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Highlights from
fca 2.2

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fca 2.2

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14 Sep 2005 (Updated )

Flow cytometric analysis GUI.

fca
fca
% 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
%       variables
%   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.
%   Help
%       Html format help can be displayed.
%
%
% University of Debrecen, PET Center/2006
% Author: Laszlo Balkay.
% email: balkay@pet.dote.hu

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