Laboratory Medical immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
Cytometry A. 2020 Nov;97(11):1180-1186. doi: 10.1002/cyto.a.24187. Epub 2020 Jul 15.
When it comes to data storage, the field of flow cytometry is fairly standardized, thanks to the flow cytometry standard (FCS) file format. The structure of FCS files is described in the FCS specification. Software that strictly complies with the FCS specification is guaranteed to be interoperable (in terms of exchange via FCS files). Nowadays, software interoperability is crucial for eco system, as FCS files are frequently shared, and workflows rely on more than one piece of software (e.g., acquisition and analysis software). Ideally, software developers strictly follow the FCS specification. Unfortunately, this is not always the case, which resulted in various nonconformant FCS files being generated over time. Therefore, robust FCS parsers must be developed, which can handle a wide variety of nonconformant FCS files, from different resources. Development of robust FCS parsers would greatly benefit from a fully fledged set of testing files. In this study, readability of 211,359 public FCS files was evaluated. Each FCS file was checked for conformance with the FCS specification. For each data set, within each FCS file, validated parse results were obtained for the TEXT segment. Highly space efficient testing files were generated. FlowCore was benchmarked in depth, by using the validated parse results, the generated testing files, and the original FCS files. Robustness of FlowCore (as measured by testing against 211,359 files) was improved by re-implementing the TEXT segment parser. Altogether, this study provides a comprehensive resource for FCS parser development, an in-depth benchmark of FlowCore, and a concrete proposal for improving FlowCore. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC on behalf of International Society for Advancement of Cytometry.
当涉及到数据存储时，由于流式细胞术标准 (FCS) 文件格式，流式细胞术领域相当标准化。FCS 文件的结构在 FCS 规范中进行了描述。严格遵守 FCS 规范的软件保证具有互操作性（通过 FCS 文件进行交换）。如今，软件互操作性对于生态系统至关重要，因为 FCS 文件经常被共享，并且工作流程依赖于不止一个软件（例如，采集和分析软件）。理想情况下，软件开发人员严格遵循 FCS 规范。不幸的是，情况并非总是如此，这导致随着时间的推移生成了各种不符合规范的 FCS 文件。因此，必须开发强大的 FCS 解析器，这些解析器可以处理来自不同资源的各种不符合规范的 FCS 文件。强大的 FCS 解析器的开发将极大地受益于全面的测试文件集。在这项研究中，评估了 211,359 个公共 FCS 文件的可读性。每个 FCS 文件都检查其是否符合 FCS 规范。对于每个数据集，在每个 FCS 文件中，都为 TEXT 段获得了经过验证的解析结果。生成了高效利用空间的测试文件。通过使用经过验证的解析结果、生成的测试文件和原始 FCS 文件，对 FlowCore 进行了深入的基准测试。通过重新实现 TEXT 段解析器，提高了 FlowCore 的稳健性（通过针对 211,359 个文件进行测试来衡量）。总的来说，这项研究为 FCS 解析器的开发提供了全面的资源，对 FlowCore 进行了深入的基准测试，并提出了改进 FlowCore 的具体建议。2020 年作者。流式细胞术发表由 Wiley 期刊代表国际细胞分析协会出版。
