CAFE (Cell Analyzer for Flow Experiment)

CAFE is an open-source, free, no-code, web-app platform for high-dimensional spectral flow cytometry data (SFCM) analysis. CAFE has been developed in Python and it can run seamlessly on regular computers operating on either Windows or macOS/Linux. The application will allow the analysis and visualization of SFCM data to produce high-resolution publication-ready figures that support reproducible research of immune cell populations.

Example data for testing available at FigShare: 01. Downsampled-CSV 02. Processed-H5AD

Update: CAFE is now accepted for publication in Bioinformatics

Md Hasanul Banna Siam, Md Akkas Ali, Donald Vardaman, Satwik Acharyya, Mallikarjun Patil, Daniel J Tyrrell, CAFE: An Integrated Web App for High-Dimensional Analysis and Visualization in Spectral Flow Cytometry, Bioinformatics, 2025;, btaf176, https://doi.org/10.1093/bioinformatics/btaf176

Documentation

Click here to access the guide for installation and running CAFE

CAFE Interface

How to Download CAFE

Step 1: Download the tool as a ZIP file

1. Click the Releases button on the right side of this page.
2. Locate the latest release
3. Select CAFE_version.zip file to download.

Step 2: Extract the ZIP File & Install the tool

1. Extract the files
2. Navigate to the " ./CAFE " folder path where you will find the following files: cafe.py, pixi.toml, cafe.yaml etc.
3. Then, follow the instructions below to run the tool using Pixi or Conda.

Quick Installation

Using Pixi Package Manager

For Mac/Linux
Run the following command to install Pixi for Mac/Linux:

curl -fsSL https://pixi.sh/install.sh | PIXI_VERSION=v0.34.0 bash

For Windows,
(1) first run the following code:

iwr -useb https://pixi.sh/install.ps1 | iex

(2) Then run the code below to restore Pixi to a specific version:

pixi self-update --version 0.34.0

Run CAFE

# Open terminal app (or Windows Powershell)

# Navigate to the directory where your CAFE tool’s file (pixi.toml) is present.
cd ./path/to/cafe

# Run the tool with pixi
pixi run cafe

Workflow

Known Issues

Windows OS has known issues with Scanpy and thus generates a higher number of clusters with a given Leiden resolution value. A numpy conflict may provide a value error message, ignore the warning. For optimal performance, consider using WSL to download the CAFE folder from Github using git clone and run the app using Pixi.

git clone https://github.com/mhbsiam/cafe.git

Here is a tutorial on how to install and activate WSL on a Windows computer. Finally, while reporting data generated using CAFE, mentioning the operating system used for data generation is highly recommended for replicability.

Citation

If you use CAFE in your research, please cite our paper:

Md Hasanul Banna Siam, Md Akkas Ali, Donald Vardaman, Satwik Acharyya, Mallikarjun Patil, Daniel J Tyrrell, CAFE: An Integrated Web App for High-Dimensional Analysis and Visualization in Spectral Flow Cytometry, Bioinformatics, 2025;, btaf176, https://doi.org/10.1093/bioinformatics/btaf176

Donald Vardaman, Md Akkas Ali, Md Hasanul Banna Siam, Chase Bolding, Harrison Tidwell, Holly R. Stephens, Mallikarjun Patil, and Daniel J. Tyrrell. "Development of a Spectral Flow Cytometry Analysis Pipeline for High-Dimensional Immune Cell Characterization." The Journal of Immunology (2024). https://doi.org/10.4049/jimmunol.2400370.