DeepBacs – Bacillus subtilis fluorescence segmentation dataset

Training and test images of live B. subtilis cells expressing FtsZ-GFP for the task of segmentation. Additional information can be found on this github wiki. The example shows the fluorescence widefield image of live B. subtilis cells expressing FtsZ-GFP and the manually annotated segmentation mask. Data type: Paired fluorescence and segmented mask images Microscopy data type: 2D widefield images (fluorescence) Microscope: Custom-built 100x inverted microscope bearing a 100x TIRF objective (Nikon CFI Apochromat TIRF 100XC Oil); images were captured on a Prime BSI sCMOS camera (Teledyne Photometrics) Cell type: B. subtilis strain SH130 grown under agarose pads File format: .tiff (8-bit) or .png (8-bit) For segmented masks, binary masks are used for training of CARE/U-Net models, 8-bit .tif ROI maps for training of StarDist models and .png images for training of pix2pix models Image size: 1024 x 1024 px² (Pixel size: 65 nm) Image preprocessing: Images were denoised using PureDenoise and resulting 32-bit images were converted into 8-bit images after normalizing to 1% and 99.98% percentiles. Images were manually annotated using the Labkit Fiji plugin Author(s): Mia Conduit1,2, Séamus Holden1,3 Contact email: [e-mail] Affiliation: 1) Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX UK 2) ORCID: 0000-0002-7169-907X Associated publications: Whitley et al., 2021, Nature Communications, https://doi.org/10.15252/embj.201696235

本数据集包含用于分割任务的、表达FtsZ-GFP融合蛋白的活枯草芽孢杆菌（B. subtilis）细胞的训练与测试图像。更多详细信息可查阅该GitHub维基页面。示例展示了表达FtsZ-GFP融合蛋白的活枯草芽孢杆菌细胞的荧光宽场图像，以及手动标注的分割掩码。
数据类型：成对的荧光图像与分割掩码图像
显微数据类型：二维宽场荧光图像
显微镜：定制化100倍倒置显微镜，搭载100倍全内反射荧光（Total Internal Reflection Fluorescence, TIRF）物镜（尼康CFI Apochromat TIRF 100XC 油浸物镜）；图像通过Prime BSI sCMOS相机（Teledyne Photometrics公司）采集
细胞样本：枯草芽孢杆菌菌株SH130，于琼脂糖垫上培养
文件格式：.tiff（8位）或.png（8位）
分割掩码说明：针对CARE/U-Net模型训练采用二值掩码，针对StarDist模型训练采用8位.tiff格式的感兴趣区域（Region of Interest, ROI）映射图，针对pix2pix模型训练采用.png格式图像
图像尺寸：1024×1024像素²，像素大小为65 nm
图像预处理：使用PureDenoise工具对图像进行降噪处理，将所得32位图像按1%与99.98%百分位进行归一化后转换为8位图像；图像标注采用Fiji软件的Labkit插件完成手动标注
作者：Mia Conduit1,2、Séamus Holden1,3
联系邮箱：[e-mail]
所属机构：1) 英国纽卡斯尔大学生物科学研究所细菌细胞生物学中心，邮编NE2 4AX；2) ORCID：0000-0002-7169-907X
相关出版物：Whitley等人，2021年，《Nature Communications》，https://doi.org/10.15252/embj.201696235