"},{"issue":"5","key":"pcbi.1010965.ref006","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1097\/00062752-200109000-00002","article-title":"Mechanisms of platelet aggregation","volume":"8","author":"B Savage","year":"2001","journal-title":"Current opinion in hematology"},{"issue":"2-3","key":"pcbi.1010965.ref007","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1159\/000089930","article-title":"Coagulation under flow: the influence of flow-mediated transport on the initiation and inhibition of coagulation","volume":"34","author":"AL Fogelson","year":"2005","journal-title":"Pathophysiology of Haemostasis and Thrombosis"},{"issue":"1","key":"pcbi.1010965.ref008","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1005291","article-title":"A general shear-dependent model for thrombus formation","volume":"13","author":"A Yazdani","year":"2017","journal-title":"PLOS Computational Biology"},{"issue":"2","key":"pcbi.1010965.ref009","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1515\/rnam-2012-0011","article-title":"Continuous mathematical model of platelet thrombus formation in blood flow","volume":"27","author":"A Tokarev","year":"2012","journal-title":"Russian Journal of Numerical Analysis and Mathematical Modelling"},{"issue":"5","key":"pcbi.1010965.ref010","doi-asserted-by":"crossref","first-page":"2539","DOI":"10.1529\/biophysj.107.127670","article-title":"Platelet adhesive dynamics. 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