Keikhosravi Adib, Almansour Faisal, Bohrer Christopher H, Fursova Nadezda A, Guin Krishnendu, Sood Varun, Misteli Tom, Larson Daniel R, Pegoraro Gianluca
High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
Sci Rep. 2024 Aug 8;14(1):18426. doi: 10.1038/s41598-024-66600-1.
High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software programs for image analysis workflows typically do not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, nucleus registration, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new analysis modules for existing analysis pipelines and to adding new analysis modules. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI software platform for a variety of cell biology applications.
高通量成像（HTI）通过大量实验扰动生成复杂的成像数据集。用于图像分析工作流程的商业HTI软件程序通常不允许在分析模块中进行完全定制和采用新的图像处理算法。虽然开源HTI分析平台在工作流程中提供了诸如细胞核分割、斑点检测或细胞追踪等单个模块，但它们在集成新的分析模块或算法方面往往受到限制。在此，我们引入高通量图像处理软件（HiTIPS）以扩展现有HTI分析能力的范围和定制性。HiTIPS整合了先进的图像处理和机器学习算法，用于自动细胞和细胞核分割、斑点信号检测、细胞核追踪、细胞核配准、斑点追踪以及斑点信号强度定量。此外，HiTIPS具有图形用户界面，可用于为现有分析流程集成新的分析模块以及添加新的分析模块。为证明HiTIPS的实用性，我们展示了高通量DNA荧光原位杂交（FISH）、免疫荧光（IF）以及单细胞转录活细胞成像的三个图像分析工作流程示例。总之，我们证明HiTIPS是一个适用于多种细胞生物学应用的用户友好、灵活且开源的HTI软件平台。
