diff --git a/+gui/GuiFile.m b/+gui/GuiFile.m
index e9bfc4b5..1eae4a97 100644
--- a/+gui/GuiFile.m
+++ b/+gui/GuiFile.m
@@ -289,7 +289,8 @@ function autosave_timer(a,b,obj)
 p.mainGui=obj.getPar('mainGui');
 p.saveroi=false;
 if obj.guihandles.autosavecheck.Value
-    savesml(obj.locData,'settings/temp/autosave_sml',p)
+    settingsdir=obj.getPar('SettingsDirectory');
+    savesml(obj.locData,[settingsdir filesep 'temp' filesep 'autosave_sml'],p)
     time=datetime('now');
     disp(['autosave: ' num2str(time.Hour) ':' num2str(time.Minute)])
 end
diff --git a/+gui/GuiPluginGroup.m b/+gui/GuiPluginGroup.m
index 921817ab..dd6d892b 100644
--- a/+gui/GuiPluginGroup.m
+++ b/+gui/GuiPluginGroup.m
@@ -197,7 +197,7 @@ function processorselect_callback(object,data,obj)
 
 function menu_callback(callobj,b,obj)
 guimodules=obj.getPar('guimodules');
-% guimodules=readstruct('settings/temp/guimodules.txt',[],true);
+
 switch callobj.Label
     case 'add plugin'
         plugins=obj.getPar('menu_plugins');
@@ -223,7 +223,8 @@ function menu_callback(callobj,b,obj)
 %         guimodules.(pluginname{1}).(pluginname{2}).(pluginname{3})=pluginname;
 %         save(obj.guipluginpath,'guimodules')
     case 'add workflow'
-        [file,path]=uigetfile(['settings/workflows/*.mat']);
+        settingsdir=obj.getPar('SettingsDirectory');
+        [file,path]=uigetfile([settingsdir '/workflows/*.mat']);
         if ~file
             return
         end
@@ -276,28 +277,7 @@ function menu_callback(callobj,b,obj)
         classname=obj.plugins.allclassnames{selection};
         guimodules.(obj.maindir{1}).(obj.maindir{2}).(classname).name=newname;
         obj.setprocessorlist;
-%     case 'reset: use all plugins'
-%         answ=questdlg('Delete all settings for pluginlist? Effect takes place after restarting the application');
-%         
-%         if strcmp(answ,'Yes')
-%             obj.setGlobalSetting('guiPluginConfigFile','');
-%         end
-%             delete('settings/temp/guimodules.txt')
-%             return
-%         end
-%     case 'load plugin structure'
-%         fs='settings/*.txt';
-%         [f,path]=uigetfile(fs,'load gui plugin structure file');
-%         if f
-%             guimodules=readstruct([path f],[],1);
-%             msgbox('please restart SMAP')
-%         end
-%     case 'save plugin structure'
-%         fs='settings/guiplugins.txt';
-%         [f,path]=uiputfile(fs,'save gui plugin structure file');
-%         if f
-%              writestruct([path f],guimodules);
-%         end
+
         
     case 'detach'
         f=figure('MenuBar','none','Toolbar','none');
@@ -311,7 +291,7 @@ function menu_callback(callobj,b,obj)
 for k=1:length(allclasses)
     guimodules.(obj.maindir{1}).(obj.maindir{2}).(allclasses{k}).position=k;
 end
-%  writestruct('settings/temp/guimodules.txt',guimodules);
+
  obj.setPar('guimodules',guimodules);
 end
 
diff --git a/+gui/GuiPluginWindow.m b/+gui/GuiPluginWindow.m
index f8ed25e7..a9582212 100644
--- a/+gui/GuiPluginWindow.m
+++ b/+gui/GuiPluginWindow.m
@@ -106,7 +106,7 @@ function addplugingroup(obj,name,screenname)
 
 function menu_callback(callobj,b,obj)
 guimodules=obj.getPar('guimodules');
-% guimodules=readstruct('settings/temp/guimodules.txt',[],true);
+
 switch callobj.Label    
     case 'add'
         name=inputdlg('name of new tab');
@@ -126,7 +126,8 @@ function menu_callback(callobj,b,obj)
             guimodules.(obj.maindir)=rmfield(guimodules.(obj.maindir),fieldr); 
         end
     case 'add workflow'
-        [file,path]=uigetfile(['settings/workflows/*.mat']);
+        settingsdir=obj.getPar('SettingsDirectory');
+        [file,path]=uigetfile([settingsdir '/workflows/*.mat']);
         if file
             [~,name]=fileparts(file);
             name=name(1:min(end,16));
@@ -167,7 +168,6 @@ function menu_callback(callobj,b,obj)
         selected.Parent=hnew;
 end
 obj.setPar('guimodules',guimodules);
-%  writestruct('settings/temp/guimodules.txt',guimodules);
 end
 
