Introduction to Biomedical Image Analysis (for Beginners)

<p>Small dataset of the zebrafish brain vasculature&nbsp;acquired at 3 days post fertilization (dpf) with a Zeiss Z.2 light-sheet microscope. Transgenic reporter line&nbsp;used: blood vessels&nbsp;<em>Tg(kdrl:HRAS-mCherry)</em>^{<em>s916</em>}&nbsp;labels EC membrane (Chi et al., 2008).</p> <p>Data were acquired by Elisabeth Kugler at the University of Sheffield conforming&nbsp;to UK Home Office regulations and were performed under Home Office Project Licence 70/8588 held by TJAC. - Data are part of the publication: Kugler et al., 2019 as well as Dr Kugler&#39;s thesis.</p> <p>Dataset consists only of 3 samples and is used as a sample dataset to train students in biomedical image analysis.</p> <p>Image Acquisition Details:<br> Datasets in Sheffield were obtained using a Zeiss Z.1 light sheet microscope with a water-dipping detection objective (Plan-Apochromat 20&times;/1.0 Corr nd&nbsp;=&nbsp;1.38) and a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data were acquired with activated pivot scan, dual-sided illumination and online fusion; properties of acquired data are as follows: 0.7&times; zoom, 16bit image depth, 1,920&nbsp;&times;&nbsp;1,920px image size and minimum z-stack interval (approx. 0.33&nbsp;&times;&nbsp;0.33&times; 0.5&nbsp;&mu;m). Green and red fluorophores were excited using 488&nbsp;nm and 561&nbsp;nm laser, respectively. Used filters in sequential tracks for multi-colour images were LP560 for both and BP505-545 and LP585, respectively. Samples were embedded in 1% or 2% LMP-agarose containing 200&nbsp;mg/l Tricaine (MS-222, Sigma). The image acquisition chamber was filled with E3 plus Tricaine (200&nbsp;mg/ml) and maintained at 28&deg;C.</p>