Vasculature Segmentation Validation Dataset - Part III - Biological Difference Dataset 1/2 (Exsanguination)

<p>Dataset to allow exploration of data enhancement, segmentation, and validation&nbsp;for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications</p> <p><strong>Dataset description</strong></p> <p><strong>Exsanguination</strong>: Example data of the head vasculature of 4dpf of zebrafish. Data acquisition before and after exsanguination by opening of the heart cavity with forceps in Tg(kdrl:HRAS-mCherry)s916 (4dpf; n=16 embryos from 2 experimental repeats).</p> <p><br> <strong>Data acquisition</strong>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588&nbsp;held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993).&nbsp;Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995).</p> <p>Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma).&nbsp;Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective,&nbsp;dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28&deg;C,&nbsp;with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth,&nbsp;voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 &micro;m).&nbsp;</p> <p><strong>Contact</strong>: kugler.elisabeth[at]gmail.com</p> <p><strong>Useful code links</strong>:&nbsp;</p> <p>https://github.com/ElisabethKugler/ZFVascularQuantification<br> https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis</p>