 function module=makewf(obj,name, file)
diff --git a/+gui/SEAnnotation.m b/+gui/SEAnnotation.m
index ec36a4b5..e10f7061 100644
--- a/+gui/SEAnnotation.m
+++ b/+gui/SEAnnotation.m
@@ -164,7 +164,7 @@ function keypress(object,data,obj,focus)
 end
 
 function loadlist_callback(a,b,obj)
-[f p]=uigetfile('settings/*.txt');
+[f p]=uigetfile([obj.getPar('SettingsDirectory') '/*.txt']);
 if f
     loadlist(obj,[p f])
 end
diff --git a/+gui/private/makeplugincallfile.m b/+gui/private/makeplugincallfile.m
index 2fa6b9f3..2e9bef1c 100644
--- a/+gui/private/makeplugincallfile.m
+++ b/+gui/private/makeplugincallfile.m
@@ -2,18 +2,13 @@
 if ~isdeployed
     addpath('plugins')
     addpath('plugins/shared');
-%     addpath('settings/workflows');
     
     try
     pold=plugin;
     catch
         pold=[];
     end
-%     outputdir='+plugintemp';
-%     if ~exist(outputdir,'dir')
-%         mkdir(outputdir)
-%         rehash
-%     end
+
     
     strcase={};
     strlist={};
diff --git a/+interfaces/imageloaderSMAP.m b/+interfaces/imageloaderSMAP.m
index 1a2446b1..b482a9b3 100644
--- a/+interfaces/imageloaderSMAP.m
+++ b/+interfaces/imageloaderSMAP.m
@@ -8,7 +8,7 @@
         waittime=5;
         currentImageNumber;
         allmetadatatags;
-        calibrationFile='settings/cameras.mat';
+        calibrationFile;
         allowmultiplefiles=true;
         ismultichannel=false;
         multiloader={};
@@ -17,6 +17,7 @@
     methods
        function obj=imageloaderSMAP(varargin)
            obj.metadata=interfaces.metadataSMAP;
+           obj.calibrationFile=[obj.getGlobalSetting('SettingsDirectory') '/cameras.mat'];
            if nargin>2 && ~isempty(varargin{3})
                if isa(varargin{3},'interfaces.ParameterData')
                     obj.P=varargin{3};
diff --git a/plugins/+Analyze/+sr3D/Biplane_getPSFxy.m b/plugins/+Analyze/+sr3D/Biplane_getPSFxy.m
index 9f3abb23..626c2a02 100644
--- a/plugins/+Analyze/+sr3D/Biplane_getPSFxy.m
+++ b/plugins/+Analyze/+sr3D/Biplane_getPSFxy.m
@@ -123,7 +123,7 @@ function loadbutton(obj,a,b)
 % pard.datapart.position=[3,1];
 
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[8,1];
 pard.Tfile.Width=3;
 
diff --git a/plugins/+File/+Load/Loader_csvAndMore.m b/plugins/+File/+Load/Loader_csvAndMore.m
index f0d0440d..5bbc51bf 100644
--- a/plugins/+File/+Load/Loader_csvAndMore.m
+++ b/plugins/+File/+Load/Loader_csvAndMore.m
@@ -1,6 +1,6 @@
 classdef Loader_csvAndMore<interfaces.DialogProcessor
     properties
-        loaderpath='settings/csvloaderconversion/';
+        loaderpath;
         notfound=false;
     end
     methods
diff --git a/plugins/+File/+Load/Loader_minflux.m b/plugins/+File/+Load/Loader_minflux.m
index 0bdd5038..022e2392 100644
--- a/plugins/+File/+Load/Loader_minflux.m
+++ b/plugins/+File/+Load/Loader_minflux.m
@@ -31,18 +31,7 @@ function clear(obj,file,isadd)
                 obj.locData.clear;
             end
         end
-%         function initGui(obj)
-%             obj.loaderpath='settings/csvloaderconversion/';
-%             files=dir([obj.loaderpath '*.txt']);
-%             string={'New format', files(:).name};
-%             obj.guihandles.importdef.String=string;
-% %             obj.guihandles.importdef.Callback=@obj.csvconvert_callback;
-%         end
-%         function csvconvert_callback(obj,object,b)
-%            if object.Value==1
-%                newformat(obj);
-%            end
-%         end
+
     end
 end
 
diff --git a/plugins/+File/+Load/Loader_sml_Tiff.m b/plugins/+File/+Load/Loader_sml_Tiff.m
index 6063eaf4..4811004d 100644
--- a/plugins/+File/+Load/Loader_sml_Tiff.m
+++ b/plugins/+File/+Load/Loader_sml_Tiff.m
@@ -183,7 +183,7 @@ function loadTfile(obj,a,b)
 pard.replacestring.TooltipString='replace string.';
 
