Single cell annotations in 3D bacterial biofilms of Vibrio cholerae

This repository contains the data to reproduce the study `Single-cell segmentation in bacterial biofilms with optimized convolutional neural networks enables tracking of cell lineages and measurements of growth rates` by Jelli, Ohmura, Netter, et al. It contains the following four subfolders: - `training-data-from-experimentally-acquired-images`: the dataset that was created to train segmentation models<br> - `trained-models`: contains five models trained on the trainind dataset to be used for predictions<br> - `segmentation-predictions-for-different-species`: segmentations based on a trained model on biofilms of different species<br> - `training-data-synthetic`: Synthetic microscope images and their corresponding label images together with scripts to create the data本仓库包含用于复现Jelli、Ohmura、Netter等作者的研究《基于优化卷积神经网络（convolutional neural networks）的细菌生物膜单细胞分割可实现细胞谱系追踪与生长速率测量》的相关数据。该仓库包含以下四个子文件夹： - `实验采集图像训练数据集（training-data-from-experimentally-acquired-images）`：专为训练分割模型构建的数据集 - `已训练模型（trained-models）`：包含5个基于上述训练数据集训练得到、可用于预测任务的模型 - `不同物种生物膜分割预测结果（segmentation-predictions-for-different-species）`：基于已训练模型对不同物种生物膜生成的分割结果 - `合成训练数据集（training-data-synthetic）`：包含合成显微镜图像、对应的标签图像以及用于生成该数据的脚本文件