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Flow Cytometry GUI for Matlab

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Flow Cytometry GUI for Matlab

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10 Sep 2012 (Updated )

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

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Description

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

Acknowledgements

Subaxis Subplot, Fast Points In Polygon Test, Distance From A Point To Polygon, Gui Layout Toolbox, and 2 D Polygon Interior Detection inspired this file.

Required Products Image Processing Toolbox
Statistics Toolbox
MATLAB
MATLAB release MATLAB 7.11 (R2010b)
Other requirements This GUI was built with the aid of the 'GUI layout toolbox' (file exchange submission, see link above), and it is required for its functionality, download it and run the 'install.m' file there.
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Comments and Ratings (4)
24 Nov 2013 Nitai Steinberg

Dear Joakim Sandstedt,
Thank you for your comment, I am happy you use this software and like it.
About the error message you encounter, it looks like it relates to the "GUI Layout Toolbox" I used to build this GUI (http://www.mathworks.com/matlabcentral/fileexchange/27758-gui-layout-toolbox).
I don't know what cause this specific error, but if I have to guess, it might be related to the Matlab version that you use.
Do you encounter problems in changing the window size? or is it just this error that appears in the beginning and that's it?
If you want you can address the people that wrote the toolbox and describe what you experience. I am sorry but I am not familiar with their code, I just used it, so I can't help you more than this...
In any case I hope you can still work with this software, and please tell me about any other problem you encounter, and I hope I could be more helpful :)
Good luck,
Nitai

21 Nov 2013 Joakim Sandstedt

Dear Nitai Steinberg!

Thank you for an excellent application for analysis of FACS data which I also plan to use for quantification of immunocytochemistry data obtained from CellProfiler. I'm quite new to the Matlab script language, but I noticed when I started the program the following error message:
"
Error using set
Values must be finite and non-NaN

Error in uiextras.Container/repositionChild (line 376)
set( child, propname, position );

Error in uiextras.VBox/redraw (line 88)
obj.repositionChild( child, newPosition );

Error in uiextras.Container/onResized (line 326)
obj.redraw();

Error in uiextras.Container>@(varargin)obj.onResized(varargin{:}) (line 90)
obj.Listeners{end+1,1} = handle.listener( containerObj, findprop(
containerObj, 'PixelBounds' ), 'PropertyPostSet', @obj.onResized );
"

The application seems to be working correctly, so this might not be anything of importance. Thanks again for a very nice application.

Kind regards

Joakim Sandstedt M.D., PhD student

Department of Clinical Chemistry and Transfusion Medicine,
Institute of Biomedicine, The Sahlgrenska Academy

02 Apr 2013 Nitai Steinberg

Hi Nicole,
Thank you very much for the feedback, it is very important to me.
About the issues you raised:
- I also have Windows machine, and I didn't experienced these problems. I used "\" and not "/" as far as I noticed... (at least in 'private\rorchach.mat' I used "\" and I tried to look for "/" in the file and saw it only in divisions). But please tell me if I am mistaken.
- As for the implementation of the logicle display, I need help, I am not sure I know how to do it efficiently.
- I didn't experience the issue with the little log scale tick marks in 2D plots... If you could tell me exactly which settings you used, or even send me a screenshot it would be helpful.
- About multiple plot of the same file using different X and Y axes for each plot, there is no such option for now. I need to think about it, another person raised a similar issue regarding the multiple plots. I created it for my own use, but I understand that there are many things I didn't think about. Maybe I could try to change it in future version...
Thanks again for your feedback!
Nitai

27 Mar 2013 Nicole

This is an excellent flow cytometry toolkit/gui for matlab. What I like most about this plug-in is the fact that I don't have to be a matlab master to use it. I hope you continue to develop it since it has a lot of potential.

Bugs:
- There are some path issues in using this plugin on a Windows installation of matlab involving \ vs /. Once repaired, the software works as advertised. (I fixed it awhile ago on my copy, so I fear I've forgotten which files are affected. But at the very least, do a search for "private/rorschach.mat" in FCGUImain.m and change to "private\rorschach.mat" if you have a Windows machine. I seem to remember at least one other file needs a similarly trivial change.)

Feature Requests:
- As you said in "open issues," implementing a logicile/biexponential display would be very beneficial.
- When I try to make a multiple plot figure of 2D histograms, and set them to have the same x/y scale (i.e. 1:1), the little log scale tick marks don't follow suit. I end up deleting them by hand.
- While I can clearly see how to make a multiple plot of several different files, using the same dyes for their x and y axes, I don't see how to make a multiplot of the same file using different dyes for the x and y axes.

Thank you for your hard work on this plug in.

Updates
11 Sep 2012

There was a mistake in the 'inpoly' version I put in the .zip folder, now it is the correct form.

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