Flow Cytometry GUI for Matlab

This GUI was built in order to make Flow Cytometry data analyses in Matlab – gating, statistics etc.

Elaborate documentation can be found in the 'FCGUI_help.pdf' file.
Some of its functionalities:
* Present scatter plot (+density color map) or histograms (+values of statistical measures), of FC data and of gates, X and Y axis selection among the different parameters that were collected, linear or logarithmic display, and option to export the plot to a separate Matlab figure
* Move between FC files keeping the same display setting
* Gating in different methods: manually – draw a shape on the plot, automatically – select # cells from a center (circle, or according to the density of cells in plot), quadrants, thresholds on histogram plot, and logical operations on the created gates
* Saving the data of cells included in a gate, or the gate coordinates, into .mat files, and load it on a different FC data file
* Make calculations on the collected parameters for each cell (e.g. normalize fluorescence to SSC)
* Make a multiplot figure of scatter plots or histograms, of a few FC data files.
This GUI was built with the aid of the 'GUI layout toolbox' (file exchange submission, see link below), and it is required for its functionality, download it and run the 'install.m' file there.
This submission includes the following file exchange submissions: 'Fast points-in-polygon test' by Darren Engwirda, ' Distance from a point to polygon' by Alejandro Weinstein, 'Subaxis - Subplot' by Aslak Grinsted, see links below.
Please, help to improve it:
1. Report any bug or inconvenience you experience.
2. Make suggestions on how to improve it.
3. Modify the code and share what you changed.
Some open issues:
1. Logicle (biexponential) display is missing. An implementation of the logicle transformation in Matlab is needed (see Parks et al. 2006, and Moore and Parks 2012 papers).
2. 'Fast points-in-polygon test' by Darren Engwirda, was found to be faster here in the .mex file version (see '2D polygon interior detection' by Bruno Luong). It was not included here to simplify installation and compatibility issues (see remark in help file section 1 for how to use it here).

Nitai Steinberg
At Prof. Yitzhak Pilpel Lab,
Molecular Genetics Department
The Weizmann Institute of Science