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In vivo positron emission tomography (PET) and magnetic resonance imaging (MRI) support non-invasive assessment of the spatiotemporal expression of proteins of interest and functional/structural changes. Our work promotes the use of a volumetric analysis on multimodal imaging datasets to assess the spatio-temporal dynamics and interaction of two imaging biomarkers, with a special focus on two neuroinflammation-related biomarkers, the translocator protein (TSPO) and matrix metalloproteinases (MMPs), in the acute and chronic post-ischemic phase. To improve our understating of the neuroinflammatory reaction and tissue heterogeneity during the post ischemic phase, we aimed (i) to assess the spatio-temporal distribution of two radiotracers, [18F]DPA-714 (TSPO) and [18F]BR-351 (MMPs), (ii) to investigate their spatial interaction, including exclusive and overlapping areas, and (iii) their relationship with the T 2 w-MRI ischemic lesion in a transient middle cerebral artery occlusion (tMCAo) mouse model using an atlas-based volumetric analysis. As described by Zinnhardt et al. (2015) , a total of N = 30 C57BL/6 mice underwent [18F]DPA-714 and [18F]BR-351 PET-CT and subsequent MR imaging 24–48 h (n = 8), 7 ± 1 days (n = 8), 14 ± 1 days (n = 7), and 21 ± 1 days (n = 7) after 30 min transient middle cerebral artery occlusion (tMCAo). To further investigate the spatio-temporal distribution of [18F]DPA-714 and [18F]BR-351, an atlas-based ipsilesional volume of interest (VOI) was applied to co-registered PET-CT images and thresholded by the mean uptake + 2.5*standard deviation of a contralateral striatal control VOI. Mean lesion-to-contralateral ratios (L/C), volume extension (V in voxel), percentages of overlap and exclusive tracer uptake areas were determined. Both tracer volumes were also compared to the lesion extent depicted by T 2 w-MR imaging. Both imaging biomarkers showed a constant small percentage of overlap across all time points (14.0 ± 14.2%). [18F]DPA-714 reached its maximum extent and uptake at day 14 post ischemia (V = 12,143 ± 6262 voxels, L/ C = 2.32 ± 0.48). The majority of [18F]DPA-714 volume (82.4 ± 16.1%) was exclusive for [18F]DPA-714 and showed limited overlap with [18F]BR-351 and T 2 w-MRI lesion volumes. On the other hand, [18F]BR-351 reached its maximum extent already 24–48 h after tMCAo (V = 7279 ± 4518 voxels) and significantly decreased at day 14 (V = 1706 ± 1202 voxels). Focal spots of residual activity were still observed at day 21 post ischemia (L/ C = 2.10 ± 0.37). The majority of [18F]BR-351 volume was exclusive for [18F]BR-351 (81.50 ± 25.07%) at 24–48 h and showed 64.84 ± 28.29% of overlap with [18F]DPA-714 from day 14 post ischemia while only 9.28 ± 13.45% of the [18F]BR-351 volume were overlapping the T 2 w-MRI lesion. The percentage of exclusive area of [18F]DPA-714 and [18F]BR-351 uptakes regarding T 2 w-MR lesion increased over time, suggesting that TSPO and MMPs are mostly localized in the peri‑infarct region at latter time points. This study promotes the use of an unbiased volumetric analyses of multi-modal imaging data sets to improve the characterization of pathological tissue heterogeneity. This approach improves our understanding of (i) the dynamics of disease-related multi-modal imaging biomarkers, (ii) their spatiotemporal interactions and (iii) the post-ischemic tissue heterogeneity. Our results indicate acute MMPs activation after tMCAo preceding TSPO-dependent (micro-)gliosis. The spatial distribution of MMPs and gliosis is regionally independent with only minor (< 20%) overlapping areas in peri‑infarct regions. [ABSTRACT FROM AUTHOR]