Extract text from flow cytometry files (FCS)
To convert FCS cytometry files to another format, you need FlowJo or other Data software.
To convert other file formats to the "Scientific Data File" file type, you need software like FlowJo or a similar tool.
The .FCS file format is the global standard for storing list-mode data generated by flow cytometry instruments. These binary files contain complex, high-dimensional matrices detailing the physical and chemical characteristics of millions of individual cells or particles, alongside critical metadata regarding the instrument's laser configuration and optical filters. The format is managed by the International Society for Advancement of Cytometry and is widely supported by dedicated analytical software like FlowJo and FCS Express.
The main disadvantage of the .FCS format is its rigid reliance on specialized, proprietary software. Viewing or analyzing the raw data requires expensive licenses that often cost hundreds or thousands of dollars annually. Furthermore, .FCS files are entirely unreadable by standard office applications or web browsers, making it extremely difficult to share preliminary results with non-specialist collaborators or data scientists. The binary structure also means that simple data extraction tasks require specific programmatic libraries in R or Python.
To bypass these limitations, convert your .FCS files to accessible text-based formats. For data modeling, spreadsheet review, or sharing, convert .FCS to CSV or TXT. Keep in mind that converting to raw text will strip out workspace gating hierarchies and compensation matrices.
*(Note: In very rare cases, a .FCS file may be a Save State created by the FCEUX NES emulator, or an obsolete spreadsheet from the 1980s software First Choice.)*
Convert.Guru analyzes your FCS file, detects the exact format, and lets you read the text inside.
Users also converted FSC, ZIP, FSC SEARCH, CSV, FCA, FCSTD, CFS, CZI, PDF, 002, JPG, XLSX and IPYNB files.
If you want to convert FCS file to CSV, JSON, XML, YAML, YML, TOML, INI, CFG, CONF, DAT, DB or SQL, you can use FlowJo or similar software from the "Flow Cytometry Data Storage" category. In the File menu, look for Save As… or Export….
To convert DBF, XML, SQLITE, XLSX, SQL, TSV, ACCDB, YAML, MDB, CSV, ODS or JSON files to FCS, try FlowJo or another comparable tool in the "Flow Cytometry Data Storage" category.
The history of Convert.Guru began over 25 years ago in California with Tom Simondi’s file-format database. A former contributor to Space Shuttle development and a software pioneer of the 1980s, Simondi established a trusted resource for file type analysis that was even referenced by Microsoft Windows XP. Today, we use modern technology to process and convert thousands of file formats while continually improving our FCS converter.