Zebrafish Brain Vasculature and EC Nuclei 3dpf Light-Sheet (For StarDist)

Small dataset of the zebrafish brain vasculature and endothelial cell nuclei acquired at 3 days post fertilization (dpf) with a Zeiss Z.2 light-sheet microscope. Transgenic reporter lines used: blood vessels Tg(kdrl:HRAS-mCherry)s916 labels EC membrane (Chi et al., 2008) and EC nuclei Tg(kdr:nls-eGFP)zf109 labels EC nuclei (Blum et al., 2008). Data were acquired by Elisabeth Kugler in 2018 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 on StarDist (https://github.com/stardist/; Schmidt, et al. 2018; Weigert, et al. 2020). 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.

本数据集为受精后3天（days post fertilization, dpf）的斑马脑血管系统与血管内皮细胞核显微成像数据集，采用蔡司Z.2光片显微镜（Zeiss Z.2 light-sheet microscope）采集。
所用转基因报告品系包括：标记血管内皮（endothelial cell, EC）细胞膜的Tg(kdrl:HRAS-mCherry)s916（Chi等，2008），以及标记血管内皮细胞核的Tg(kdr:nls-eGFP)zf109（Blum等，2008）。
该数据集由Elisabeth Kugler于2018年在谢菲尔德大学采集，实验操作符合英国内政部（UK Home Office）相关规定，并使用了TJAC持有的内政部项目许可70/8588。
本数据集相关成果发表于Kugler等人2019年的研究论文及Kugler博士的学位论文。该数据集仅包含3个样本，用作面向学生开展StarDist（https://github.com/stardist/; Schmidt等，2018; Weigert等，2020）训练的示例数据集。
图像采集细节：谢菲尔德校区的数据集采用蔡司Z.1光片显微镜采集，搭配水浸式检测物镜（Plan-Apochromat 20×/1.0 Corr nd=1.38）及科学互补金属氧化物半导体（scientific complementary metal-oxide semiconductor, sCMOS）检测单元。
采集时启用了枢轴扫描、双侧照明与在线融合功能；采集参数如下：缩放倍率0.7×，图像位深16bit，图像尺寸为1920×1920像素，z轴最小步进间隔约为0.33×0.33×0.5 μm。
绿色与红色荧光分别采用488 nm与561 nm激光激发；用于多色成像的序列轨道滤光片如下：双通道通用LP560，绿色通道使用BP505-545，红色通道使用LP585。
样本包埋于1%或2%低熔点琼脂糖（low melting point agarose, LMP-agarose）中，体系含200 mg/l三卡因（Tricaine, MS-222, Sigma）。成像腔室填充含200 mg/ml三卡因的E3培养液，维持温度28℃。