Introduction to Biomedical Image Analysis (for Beginners)

Small dataset of the zebrafish brain vasculature acquired at 3 days post fertilization (dpf) with a Zeiss Z.2 light-sheet microscope. Transgenic reporter line used: blood vessels Tg(kdrl:HRAS-mCherry)s916 labels EC membrane (Chi et al., 2008). Data were acquired by Elisabeth Kugler at the University of Sheffield conforming 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's thesis. Dataset consists only of 3 samples and is used as a sample dataset to train students in biomedical image analysis. Image Acquisition Details: Datasets in Sheffield were obtained using a Zeiss Z.1 light sheet microscope with a water-dipping detection objective (Plan-Apochromat 20×/1.0 Corr nd = 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× zoom, 16bit image depth, 1,920 × 1,920px image size and minimum z-stack interval (approx. 0.33 × 0.33× 0.5 μm). Green and red fluorophores were excited using 488 nm and 561 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 mg/l Tricaine (MS-222, Sigma). The image acquisition chamber was filled with E3 plus Tricaine (200 mg/ml) and maintained at 28°C.