.. FlowCal documentation master file, created by Sebastian Castillo-Hair sphinx-quickstart on Mon Dec 7 10:49:16 2015. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. ======= FlowCal ======= ``FlowCal`` is a library for reading, analyzing, and calibrating flow cytometry data in Python. It features: * Extraction of Flow Cytometry Standard (FCS) files into numpy array-like structures * Traditional and non-standard gating, including automatic density-based two-dimensional gating. * Transformation functions that allow conversion of data from raw FCS channel numbers to arbitrary fluorescence units (a.u.). * Plotting, including generation of histograms, density plots and scatter plots. Most importantly, ``FlowCal`` automatically processes calibration beads data in order to convert fluorescence to calibrated units, **Molecules of Equivalent Fluorophore (MEF)**. The most important advantages of using MEF are 1) fluorescence can be reported independently of acquisition settings, and 2) variation in data due to instrument shift is eliminated. Finally, ``FlowCal`` includes a user-fiendly Excel User Interface to perform all of these operations automatically, without the need to write any code. Cite FlowCal ============ If you use ``FlowCal`` in your research, we would appreciate citations to the following article: Castillo-Hair S.M., Sexton J.T., *et al*. `FlowCal: A User-Friendly, Open Source Software Tool for Automatically Converting Flow Cytometry Data from Arbitrary to Calibrated Units. `_. ACS Synth. Biol. 2016. Table of Contents ================= .. toctree:: :maxdepth: 2 getting_started/index.rst fundamentals/index.rst excel_ui/index.rst python_tutorial/index.rst reference/modules.rst contribute/index.rst .. Getting Started .. --------------- .. .. toctree:: .. :maxdepth: 1 .. Download FlowCal! .. installation.rst