readfcs: Read FCS files#

readfcs is a lightweight open-source Python package that loads data and metadata from Flow Cytometry Standard (FCS) files into DataFrame and AnnData objects, allowing users to flexibly use downstream analytical tools.

With this, it fills a gap among existing FCS readers in the Python ecosystem: These are either part of comprehensive analytical packages (e.g., FlowIO by White21, cytopy by Burton21) that operate on data structures tailored to specific downstream analyses or they do not offer support for AnnData objects [Yurtsev22].

For the main data and metadata functionality, readfcs builds on fcsparser [Yurtsev22]. In addition to FCSParser, readfcs offers compensation, indexing channels by markers, and structuring metadata in AnnData.

readfcs is used by pytometry [Buttner22].


We are grateful to Maren Büttner for valuable discussions.

Author contributions#

Sunny & Alex conceived the project. Sunny developed the software.


Cite the software and this report as:

Sun S & Wolf A (2022). readfcs: Read FCS files. Lamin Blog.


  1. Yurtsev E (2022). FCSParser - a python package for reading fcs files. GitHub.

  2. White S, Quinn J, Enzor J, Staats J, Mosier S M, Almarode J, Denny T N, Weinhold K J, Ferrari G & Chan C (2021). FlowKit: A Python toolkit for integrated manual and automated cytometry analysis workflows. Frontiers in Immunology, 12. GitHub.

  3. Burton R (2021). CytoPy - a cytometry analysis framework for Python. GitHub.

  4. Büttner M, Hempel F, Ryborz T, Theis FJ & Schultze JL (2022). Pytometry: Flow & mass cytometry analytics. bioRxiv. GitHub.