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[3,1];
 pard.Tfile.Width=3;
 pard.syncParameters={{'transformationfile','Tfile',{'String'}}};
diff --git a/plugins/+Process/+Assign2C/Get2CIntImages2cam.m b/plugins/+Process/+Assign2C/Get2CIntImages2cam.m
index 89cf13ca..23a69de6 100644
--- a/plugins/+Process/+Assign2C/Get2CIntImages2cam.m
+++ b/plugins/+Process/+Assign2C/Get2CIntImages2cam.m
@@ -25,8 +25,6 @@
             settingsdir=obj.getPar('SettingsDirectory');
             f=obj.figure;
             f.Visible='on';
-%             wffile='settings/workflows/get2CIntensityImagesWF_group.mat';
-%             wffile='settings/workflows/get2CIntensityImagesWF2';
             if p.evalref && p.evaltarget && ( isempty(p.tiffileref) || strcmp(p.tiffileref,p.tiffiletarget))  %both channels on one chip
                 wffile=[settingsdir filesep 'workflows' filesep 'get2CIntensityImagesWF3_reftarget'];
                 samechip=true;
diff --git a/plugins/+Process/+Assign2C/Get2CIntLoc.m b/plugins/+Process/+Assign2C/Get2CIntLoc.m
index 55adbf8b..d93e6ab7 100644
--- a/plugins/+Process/+Assign2C/Get2CIntLoc.m
+++ b/plugins/+Process/+Assign2C/Get2CIntLoc.m
@@ -64,7 +64,7 @@ function loadbutton(obj,a,b)
 % pard.datapart.position=[3,1];
 
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[8,1];
 pard.Tfile.Width=3;
 
diff --git a/plugins/+Process/+Assign2C/old/Get2CIntImages.m b/plugins/+Process/+Assign2C/old/Get2CIntImages.m
index 42c4bab2..7a0455cc 100644
--- a/plugins/+Process/+Assign2C/old/Get2CIntImages.m
+++ b/plugins/+Process/+Assign2C/old/Get2CIntImages.m
@@ -133,7 +133,7 @@ function loadbutton(obj,a,b)
 % pard.size2roi2.position=[3,4.5];
 % pard.size2roi2.Width=0.5;
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[8,1];
 pard.Tfile.Width=3;
 
diff --git a/plugins/+Process/+Modify/MathParser.m b/plugins/+Process/+Modify/MathParser.m
index bf7db3a5..b203e5cf 100644
--- a/plugins/+Process/+Modify/MathParser.m
+++ b/plugins/+Process/+Modify/MathParser.m
@@ -4,13 +4,14 @@
 %     access.
     properties
         equationhistory
-        historyfile='settings/temp/MathParser.txt';
+        historyfile
     end
     methods
         function obj=MathParser(varargin)      
             obj@interfaces.DialogProcessor(varargin{:}) ;  
         end
         function initGui(obj)
+            obj.historyfile=[obj.getPar('SettingsDirectory') filesep 'temp' filesep 'MathParser.txt'];
             if exist(obj.historyfile,'file')
                 try
                     obj.equationhistory=readtable(obj.historyfile,'Delimiter',',');
@@ -27,7 +28,6 @@ function initGui(obj)
                 tt=struct('resultfield',{{''}},'equation',{{''}});
                 obj.equationhistory=struct2table(tt);
             end
-            obj.historyfile=[obj.getPar('SettingsDirectory') filesep 'temp' filesep 'MathParser.txt'];
         end
         
         function out=run(obj,p)
diff --git a/plugins/+Process/+Register/ApplyTransform.m b/plugins/+Process/+Register/ApplyTransform.m
index b25dbf09..ea4cff42 100644
--- a/plugins/+Process/+Register/ApplyTransform.m
+++ b/plugins/+Process/+Register/ApplyTransform.m
@@ -127,7 +127,7 @@ function loadbutton(obj,a,b)
 pard.transformz.Width=2;
 
