Nahami Avichay, Kain Dor, Cohen Yonatan, Kolodkin-Gal Yuval, Assouline Yohanan, Yona Avihu H, Kolodkin-Gal Ilana, Dorfan Yuval
Faculty of Electrical and Electronics Engineering, HIT-Holon Institute of Technology, Holon 5810201, Israel.
Scojen Institute for Synthetic Biology, Dina Recanati School of Medicine, Reichman University, Herzliya 4610101, Israel.
Microorganisms. 2025 Aug 13;13(8):1889. doi: 10.3390/microorganisms13081889.
Researchers traditionally calculate growth rates using the natural logarithm of optical density (OD), with existing script packages facilitating this process. Automatic plate readers, capable of simultaneously measuring OD across 384 cultures, significantly enhance data collection efficiency. Furthermore, these readers also measure luminescence and fluorescence, providing valuable insights into gene expression. However, current analysis software often struggle with data generated by robotic systems measuring multiple plates, limiting the integration of growth and reporter analyses. This method paper addresses three key challenges: (a) the incompatibility of robotic multi-plate systems with existing analysis software, (b) the integration of growth and reporter analyses, and (c) the development of user-friendly interfaces for non-programmers. To address these challenges, we offer optimized script packages and a relevant case study on matrix expression in response to antibiotics. Our platform facilitates the efficient and integrated analysis of multi-plate growth and reporter data.
传统上，研究人员使用光密度（OD）的自然对数来计算生长速率，现有的脚本包有助于这一过程。能够同时测量384种培养物OD的自动酶标仪显著提高了数据收集效率。此外，这些酶标仪还能测量发光和荧光，为基因表达提供有价值的见解。然而，当前的分析软件常常难以处理由测量多个平板的机器人系统生成的数据，限制了生长分析和报告基因分析的整合。本方法论文解决了三个关键挑战：（a）机器人多平板系统与现有分析软件的不兼容性，（b）生长分析和报告基因分析的整合，以及（c）为非程序员开发用户友好的界面。为应对这些挑战，我们提供了优化的脚本包以及一个关于抗生素响应下基质表达的相关案例研究。我们的平台有助于对多平板生长和报告基因数据进行高效且综合的分析。
