diff --git a/GUI/createImages/shiftCBar_BarInFig.m b/GUI/createImages/shiftCBar_BarInFig.m
index 8068166..8c5f507 100644
--- a/GUI/createImages/shiftCBar_BarInFig.m
+++ b/GUI/createImages/shiftCBar_BarInFig.m
@@ -77,8 +77,8 @@ function changepointer(hf,~)
             elseif y_new<=1.1
                 x = (y_int:((s+1-y_int)/(s+1)):(s+1))';
             else
-                ym = min((y_int)/(y_new)*ceil(y_new),64);
-                x = [linspace(1,(y_int)/(y_new)*floor(y_new),floor(y_new)) linspace(ym,64,65-ceil(y_new))]';
+                ym = min((y_int)/(y_new)*ceil(y_new),s);
+                x = [linspace(1,(y_int)/(y_new)*floor(y_new),floor(y_new)) linspace(ym,s,(s+1)-ceil(y_new))]';    
             end
             cmap_new = [interp1(ind,cmap(:,1),x) interp1(ind,cmap(:,2),x) interp1(ind,cmap(:,3),x)];
             colormap(ha,cmap_new)
diff --git a/GUI/generalFunc/messagePanel.m b/GUI/generalFunc/messagePanel.m
index 106feec..a79383c 100644
--- a/GUI/generalFunc/messagePanel.m
+++ b/GUI/generalFunc/messagePanel.m
@@ -26,7 +26,7 @@
 jText = JTextArea;
 jText.setAlignmentX(0.5);
 jpan.add(jText);
-str = sprintf('Welcome to StatSTEM v3.0, have fun analysing\nWhen using StatSTEM please cite: A. De Backer, K.H.W. van den Bos, et. al., Ultramicroscopy 171 (2016), p.104-116');
+str = sprintf('Welcome to StatSTEM v3.1, have fun analysing\nWhen using StatSTEM please cite: A. De Backer, K.H.W. van den Bos, et. al., Ultramicroscopy 171 (2016), p.104-116');
 jText.setText(str)
 jText.setEditable(false)
 jText.setFocusable(true)
diff --git a/StatSTEM.prj b/StatSTEM.prj
index b476bbf..c46e78d 100644
--- a/StatSTEM.prj
+++ b/StatSTEM.prj
@@ -1,138 +1,127 @@
-<deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
-  <configuration build-checksum="3180951167" file="C:\Users\Karel\Documents\MATLAB\StatSTEMv3.0\StatSTEM.prj" location="C:\Users\Karel\Documents\MATLAB\StatSTEMv3.0" name="StatSTEM" preferred-package-location="C:\Users\Karel\Documents\MATLAB\StatSTEMv3.0\StatSTEM\for_redistribution" preferred-package-type="package.type.exe" target="target.ezdeploy.standalone" target-name="Application Compiler">
-    <param.appname>StatSTEM</param.appname>
-    <param.icon>${PROJECT_ROOT}\StatSTEM_resources\icon.ico</param.icon>
-    <param.icons>
-      <file>${PROJECT_ROOT}\StatSTEM_resources\icon_48.png</file>
-      <file>${PROJECT_ROOT}\StatSTEM_resources\icon_32.png</file>
-      <file>${PROJECT_ROOT}\StatSTEM_resources\icon_24.png</file>
-      <file>${PROJECT_ROOT}\StatSTEM_resources\icon_16.png</file>
-    </param.icons>
-    <param.version>3.0</param.version>
-    <param.authnamewatermark />
-    <param.email>Sandra.VanAert@uantwerpen.be</param.email>
-    <param.company>EMAT</param.company>
-    <param.summary>Application for extracting structural information from scanning transmission electron microscopy images</param.summary>
-    <param.description>Scanning transmission electron microscopy images will be modeled by a superposition of Gaussian peaks describing each individual atomic column. Overlap of intensities from neighbouring columns is taken into account. Structural parameters, like column positions and scattering cross sections, can be stored in a MATLAB file format. From the modelled image, the number of atoms in each atomic column can be determined together with an atomically resolved strain map.
