/TASBEFlowAnalytics

Flow cytometry unit conversion and analytics

Primary LanguageMATLABOtherNOASSERTION

TASBE Flow Analytics

TASBE Flow Analytics is a flow cytometry analysis package. Documentation, templates, and the Excel user interface are stored in the TASBE Tutorial project and in the TASBE project website.

An introductory tutorial on flow cytometry, calibration, and data interpretation can be found in the iGEM Fluorescence Tutorials.

If you make use of the TASBE Flow Analytics package, please cite the following publication:

  • Jacob Beal, Cassandra Overney, Aaron Adler, Fusun Yaman, Lisa Tiberio, and Meher Samineni. "TASBE Flow Analytics: A Package for Calibrated Flow Cytometry Analysis," ACS Synthetic Biology, 8(7), pp 1524--1529, May 2019

Build status:

Build Status for this project

Build Status for tutorial and templates

Features

  • Runs on both Matlab and Octave, and from Python/Jupyter via oct2py
  • User-friendly Excel interface with run buttons that currently only work on Windows
  • Flow cytometry analysis
  • Plotting and comparison templates for many experiments, including comparative analysis and parametric analysis
  • Output of "point clouds", histograms, and key statistics
  • Unit conversion to ERF from multiple channels
  • Compensation for autofluorescence and spectral overlap
  • Automation-assisted gating
  • Automatic "sanity check" warnings and detailed diagnostic reports
  • Scriptable for high-throughput analysis
  • Distributed under a permissive free and open license

If you make use of the TASBE Flow Analytics package, please cite the following publication:

  • Jacob Beal, Cassandra Overney, Aaron Adler, Fusun Yaman, Lisa Tiberio, and Meher Samineni, "TASBE Flow Analytics: A Package for Calibrated Flow Cytometry Analysis," ACS Synthetic Biology, online May 2019.

Installation

  • Dependencies:

    • If you are using Matlab, TASBE prefers to have the stats package installed (though it can use alternate code)

    • If you are using Octave, TASBE depends on the io package (recommended version 2.4.10)

      • This can typically be installed with octave --no-gui --quiet --eval "pkg install -forge io"

  • Installation on Apple OSX or GNU/Linux using the shell:

    git clone https://github.com/TASBE/TASBEFlowAnalytics.git
cd TASBEFlowAnalytics
make install

    This will add the TASBEFlowAnalyics directory to the Matlab and/or GNU Octave searchpath. If both Matlab and GNU Octave are available on your machine, it will install TASBEFlowAnalyics for both.

  • Installation on Windows (or manual installation on Mac/Linux):

    • Download the package from GitHub

    • Start Matlab or Octave

    • Go to the TASBEFlowAnalytics directory

    • Run the installation command by hand:

      tasbe_set_path(); savepath();

  • Optional: If you want to run the test files, install MOxUnit, and install the tutorial/example package from GitHub in a sibling directory to TASBEFlowAnalytics named TASBEFlowAnalyics-Tutorial.

Usage

In use of this package, you will typically want to split your processing into three stages:

  • Creation of a ColorModel that translates raw FCS to comparable unit data
  • Using a ColorModel for batch processing of experimental data
  • Comparison and plotting of the results of batch processing

Example files are provided in the TASBE Tutorial that show how these stages typically work.