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Since multiple hemodynamic variables can simultaneously exhibit transient and spatiotemporally heterogeneous behavior, there is an exigent need for analysis tools that employ multiple variables to characterize the anomalous hemodynamics within the TME. To address this, we developed a new toolkit called HemoSYS for quantifying the hemodynamic landscape within angiogenic microenvironments. It employs multivariable time-series data such as <jats:italic>in vivo<\/jats:italic> tumor blood flow (BF), blood volume (BV) and intravascular oxygen saturation (Hb<jats:sub>sat<\/jats:sub>) acquired concurrently using a wide-field multicontrast optical imaging system. The HemoSYS toolkit consists of propagation, clustering, coupling, perturbation and Fourier analysis modules. We demonstrate the utility of each module for characterizing the <jats:italic>in vivo<\/jats:italic> hemodynamic landscape of an orthotropic breast cancer model. With HemoSYS, we successfully described: (i) the propagation dynamics of acute hypoxia; (ii) the initiation and dissolution of distinct hemodynamic niches; (iii) tumor blood flow regulation via local vasomotion; (iv) the hemodynamic response to a systemic perturbation with carbogen gas; and (v) frequency domain analysis of hemodynamic heterogeneity in the TME. HemoSYS (freely downloadable via the internet) enables vascular phenotyping from multicontrast <jats:italic>in vivo<\/jats:italic> optical imaging data. Its modular design also enables characterization of non-tumor hemodynamics (e.g. brain), other preclinical disease models (e.g. stroke), vascular-targeted therapeutics, and hemodynamic data from other imaging modalities (e.g. MRI).<\/jats:p>","DOI":"10.1038\/s41598-020-58918-3","type":"journal-article","created":{"date-parts":[[2020,2,11]],"date-time":"2020-02-11T11:02:39Z","timestamp":1581418959000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["HemoSYS: A Toolkit for Image-based Systems Biology of Tumor Hemodynamics"],"prefix":"10.1038","volume":"10","author":[{"given":"Janaka","family":"Senarathna","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ayush","family":"Prasad","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akanksha","family":"Bhargava","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stacy","family":"Gil","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nitish V.","family":"Thakor","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arvind P.","family":"Pathak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,2,11]]},"reference":[{"key":"58918_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0065-2660(10)69010-4","volume":"69","author":"AP Pathak","year":"2010","unstructured":"Pathak, A. 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