mAIcrobe validation datasets
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mAIcrobe dataset collection — Overview This repository aggregates several bacterial microscopy datasets used for cell-cycle analysis, morphometrics, and deep-learning segmentation. Used in mAIcrobe https://maicrobe.henriqueslab.org https://github.com/HenriquesLab/mAIcrobe Folder map All folder contain a README.md with details on the dataset, acquisition, and references. JE2_WT SIM images of Staphylococcus aureus JE2 WT (membrane + DNA channels) LCML1_LCML262 SIM images of CRISPRi dnaA knockdown (LCML1) and control (LCML262) StarDist_Saureus Training and test data for StarDist segmentation on S. aureus SIM images UNetSPneumo Training and test data for U-Net segmentation on Streptococcus pneumoniae phase-contrast images JE2_WT 31 fields of view (FOVs) of S. aureus JE2 WT imaged by structured illumination microscopy (SIM). Channels: membrane (NileRed) and DNA (Hoechst 33342). Dataset used to validate eHooke’s cell-cycle model; repurposed to validate morphometrics in mAIcrobe. Reference: Saraiva BM, Krippahl L, Filipe SR, Henriques R, Pinho MG. Biological Imaging. 2021;1:e3. doi:10.1017/S2633903X21000027. LCML1_LCML262 Scope: Two S. aureus datasets, membrane-labelled and imaged by SIM. LCML1: CRISPRi-mediated knockdown of dnaA. LCML262: Control strain with dCas9 and markers but no sgRNA. Each dataset contains 5 FOVs. Reference (strain resource): Reed P et al. 2024. mBio 15:e02773-23. https://doi.org/10.1128/mbio.02773-23 StarDist_Saureus Goal: Data for training/testing StarDist instance segmentation on S. aureus SIM membrane images (used in mAIcrobe). Training set: Conditions: WT JE2 (10 FOVs) and WT JE2 + PC190723 (12 FOVs; FtsZ inhibitor causing enlarged bacteria). Contents: Fluorescence images + corresponding instance masks (Labels match image filenames per subset). Test set: Condition: LCML262 (3 FOVs). Contents: Images + instance masks. References: Ferreira MG et al. (ReScale4DL) bioRxiv, 2025. https://doi.org/10.1101/2025.04.09.647871 Reed P et al. mBio, 2024. https://doi.org/10.1128/mbio.02773-23 UNetSPneumo Goal: Data for training/testing a U‑Net model on phase-contrast images of Streptococcus pneumoniae (Pen6; PenR, unencapsulated; mosaic pbp alleles). Trained with ZeroCostDL4Mic. Size (from README): 16 FOVs for training 3 FOVs for testing Structure (with filename parity between images and masks): Train/Phase Train/Labels Test/Phase Test/Labels Citations Saraiva BM, Krippahl L, Filipe SR, Henriques R, Pinho MG. eHooke: Automated image analysis of spherical bacteria. Biological Imaging. 2021;1:e3. doi:10.1017/S2633903X21000027 Reed P, Sorg M, Alwardt D, Serra L, Veiga H, Schäper S, Pinho MG. 2024. A CRISPRi-based genetic resource to study essential Staphylococcus aureus genes. mBio 15:e02773-23. https://doi.org/10.1128/mbio.02773-23 Ferreira MG, Saraiva BM, Brito AD, Pinho MG, Henriques R, Gómez-de-Mariscal E. ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation. bioRxiv, 2025. https://doi.org/10.1101/2025.04.09.647871
