FCSalyzer Files

FCSalyzer Version 0.9.22-alpha
Copyright (C) 2012-2021 Sven Mostböck
http://sourceforge.net/projects/FCSalyzer

FCSalyzer is a simple application for analysing flow cytometry data. It is based on the "What you see is what you get" principle and I hope it is intuitive to use. For more information, please visit the project web page at http://sourceforge.net/projects/FCSalyzer. FCSalyzer is a Java-based application, so you need to install Java (Version 7 or higher). To start, double-click the JAR file.

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Version 0.9.22-alpha

This version has only one bug fix:
- fixed a bug that prevented compensation in version 0.9.21-alpha

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Version 0.9.21-alpha

This version only introduces and "alternative" JAR that uses a different dialog when loading/saving files. For major feature changes, see version 0.9.19-alpha.

GUI:
+ There is now an additional "FCSalyzer_alternative.jar" provided. The only difference between the two FCSalyzer JARs is the dialog used when the user opens or saves files. "FCSalyzer.JAR" uses a dialog provided by JAVA. However, I got reports that this JAVA-internal dialog might not work on some systems (the reported system was MacOS using Japanese as system language). This JAR requires Java version 6 or higher. "FCSalyzer_alternative.JAR" uses a system-provided dialog. This JAR requires Java version 7 or higher. Please see Exporting Data for an important usage difference in this version. Users can simply try both versions and see, which works better for them. All other aspects are identical, so all FCX analysis documents can be opened and edited with either version.

Improvements:
+ FCX documents can now be provided as command line arguments to be opened by FCSalyzer during startup. Maybe useful for some users.

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Version 0.9.20-alpha

This is mainly a maintenance release for bugs that I missed in version 0.9.19-alpha. For major feature changes, see version 0.9.19-alpha.

Improvement:
+ Gates can now be re-arranged in the gate list, thus changing which gate is drawn on top.

Bug fixes:
+ Bug fixed with gate definition, that led to circular references freezing the program
+ many other smaller bugs from

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Version 0.9.19-alpha

New Features:
+ Plots and Documents can now be exported in SVG format
+ Batch operations are now possible: when epxorting plots or documents, a list of FCS files can be selected, and the export happens for each of the files.
+ A step size can now be specified that defines the distance of FCS files when using "Previous/Next datafile" on selected plot(s). The default is "1", meaning that the next datafile in the directory list is used.
+ New data can be attached as additional parameters to existing FCS data files. The data can be imported from CSV text files. All attached parameter values are stored in a combined file that carries the extension ".FCXA", separate from the FCX document. Data can be numerical, or categorical. Details on importing data is found in the "Attach Parameters" dialog. ------>>>>> This is a very new feature and there are probably some bugs - please test carefully if the results match your expectations!

Improvement:
+ Each open FCX document is now shown in an independent top window, instead of all open FCS document being contained in one single top window.
+ The calculation of compensation was changed. In previous versions, the Compensation Matrix was entered and used for calculation. However, usually the Spillover Matrix is entered and the Compensation Matrix is then calculated based on the Spillover Matrix (see http://www.bioinformin.net/cytometry/compensation.php). The earlier behaviour of FCSalyzer also introduced a bug when reading the spillover matrix from an FCS file, as the matrix was then treated like a compensation matrix (my apologies for that mistake; errors like that are the reason why FCSalyzer continues to be in alpha status). With this version 0.9.19, matrixes are treated as spillover matrix. ------>>>>> This means that 0.9.19 calculates compensation different than earlier version. Be careful when opening old FCX files, as the data might change if compensation was used. As this is a new feature there are probably some bugs - please test carefully if the results match your expectations!
+ Regions can now be deleted in the "Regions/Gate" dialog
+ The Rainbow-color map is now the default for density graphs

Bug fixes:
+ Spillover matrix was interpreted correctly for compensation calculations (see above).
+ The compensation dialog had a few bugs
+ The Font Sizes were not applied correctly. In general, font sizes larger than 12 were shown too small. This has been repaired. ------>>>>> When opening FCX documents prepared in earlier FCSalyzer version, the text might be shown in slightly different font sizes.
+ Fixed a bug when opening large FCS3 files
+ multiple minor bugs

Side-effects:
+ The shortcuts for "Next/Previous datafile" had to be changed to using "Shift-Page Down" and "Shift-Page Up".
+ FCX documents generated in earlier versions might look different now, with changed font sizes (see above)
+ FCS documents generated in earlier version might calculate and display data differently, if compensation was used (see above).