A toolkit for stroke infarct volume estimation in rodents

Rebecca Z. Weber, Davide Bernardoni, Nora H. Rentsch, Beatriz Achón Buil, Stefanie Halliday, Mark Aurel Augath, Daniel Razansky, Christian Tackenberg, Ruslan Rust

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Stroke volume is a key determinant of infarct severity and an important metric for evaluating treatments. However, accurate estimation of stroke volume can be challenging, due to the often confined 2-dimensional nature of available data. Here, we introduce a comprehensive semi-automated toolkit to reliably estimate stroke volumes based on (1) whole brains ex-vivo magnetic resonance imaging (MRI) and (2) brain sections that underwent immunofluorescence staining. We located and quantified infarct areas from MRI three days (acute) and 28 days (chronic) after photothrombotic stroke induction in whole mouse brains. MRI results were compared with measures obtained from immunofluorescent histologic sections of the same brains. We found that infarct volume determined by post-mortem MRI was highly correlated with a deviation of only 6.6 % (acute) and 4.9 % (chronic) to the measurements as determined in the histological brain sections indicating that both methods are capable of accurately assessing brain tissue damage (Pearson r > 0.9, p < 0.001). The Dice similarity coefficient (DC) showed a high degree of coherence (DC > 0.8) between MRI-delineated regions of interest (ROIs) and ROIs obtained from histologic sections at four to six pre-defined landmarks, with histology-based delineation demonstrating higher inter-operator similarity compared to MR images. We further investigated stroke-related scarring and post-ischemic angiogenesis in cortical peri‑infarct regions and described a negative correlation between GFAP+fluorescence intensity and MRI-obtained lesion size.

Original languageEnglish
Article number120518
StatePublished - 15 Feb 2024
Externally publishedYes


  • Histology
  • Immunofluorescence imaging
  • MRI
  • Photothrombotic stroke
  • Stroke size
  • Stroke volume


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