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[7,1];
 pard.Tfile.Width=3;
 
diff --git a/plugins/+Process/+Register/CombineChannels.m b/plugins/+Process/+Register/CombineChannels.m
index e607b7a3..3041efa1 100644
--- a/plugins/+Process/+Register/CombineChannels.m
+++ b/plugins/+Process/+Register/CombineChannels.m
@@ -137,7 +137,7 @@ function loadbutton(obj,a,b)
 % 
 
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[7,1];
 pard.Tfile.Width=3;
 
diff --git a/plugins/+Process/+Register/RegisterImages.m b/plugins/+Process/+Register/RegisterImages.m
index 060373b7..3c2dd4a6 100644
--- a/plugins/+Process/+Register/RegisterImages.m
+++ b/plugins/+Process/+Register/RegisterImages.m
@@ -133,7 +133,7 @@ function savebutton(obj,a,b)
 pard.syncParameters={{'filelist_short','dataselect',{'String'}}};
 
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[8,1];
 pard.Tfile.Width=3;
 
diff --git a/plugins/+Process/+Register/RegisterLocs2.m b/plugins/+Process/+Register/RegisterLocs2.m
index fb5e4ba0..dda0173b 100644
--- a/plugins/+Process/+Register/RegisterLocs2.m
+++ b/plugins/+Process/+Register/RegisterLocs2.m
@@ -222,7 +222,7 @@ function useT_callback(obj,a,b)
 pard.reflayer.Width=0.85;
 pard.reflayer.Optional=true;
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[8,1];
 pard.Tfile.Width=3;
 pard.Tfile.object.TooltipString='default file for transformation matrix. You can select new file after transformation has been calculated.';
diff --git a/plugins/+Process/+Register/RegisterLocs4Pi.m b/plugins/+Process/+Register/RegisterLocs4Pi.m
index 5e29c055..fcb36060 100644
--- a/plugins/+Process/+Register/RegisterLocs4Pi.m
+++ b/plugins/+Process/+Register/RegisterLocs4Pi.m
@@ -259,7 +259,7 @@ function useT_callback(obj,a,b)
 % pard.reflayer.object.TooltipString='layer';
 % pard.reflayer.Width=0.85;
 
-% pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+% pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 % pard.Tfile.position=[8,1];
 % pard.Tfile.Width=3;
 % pard.Tfile.object.TooltipString='default file for transformation matrix. You can select new file after transformation has been calculated.';
diff --git a/plugins/+Process/+Register/Transform2C_interleaved.m b/plugins/+Process/+Register/Transform2C_interleaved.m
index 28bb668f..5a6ae59d 100644
--- a/plugins/+Process/+Register/Transform2C_interleaved.m
+++ b/plugins/+Process/+Register/Transform2C_interleaved.m
@@ -135,7 +135,7 @@ function loadbutton(obj,a,b)
 % pard.transformz.Width=2;
 
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[7,1];
 pard.Tfile.Width=3;
 
diff --git a/plugins/+Process/+Register/hide/ManualTransform.m b/plugins/+Process/+Register/hide/ManualTransform.m
index 100a8048..cc6938b7 100644
--- a/plugins/+Process/+Register/hide/ManualTransform.m
+++ b/plugins/+Process/+Register/hide/ManualTransform.m
@@ -93,7 +93,7 @@ function updateGui(obj,event,data)
 pard.refmirror.object=struct('Style','popupmenu','String','no mirror|left-right|up-down');
 pard.refmirror.position=[4,2];
 
-pard.savefile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.savefile.object=struct('Style','edit','String','*_T.mat');
 pard.savefile.position=[8,1];
 pard.savefile.Width=3;
 
diff --git a/plugins/+Process/+Register/hide/RegisterLocs.m b/plugins/+Process/+Register/hide/RegisterLocs.m
index 1949a68a..f43a6750 100644
--- a/plugins/+Process/+Register/hide/RegisterLocs.m
+++ b/plugins/+Process/+Register/hide/RegisterLocs.m
@@ -111,7 +111,7 @@ function savebutton(obj,a,b)
 % pard.refmirror.position=[4,1];
 % pard.refmirror.object.TooltipString='mirror reference part';
 