mAIcrobe数据集合集——概览 本仓库整合了多个用于细胞周期分析、形态计量学以及深度学习分割的细菌显微镜数据集，为mAIcrobe工具所使用。 https://maicrobe.henriqueslab.org https://github.com/HenriquesLab/mAIcrobe ## 文件夹结构 所有文件夹均包含README.md文件，详述数据集相关信息、采集方式及参考文献。 ### JE2_WT 金黄色葡萄球菌JE2野生型的结构照明显微镜（Structured Illumination Microscopy, SIM）图像（包含膜通道与DNA通道） ### LCML1_LCML262 CRISPRi介导dnaA基因敲低（LCML1）及对照（LCML262）的结构照明显微镜图像 ### StarDist_Saureus 用于金黄色葡萄球菌SIM图像StarDist实例分割的训练与测试数据集 ### UNetSPneumo 用于肺炎链球菌相差图像U-Net分割的训练与测试数据集 --- ### JE2_WT 本数据集包含31个视场（FOVs）的金黄色葡萄球菌JE2野生型结构照明显微镜图像。 成像通道：膜染色通道（使用尼罗红（NileRed）染色）与DNA染色通道（使用Hoechst 33342染色）。 该数据集曾用于验证eHooke细胞周期模型，后被重新用于验证mAIcrobe的形态计量学功能。 参考文献：Saraiva BM, Krippahl L, Filipe SR, Henriques R, Pinho MG. eHooke: Automated image analysis of spherical bacteria. *Biological Imaging*. 2021;1:e3. doi:10.1017/S2633903X21000027. --- ### LCML1_LCML262 数据集概况：包含两个金黄色葡萄球菌数据集，均经膜染色后通过结构照明显微镜（SIM）采集。 LCML1：通过CRISPR干扰（CRISPR interference, CRISPRi）技术介导dnaA基因敲低的菌株。 LCML262：仅表达dCas9及标记基因、不含向导RNA（single guide RNA, sgRNA）的对照菌株。 每个数据集包含5个视场。 参考文献（菌株资源）：Reed P等. 2024. *mBio* 15:e02773-23. https://doi.org/10.1128/mbio.02773-23 --- ### StarDist_Saureus 数据集用途：用于训练与测试金黄色葡萄球菌SIM膜染色图像的StarDist实例分割模型，为mAIcrobe工具所使用。 #### 训练集 样本条件：JE2野生型（10个视场），以及添加FtsZ抑制剂PC190723的JE2野生型（12个视场，该抑制剂可导致细菌体积增大）。 数据集内容：荧光图像及对应的实例掩码（各子集内掩码标签与图像文件名一一对应）。 #### 测试集 样本条件：LCML262菌株（3个视场）。 数据集内容：图像及实例掩码。 参考文献： 1. Ferreira MG等（ReScale4DL）. bioRxiv, 2025. https://doi.org/10.1101/2025.04.09.647871 2. Reed P等. *mBio*, 2024. https://doi.org/10.1128/mbio.02773-23 --- ### UNetSPneumo 数据集用途：用于训练与测试针对肺炎链球菌（Pen6菌株，青霉素抗性、无荚膜、携带嵌合pbp等位基因）相差图像的U-Net模型，训练流程基于零成本深度学习显微工具（ZeroCostDL4Mic）。 数据集规模（来自README文件）： - 训练集：16个视场 - 测试集：3个视场 文件夹结构（图像与掩码文件名一一对应）： `Train/Phase`、`Train/Labels`、`Test/Phase`、`Test/Labels` --- ## 参考文献 1. Saraiva BM, Krippahl L, Filipe SR, Henriques R, Pinho MG. eHooke: Automated image analysis of spherical bacteria. *Biological Imaging*. 2021;1:e3. doi:10.1017/S2633903X21000027 2. Reed P, Sorg M, Alwardt D, Serra L, Veiga H, Schäper S, Pinho MG. 2024. A CRISPRi-based genetic resource to study essential Staphylococcus aureus genes. *mBio* 15:e02773-23. https://doi.org/10.1128/mbio.02773-23 3. Ferreira MG, Saraiva BM, Brito AD, Pinho MG, Henriques R, Gómez-de-Mariscal E. ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation. bioRxiv, 2025. https://doi.org/10.1101/2025.04.09.647871
