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Updated: Dec 15, 2025
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A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts
Published on: December 1, 2018
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Robust FCS Parsing: Exploring 211,359 Public Files.
Anne E Bras1, Vincent H J van der Velden1
1Laboratory Medical immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
Summary
Robust flow cytometry data analysis requires reliable parsing of Flow Cytometry Standard (FCS) files. This study evaluated 211,359 FCS files, generating testing data to improve FCS parser robustness and benchmark FlowCore software.
Area of Science:
- Biotechnology
- Bioinformatics
- Data Science
Background:
- The Flow Cytometry Standard (FCS) file format ensures data storage standardization and software interoperability.
- Software compliance with the FCS specification is crucial for seamless data exchange in multi-software workflows.
- Non-compliant FCS files are prevalent, necessitating robust parsers capable of handling diverse file structures.
Purpose of the Study:
- To evaluate the readability and conformance of a large set of public FCS files.
- To develop a comprehensive set of testing files for robust FCS parser development.
- To benchmark the FlowCore software's performance and identify areas for improvement.
Main Methods:
- Readability assessment of 211,359 public FCS files.
- Conformance checking against the FCS specification for each file.
- Generation of space-efficient testing files based on validated parse results.
- In-depth benchmarking of FlowCore using original and generated testing files.
Main Results:
- 211,359 public FCS files were evaluated for readability and conformance.
- Validated parse results were obtained for the TEXT segment of each data set.
- Highly space-efficient testing files were generated to aid parser development.
- FlowCore's robustness was enhanced through re-implementation of its TEXT segment parser.
Conclusions:
- The study provides a valuable resource for developing robust FCS parsers.
- An in-depth benchmark of FlowCore software is presented.
- A concrete proposal for improving FlowCore's performance and reliability is offered.
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