Abstract
In this data report we make available to the community a highly variable longitudinal MRI mouse brain data set of ischemic lesion after transient middle cerebral artery occlusion (tMCAo). Together with the provided semi-automated and automated segmentations, these data can be used to further improve the method proposed by Mulder et al. (2017) and also to serve as a benchmark for comparison between different approaches to segment ischemic lesions in MRI mouse brain data. It can also be used to develop and validate algorithms that further classify the stroke area into core and penumbra. • The data were collected from mice: (i) of different ages, (ii) of two different strains, (iii) at different time points after the ischemic infarct induction, (iv) from two laboratories, (v) using two different MRI systems, and (vi) using three different sets of acquisition parameters. • Segmentations of the ischemic lesions are provided as well. These were obtained by: (i) two observers using a semi-automated method and (ii) using the novel automated segmentation approach described by Mulder et al. (2017). • Type/format of data: raw files, MetaImage files, text/Excel files, analyzed data. • The following set of images associated with each of the 121 scans is included: raw Bruker MRI data (reference scan, T2 scan with all echoes, calculated T2-weighted map), automated segmentations of the ischemic lesions and semi-automated segmentations by two observers. • For 99 of these scans, an accompanying set of Bruker MR diffusion maps, containing the Diffusion-Weighted Image (DWI) and calculated Apparent Diffusion Coefficient (ADC) maps, is included. • Acquisition hardware: small-animal Bruker MRI systems (7 T and 11.7 T). • Experimental set-up: infarct was induced in male mice of different age and background, using the tMCAo model. After that, MRI scans at different time points after infarct induction were acquired. • Data sources: Leiden, Netherlands; Cologne, Germany. • Data accessibility: all related data sets (121 T2 scans + template + 99 diffusion scans) were deposited in the public Dryad Digital Repository (https://doi.org/10.5061/dryad.1m528).
Highlights
In this data report we make available to the community a highly variable longitudinal MRI mouse brain data set of ischemic lesion after transient middle cerebral artery occlusion
Together with the provided semi-automated and automated segmentations, these data can be used to further improve the method proposed by Mulder et al (2017) and to serve as a benchmark for comparison between different approaches to segment ischemic lesions in MRI mouse brain data
All animal experiments conducted at the Max Plank Institute for Metabolism Research in Cologne were performed in accordance with the German Animal Welfare Act and approved by the local authorities (Landesamt für Naturschutz, Umwelt und Verbraucherschutz NRW)
Summary
Male WT mice were subdivided into three main sets, respectively labeled as: “Leiden-Set”, “Cologne-Set-1”, “Cologne-Set-2”, depending on the city of origin and acquisition protocol. Leiden-Set: C57BL/6J mice (n = 58) were further subdivided into three age groups (3- to 5-, 12- to 14- and 20- to 24month-old). Cologne-Set-1: C57BL/6J mice (n = 6; 3-month-old) were scanned at 18 h and 4 d after infarct induction. Cologne-Set-2: Transgenic mice expressing luciferase under doublecortin control (DCX-Luc, Couillard-Després et al, 2008) (n = 10; 2- and 12-month-old) were scanned at 48 h after infarct induction. All animal experiments performed at the Leiden University Medical Center (LUMC) were approved by the local committee for animal health, ethics, and research of LUMC. All animal experiments conducted at the Max Plank Institute for Metabolism Research in Cologne were performed in accordance with the German Animal Welfare Act and approved by the local authorities (Landesamt für Naturschutz, Umwelt und Verbraucherschutz NRW).
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