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[8,1];
 pard.Tfile.Width=3;
 pard.Tfile.object.TooltipString='default file for transformation matrix. You can select new file after transformation has been calculated.';
diff --git a/plugins/+WorkflowModules/+Loaders/CameraConverter.m b/plugins/+WorkflowModules/+Loaders/CameraConverter.m
index beb64c2a..60c3dc0b 100644
--- a/plugins/+WorkflowModules/+Loaders/CameraConverter.m
+++ b/plugins/+WorkflowModules/+Loaders/CameraConverter.m
@@ -2,7 +2,7 @@
 %     Interprets metadata and converts camera ADUs into photons- Metadata
 %     can be overwritten manually or loaded from a SMAP _sml.mat data file.
     properties
-        calfile='settings/CameraCalibration.xls';
+        calfile;
         loc_cameraSettings=interfaces.metadataSMAP;
         loc_cameraSettingsStructure=struct('EMon',1,'emgain',1,'conversion',1,'offset',400,'cam_pixelsize_um',0.1,...
             'roi',[],'exposure',1,'timediff',0,'comment','','correctionfile','');        
@@ -47,8 +47,7 @@ function initGui(obj)
            obj.guihandles.calibrate.Callback={@calibrate_callback,obj};
             obj.outputParameters={'loc_cameraSettings'};
            obj.addSynchronization('loc_fileinfo_set',[],[],@obj.setmetadata)
-            obj.inputParameters={'diffrawframes'};
-           
+            obj.inputParameters={'diffrawframes'};          
         end
         function setmetadata(obj,overwrite)
             if nargin<2
diff --git a/plugins/+WorkflowModules/+LocProcessors/LocSaver.m b/plugins/+WorkflowModules/+LocProcessors/LocSaver.m
index 616348b7..c7af7a00 100644
--- a/plugins/+WorkflowModules/+LocProcessors/LocSaver.m
+++ b/plugins/+WorkflowModules/+LocProcessors/LocSaver.m
@@ -291,7 +291,7 @@ function outputfields_callback(a,b,obj)
 end
 
 function imout=makeSRimge(obj,locDatatemp)
-channelfile=[obj.getPar('maindirectory')  '/settings/workflows/FitTif_Channelsettings.mat'];
+channelfile=[obj.getPar('SettingsDirectory')  '/workflows/FitTif_Channelsettings.mat'];
 pall=load(channelfile);
 p=pall.globalParameters;
 p.lutinv=false;
diff --git a/plugins/+WorkflowModules/+Peakfinders/PeakCombiner.m b/plugins/+WorkflowModules/+Peakfinders/PeakCombiner.m
index bfbe3361..925d9eab 100644
--- a/plugins/+WorkflowModules/+Peakfinders/PeakCombiner.m
+++ b/plugins/+WorkflowModules/+Peakfinders/PeakCombiner.m
@@ -221,7 +221,7 @@ function loadbutton(obj,a,b)
 
 
 function pard=guidef(obj)
-pard.Tfile.object=struct('Style','edit','String','settings/temp/temp_T.mat');
+pard.Tfile.object=struct('Style','edit','String','*_T.mat');
 pard.Tfile.position=[1,1];
 pard.Tfile.Width=3;
 
diff --git a/shared/imageloaders/CameraManager.m b/shared/imageloaders/CameraManager.m
index a1dd5188..7b5d3259 100644
--- a/shared/imageloaders/CameraManager.m
+++ b/shared/imageloaders/CameraManager.m
@@ -12,7 +12,7 @@
         currentstate=1;
         lastcamtableselected=[];
         defaultpath;
-        cameraSettingsFile='settings/cameras.mat';
+        cameraSettingsFile;
     end
     
     methods
@@ -46,6 +46,7 @@ function loadimages(obj,file)
                 end
         end
         function makeGui(obj)
+            obj.cameraSettingsFile=obj.getGlobalSetting('cameraSettingsFile');
             makeGui(obj)
         end
         function pard=guidef(obj)
diff --git a/shared/imageloaders/imageloaderMMsingle.m b/shared/imageloaders/imageloaderMMsingle.m
index 37103533..3a6924a3 100644
--- a/shared/imageloaders/imageloaderMMsingle.m
+++ b/shared/imageloaders/imageloaderMMsingle.m
@@ -3,7 +3,6 @@
     %   Detailed explanation goes here
     
     properties
-%         calfile='settings/CameraCalibration.xls';
         separate
         separatefiles
     end
diff --git a/shared/imageloaders/imageloaderOME.m b/shared/imageloaders/imageloaderOME.m
index 890b00b7..37c5f22b 100644
--- a/shared/imageloaders/imageloaderOME.m
+++ b/shared/imageloaders/imageloaderOME.m
@@ -3,7 +3,7 @@
     %   Detailed explanation goes here
     
     properties
-        calfile='settings/CameraCalibration.xls';
+%         calfile;
         reader
         seriesnumber=0;
 %         allmetadatatags