-
-When using this program please cite: A. De Backer, Ultramicroscopy 171 (2016), p.104-116</param.description>
-    <param.screenshot>${PROJECT_ROOT}\GUI\splash.png</param.screenshot>
-    <param.guid />
-    <param.installpath.string>\EMAT\StatSTEM\</param.installpath.string>
-    <param.installpath.combo>option.installpath.programfiles</param.installpath.combo>
-    <param.logo />
-    <param.install.notes />
-    <param.target.install.notes />
-    <param.intermediate>${PROJECT_ROOT}\StatSTEM\for_testing</param.intermediate>
-    <param.files.only>${PROJECT_ROOT}\StatSTEM\for_redistribution_files_only</param.files.only>
-    <param.output>${PROJECT_ROOT}\StatSTEM\for_redistribution</param.output>
-    <param.logdir>${PROJECT_ROOT}\StatSTEM</param.logdir>
-    <param.enable.clean.build>false</param.enable.clean.build>
-    <param.user.defined.mcr.options />
-    <param.target.type>subtarget.standalone</param.target.type>
-    <param.support.packages />
-    <param.web.mcr>true</param.web.mcr>
-    <param.package.mcr>false</param.package.mcr>
-    <param.no.mcr>false</param.no.mcr>
-    <param.web.mcr.name>StatSTEM3.0</param.web.mcr.name>
-    <param.package.mcr.name>MyAppInstaller_mcr</param.package.mcr.name>
-    <param.no.mcr.name>MyAppInstaller_app</param.no.mcr.name>
-    <param.windows.command.prompt>true</param.windows.command.prompt>
-    <param.create.log>false</param.create.log>
-    <param.log.file />
-    <unset>
-      <param.authnamewatermark />
-      <param.guid />
-      <param.installpath.string />
-      <param.installpath.combo />
-      <param.logo />
-      <param.target.install.notes />
-      <param.intermediate />
-      <param.files.only />
-      <param.output />
-      <param.logdir />
-      <param.enable.clean.build />
-      <param.user.defined.mcr.options />
-      <param.target.type />
-      <param.support.packages />
-      <param.web.mcr />
-      <param.package.mcr />
-      <param.no.mcr />
-      <param.package.mcr.name />
-      <param.no.mcr.name />
-      <param.windows.command.prompt />
-      <param.create.log />
-      <param.log.file />
-    </unset>
-    <fileset.main>
-      <file>${PROJECT_ROOT}\StatSTEM.m</file>
-    </fileset.main>
-    <fileset.resources>
-      <file>${PROJECT_ROOT}\functions</file>
-      <file>${PROJECT_ROOT}\GUI</file>
-      <file>${PROJECT_ROOT}\StatSTEM.m</file>
-    </fileset.resources>
-    <fileset.package>
-      <file>${PROJECT_ROOT}\Database</file>
-      <file>${PROJECT_ROOT}\Examples</file>
-      <file>${PROJECT_ROOT}\LICENSE.txt</file>
-    </fileset.package>
-    <fileset.depfun />
-    <build-deliverables>
-      <file location="${PROJECT_ROOT}\StatSTEM\for_testing" name="splash.png" optional="false">C:\Users\Karel\Documents\MATLAB\StatSTEMv3.0\StatSTEM\for_testing\splash.png</file>
-      <file location="${PROJECT_ROOT}\StatSTEM\for_testing" name="readme.txt" optional="true">C:\Users\Karel\Documents\MATLAB\StatSTEMv3.0\StatSTEM\for_testing\readme.txt</file>
-      <file location="${PROJECT_ROOT}\StatSTEM\for_testing" name="StatSTEM.exe" optional="false">C:\Users\Karel\Documents\MATLAB\StatSTEMv3.0\StatSTEM\for_testing\StatSTEM.exe</file>
-    </build-deliverables>
-    <workflow />
-    <matlab>
-      <root>C:\Program Files\MATLAB\R2017a</root>
-      <toolboxes>
-        <toolbox name="fixedpoint" />
-        <toolbox name="matlabcoder" />
-        <toolbox name="matlabhdlcoder" />
-        <toolbox name="embeddedcoder" />
-        <toolbox name="polyspacebugfinder" />
-      </toolboxes>
-      <toolbox>
-        <fixedpoint>
-          <enabled>true</enabled>
-        </fixedpoint>
-      </toolbox>
-      <toolbox>
-        <matlabcoder>
-          <enabled>true</enabled>
-        </matlabcoder>
-      </toolbox>
-      <toolbox>
-        <matlabhdlcoder>
-          <enabled>true</enabled>
-        </matlabhdlcoder>
-      </toolbox>
-      <toolbox>
