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FCSalyzer Version 0.9.6-alpha
Copyright (C) 2012 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 0.9.6-alpha

This is a bugfix-release. Please note that this is an alpha Version. It probably contains a lot of bugs. It is not guaranteed that documents from earlier versions can be opened.

fixed bugs:
+ gate was not set correctly when copying statistics
+ statistics and annotations were not linked to the plot after loading
+ improved speed of statistics calculations
+ gates were not working with histograms
+ low event count made problems in histograms, in general, tick calculation is not good
+ font size of comments were not saved correctly
+ plots now always start with FCS/SSC
+ shift-click to select a plot did not work
+ parameters that are irrelevant for compensation were removed from the compensation dialog: time, FCS, SSC 
+ printing has been improved

known bugs:
- sometimes: change gate color or changing region name does not work

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Version 0.9.5-alpha

This is an early release with FCS3 support. Please note that this is an alpha Version. It probably contains a lot of bugs. It is not guaranteed that documents from earlier versions can be opened.

new features:
- FCS3 is now supported, including log-transformation and compensation
- other stuff might have changed compared to earlier versions. It has been too long, I can't really remember.

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Version 0.9.4

bug fixes:
+ files can be saved. I have no clue how or when that broke.
+ fixed cursor changes.

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Version 0.9.3

new features:
+ Plots can now be arranged. They can be moved in small steps using the keyboard (CTRL- + arrow keys) or aligned along a border /left, right, top, bottom).
+ Statistics can now be exported to a tab-delimited text file. This can be done in the "File" menu.

bug fixes:
+ histogram and density plots now observe the "coloring according to aplied gate" option
+ density plots show overlay
+ fixed buggy font sizes of plots 
+ fixed color settings of plots after duplication
+ the cursor changes to the wait-cursor when drawing plots with a lot of events

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Version 0.9.2

new features:
+ density graphs
+ overlays: all plots now support overlays. Please use "Format plot/overlay" in the "Plot" menu. 

multiple bug fixes, but I am sure plenty are still around.

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Version 0.9.1

no new features, just bug fixes:
+ gates are updated when region or gate names change
+ histograms are redrawn when regions change
+ marker and quadrant changes are reflected in statistics
+ quadrant labels are correct in statistics
+ labels for histogram y-axis now work for very low event counts

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Version 0.9.0

This is the first version to be released. It allows basic functionality, but also has some known issues.
Give it a try, but don't expect it to replace your regular analysis program (yet).

+ analyses FCS2.0 data files
+ allows dot plots and histograms
+ has regions and gates, quadrants and markers - and associated statistics

- sometimes a file document can't be loaded properly
- changing the data file and other things might not be reflected immediately in the respective plots

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This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program (License.txt).  If not, see <http://www.gnu.org/licenses/>.
Source: Readme.txt, updated 2016-03-04