Code covered by the BSD License
Laszlo Balkay (view profile)
14 Sep 2005
26 May 2006)
Flow cytometric analysis GUI.
% fca - flow cytometric analysis
% This Matlab GUI enables you to perform evaluation on FCS format
% data files measured by flow cytometry. The following features are
% included (version 2.2):
% - reading FCS 2.0 and FCS 3.0 list mode (LM) file format. The user can
% multiselect more LM files in the "Open LM File" dialog box defining a set
% of LM files to be evaluate.
% - lineplot, dotplot and 3Dplot can be defined with easy way by a special GUI
% 1. To define lineplot you should select the desired LM parameter by left
% click and define it as lineplot by right click
% 2. To define dotplot or 3Dplot you should select the desired LM parameters
% by left click WITH pressing the CTRL key down and define them as dotplot
% or 3Dplot by right click
% 3. To delete a lineplot, dotplot or 3Dplot you should select the desired plot
% by left click and remove by right click
% /For more info, press the Help button on the HistogramSetup window/
% - ROIs can be drawn on the dotplots to define filtered population. Use normal
% (left)button clicks to add vertices to the polygon and right-click to close the
% vertex. If more ROI you have at different dotplot, the intersection will be
% determined of the events. Only the filtered events will be displayed
% on lineplots and they will have red color in dotplot figures.
% - defined ROIs can be moved by mouse dragging
% - the mean and the stdev parameters are always displayed in all lineplot
% - the setup of histograms (definition of lineplots, dotplots, ROIs)
% can be saved and reloaded for later processing
% - pressing the “result2xls” or “Hdr2xls” buttons on main window, statistical
% results (mean, stdev) can be saved directly to an Excel sheet
% including optional header line. The current excel sheet can be defined by
% the "Select excel File for Results" menu item or it is generated automatically
% under the directory where the opened LM files exist. In the second case the
% name of the excel sheet will be given for the next way: fca_'LMmainname'.xls,
% where 'LMmainname' means the filename of the currently opened LM file without
% extension. The program writes the results to the worksheet named 'results'.
% - using the “Export2xls” button on the LinePlot window, the user can
% export the histogram data (X,Y coordinates) of a lineplot to Excel
% file for creating custom plots with different lineplots. The naming convention
% of the Excel file is same as above, but the worksheet name will be
% different: 'LMfilname_8dot3format'+'PARname', where 'PARname' is the LM parameter
% name of the current lineplot, and 'LMfilname_8dot3_format' is the short version
% (old DOS 8.3 format) of the opened LM file name.
% - the scale of the Y axis of the lineplots can be changed by double clicking
% on the Y scale
% - pressing the “Export2hist” button on the LinePlot window, the line plots
% can be saved directly to FCS Histogram (single parameter binary) file.
% This might be useful option if the user wants to perform cell cycle analysis
% with the Cylchred.exe(Cardiff University) program.
% - the user can navigate across the current set of LM files using the "Previous LM"
% and "Next LM" buttons, enabling an efficient way to evaluate the next(previous)
% LM file.
% On the main window the buttons have "ToolTip String" describing the purpose of the
% given button. Some menu item are defined helping the work with FCA. The next
% section gives a short description of the Menu Items:
% File | Open FCS file
% LM file or a set of LM files can be select using a standard dialog box. The
% user can select multiple files by holding down the Shift or Ctrl key
% and clicking on a file.
% File | Show FCS hdr
% Selecting this item the most important LM header info can be displayed. This
% is a special matlab structure, which also contains the whole data part
% of the LM file.
% File | Close FCS file
% The current LM file can be closed along with deleting the all histograms and
% File | Save FCS as txt
% The LM data can be saved as tab separated txt file. If ROIs are defined on
% histograms only the filtered events will be selected for saving.
% File | Exit
% Quit the "fca" program.
% Excel options | Select Excel File for Results
% Defining an Excel file for the results the user should activate this item.
% New or existing excel file can be selected both. If the user select
% an existing file the program will prompt a warning as "Do you want
% to replace it?", but it does mean to delete the previous one. The program just
% read the name of the file.
% Excel options | Open Current Excel File
% During the data evaluation the current excel file should be closed
% enabling the Matlab to write the data to the xls file. To check the
% content of the xls file the user can select this menu item, the
% program will open the excel file. The user have to close the xls file
% again before continue the data evaluation.
% /hint: the current excel file can be also opened by selecting and right
% clicking on the "Current excel file name" edit box./
% Excel options | Set Current Excel Row
% The first 'active' row in the current excel file can be displayed or
% redefined selecting this menu item. This is "row number" where the
% next data will be written when the user press the "Result2xls" or
% "Hdr2xls" button.
% Html format help can be displayed.
% University of Debrecen, PET Center/2006
% Author: Laszlo Balkay.
% email: firstname.lastname@example.org
Published with MATLAB® 7.0.4