-        <embeddedcoder>
-          <enabled>true</enabled>
-        </embeddedcoder>
-      </toolbox>
-      <toolbox>
-        <polyspacebugfinder>
-          <enabled>true</enabled>
-        </polyspacebugfinder>
-      </toolbox>
-    </matlab>
-    <platform>
-      <unix>false</unix>
-      <mac>false</mac>
-      <windows>true</windows>
-      <win2k>false</win2k>
-      <winxp>false</winxp>
-      <vista>false</vista>
-      <linux>false</linux>
-      <solaris>false</solaris>
-      <osver>6.1</osver>
-      <os32>false</os32>
-      <os64>true</os64>
-      <arch>win64</arch>
-      <matlab>true</matlab>
-    </platform>
-  </configuration>
+<deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
+  <configuration build-checksum="3180951167" file="C:\Users\thoma\Desktop\StatSTEM\StatSTEM.prj" location="C:\Users\thoma\Desktop\StatSTEM" name="StatSTEM" preferred-package-location="C:\Users\Karel\Documents\MATLAB\StatSTEMv3.0\StatSTEM\for_redistribution" preferred-package-type="package.type.exe" target="target.ezdeploy.standalone" target-name="Application Compiler">
+    <param.appname>StatSTEM</param.appname>
+    <param.icon>${PROJECT_ROOT}\StatSTEM_resources\icon.ico</param.icon>
+    <param.icons>
+      <file>${PROJECT_ROOT}\StatSTEM_resources\icon_48.png</file>
+      <file>${PROJECT_ROOT}\StatSTEM_resources\icon_32.png</file>
+      <file>${PROJECT_ROOT}\StatSTEM_resources\icon_24.png</file>
+      <file>${PROJECT_ROOT}\StatSTEM_resources\icon_16.png</file>
+    </param.icons>
+    <param.version>3.1</param.version>
+    <param.authnamewatermark />
+    <param.email>Sandra.VanAert@uantwerpen.be</param.email>
+    <param.company>EMAT</param.company>
+    <param.summary>Application for extracting structural information from scanning transmission electron microscopy images</param.summary>
+    <param.description>Scanning transmission electron microscopy images will be modeled by a superposition of Gaussian peaks describing each individual atomic column. Overlap of intensities from neighbouring columns is taken into account. Structural parameters, like column positions and scattering cross sections, can be stored in a MATLAB file format. From the modelled image, the number of atoms in each atomic column can be determined together with an atomically resolved strain map.
+
+When using this program please cite: A. De Backer, Ultramicroscopy 171 (2016), p.104-116</param.description>
+    <param.screenshot>${PROJECT_ROOT}\GUI\splash.png</param.screenshot>
+    <param.guid />
+    <param.installpath.string>\EMAT\StatSTEM\</param.installpath.string>
+    <param.installpath.combo>option.installpath.programfiles</param.installpath.combo>
+    <param.logo />
+    <param.install.notes />
+    <param.target.install.notes />
+    <param.intermediate>${PROJECT_ROOT}\StatSTEM\for_testing</param.intermediate>
+    <param.files.only>${PROJECT_ROOT}\StatSTEM\for_redistribution_files_only</param.files.only>
+    <param.output>${PROJECT_ROOT}\StatSTEM\for_redistribution</param.output>
+    <param.logdir>${PROJECT_ROOT}\StatSTEM</param.logdir>
+    <param.enable.clean.build>false</param.enable.clean.build>
+    <param.user.defined.mcr.options />
+    <param.target.type>subtarget.standalone</param.target.type>
+    <param.support.packages />
+    <param.web.mcr>true</param.web.mcr>
+    <param.package.mcr>false</param.package.mcr>
+    <param.no.mcr>false</param.no.mcr>
+    <param.web.mcr.name>StatSTEM3.1</param.web.mcr.name>
+    <param.package.mcr.name>MyAppInstaller_mcr</param.package.mcr.name>
+    <param.no.mcr.name>MyAppInstaller_app</param.no.mcr.name>
+    <param.windows.command.prompt>true</param.windows.command.prompt>
+    <param.create.log>false</param.create.log>
+    <param.log.file />
+    <param.native.matlab>false</param.native.matlab>
+    <param.checkbox>false</param.checkbox>
+    <param.example />
+    <param.help.text>Syntax 
+	  -? 
