Gastruloid phenotype live cell imaging dataset

Overview The images were taken every 6 hours for 2 days (48 hours), resulting in 9 frames per gastruloid. 1,058 total gastruloids were grown, evenly split between euploid (array1) and aneuploid (array2) conditions, resulting in ~9,500 images, of which 9,252 are included here (with the remaining removed due to substaintial technical artifacts obscuring a large (>50%) portion of the gastruloid). Each image is a 128x128 pixel png file. To increase contrast and reduce background lighting effects, we applied a gaussian blur (sigma=50) and background removal before normalization. The filenames contain metadata about each of the images in the form: <collection_date>_<staining>_<array1/array2>_<sample_number>_<timepoint>.png Curation Time-series transmitted light and fluorescence imaging of the gastruloids were performed using a custom microscopy system enclosed within an incubation chamber maintaining constant temperature, CO2, and humidity levels as previously described. Notably, the system consisted of an inverted MVX10 MacroView fluorescence microscope (Evident Scientific, Tokyo, Japan) with a 2x wide-field objective and was illuminated by a Lumen 200 mercury lamphouse (Prior Scientific Inc., Rockland, MA) through a 8907 ET - ECFP/EYFP/DsRed filter set (Chroma Technology Corp, Bellow Falls, VT). Images were acquired every 6 h over 48 h at 4x magnification (1.7 µm/pixel). The python file used to do background correction and normalization of the images in this dataset is also includuded in this repository. The primary codebase associated with this project can be found here.## 概述 本数据集的图像每6小时采集一次，采集周期为2天（总计48小时），每个类原肠胚（gastruloid）可获得9帧图像。本次共培养了1058个类原肠胚，按实验条件均分为整倍体组（array1）与非整倍体组（array2），理论上可产生约9500张图像，本次收录其中9252张（剩余图像因存在严重技术伪影遮挡了类原肠胚50%以上的区域而被剔除）。每张图像均为128×128像素的PNG格式文件。为提升图像对比度并减弱背景光照影响，我们在归一化处理前对图像施加了高斯模糊（σ=50）并进行了背景移除操作。图像文件名以如下格式包含了各图像的元数据：<采集日期>_<染色方式>_<array1/array2>_<样本编号>_<时间点>.png ## 数据集整理 类原肠胚的时序明场与荧光成像采用定制化显微镜系统完成，该系统置于可维持恒定温度、CO₂浓度与湿度的培养舱内，具体配置如既往研究所述。值得注意的是，该系统搭载日本东京Evident Scientific公司生产的倒置MVX10 MacroView荧光显微镜，配备2×宽场物镜；照明系统采用Prior Scientific Inc.（美国马萨诸塞州罗克兰）的Lumen 200汞灯光源，并通过Chroma Technology Corp（美国佛蒙特州贝洛福尔斯）的8907 ET-ECFP/EYFP/DsRed滤光组进行滤光。图像每6小时采集一次，持续48小时，采集时放大倍率为4×（像素分辨率1.7μm/像素）。 本数据集图像的背景校正与归一化处理所用的Python脚本也已包含在本代码仓库中。本项目关联的核心代码库可在此处获取。