+	 
+ Input Arguments 
+	 -?  print help on how to use the application 
+	 input arguments</param.help.text>
+    <unset>
+      <param.authnamewatermark />
+      <param.guid />
+      <param.installpath.string />
+      <param.installpath.combo />
+      <param.logo />
+      <param.install.notes />
+      <param.target.install.notes />
+      <param.intermediate />
+      <param.files.only />
+      <param.output />
+      <param.logdir />
+      <param.enable.clean.build />
+      <param.user.defined.mcr.options />
+      <param.target.type />
+      <param.support.packages />
+      <param.web.mcr />
+      <param.package.mcr />
+      <param.no.mcr />
+      <param.package.mcr.name />
+      <param.no.mcr.name />
+      <param.windows.command.prompt />
+      <param.create.log />
+      <param.log.file />
+      <param.native.matlab />
+      <param.checkbox />
+      <param.example />
+    </unset>
+    <fileset.main>
+      <file>${PROJECT_ROOT}\StatSTEM.m</file>
+    </fileset.main>
+    <fileset.resources>
+      <file>${PROJECT_ROOT}\functions</file>
+      <file>${PROJECT_ROOT}\GUI</file>
+      <file>${PROJECT_ROOT}\StatSTEM.m</file>
+    </fileset.resources>
+    <fileset.package>
+      <file>${PROJECT_ROOT}\Database</file>
+      <file>${PROJECT_ROOT}\Examples</file>
+      <file>${PROJECT_ROOT}\LICENSE.txt</file>
+    </fileset.package>
+    <fileset.depfun />
+    <build-deliverables>
+      <file location="${PROJECT_ROOT}\StatSTEM\for_testing" name="splash.png" optional="false">C:\Users\thoma\Desktop\StatSTEM\StatSTEM\for_testing\splash.png</file>
+      <file location="${PROJECT_ROOT}\StatSTEM\for_testing" name="StatSTEM.exe" optional="false">C:\Users\thoma\Desktop\StatSTEM\StatSTEM\for_testing\StatSTEM.exe</file>
+      <file location="${PROJECT_ROOT}\StatSTEM\for_testing" name="readme.txt" optional="true">C:\Users\thoma\Desktop\StatSTEM\StatSTEM\for_testing\readme.txt</file>
+    </build-deliverables>
+    <workflow />
+    <matlab>
+      <root>C:\Program Files\MATLAB\R2019b</root>
+      <toolboxes>
+        <toolbox name="matlabcoder" />
+      </toolboxes>
+      <toolbox>
+        <matlabcoder>
+          <enabled>true</enabled>
+        </matlabcoder>
+      </toolbox>
+    </matlab>
+    <platform>
+      <unix>false</unix>
+      <mac>false</mac>
+      <windows>true</windows>
+      <win2k>false</win2k>
+      <winxp>false</winxp>
+      <vista>false</vista>
+      <linux>false</linux>
+      <solaris>false</solaris>
+      <osver>10.0</osver>
+      <os32>false</os32>
+      <os64>true</os64>
+      <arch>win64</arch>
+      <matlab>true</matlab>
+    </platform>
+  </configuration>
 </deployment-project>
\ No newline at end of file
diff --git a/StatSTEM_manual.pdf b/StatSTEM3.1_manual.pdf
similarity index 100%
rename from StatSTEM_manual.pdf
rename to StatSTEM3.1_manual.pdf