From cfa872fcb5943d8b8e0a822fa0a3d0afc2d9c9a0 Mon Sep 17 00:00:00 2001
From: Jonas Ries <jonas.ries@gmail.com>
Date: Fri, 4 Dec 2020 12:34:33 +0100
Subject: [PATCH 1/4] Gauss for BP

---
 other/BP_Gauss_analysis.m |  74 ++++++++++++++++++++++++++++++++++++++
 settings/cameras.mat      | Bin 18664 -> 18689 bytes
 2 files changed, 74 insertions(+)
 create mode 100644 other/BP_Gauss_analysis.m

diff --git a/other/BP_Gauss_analysis.m b/other/BP_Gauss_analysis.m
new file mode 100644
index 00000000..08f6db30
--- /dev/null
+++ b/other/BP_Gauss_analysis.m
@@ -0,0 +1,74 @@
+
+pixs=100;
+dz=10;
+
+%% BEADS: calibrate sx
+figure(88);
+
+sx=g.locData.loc.PSFxnm/pixs;
+sy=g.locData.loc.PSFynm/pixs;
+frame=g.locData.loc.frame;
+z=frame*dz;
+plot(frame,sx,'.',frame,sy,'.')
+
+ds=sx.^2-sy.^2;
+figure(89)
+plot(frame,ds,'.')
+
+range=[45,95];
+
+inr=frame>range(1)&frame<range(2);
+
+figure(89)
+hold off
+plot(ds(inr),z(inr),'.')
+
+calbead=fit(ds(inr),z(inr),'poly4');
+hold on
+plot(ds(inr),calbead(ds(inr)))
+
+maxrangeds=[min(ds(inr)) max(ds(inr))];
+
+%% data: calculate z
+outz=1000;
+sx=g.locData.loc.PSFxnm/pixs;
+sy=g.locData.loc.PSFynm/pixs;
+ds=sx.^2-sy.^2;
+z=calbead(ds);
+g.locData.loc.znm=z-750;
+
+outofrange=ds<maxrangeds(1) | ds>maxrange(2);
+g.locData.loc.znm(outofrange)=outz;
+
+%% data: average x,y
+trafo=g.locData.files.file.transformation;
+inref=trafo.getRef(g.locData.loc.xnm,g.locData.loc.ynm);
+cr=[g.locData.loc.xnm(inref),g.locData.loc.ynm(inref)];
+ct=[g.locData.loc.xnm(~inref),g.locData.loc.ynm(~inref)];
+ctt=trafo.transformToReference(2,ct/pixs)*pixs;
+lr.x=g.locData.loc.xnm;lr.y=g.locData.loc.ynm;lr.frame=g.locData.loc.frame;
+ft=g.locData.loc.frame(~inref);
+locpt=g.locData.loc.locprecnm(~inref);
+lt.x=ctt(:,1);lt.y=ctt(:,2);lt.frame=ft;
+[iA,iB]=matchlocsall(lr,lt,0,0,500);
+
+normw=1./g.locData.loc.locprecnm(iA).^2+1./locpt(iB).^2;
+xav=(lr.x(iA)./g.locData.loc.locprecnm(iA).^2+lt.x(iB)./locpt(iB).^2)./normw;
+yav=(lr.y(iA)./g.locData.loc.locprecnm(iA).^2+lt.y(iB)./locpt(iB).^2)./normw;
+
+figure(91)
+plot(lr.y(iA),lt.y(iB),'.')
+
+
+% plot(g.locData.loc.xnm(inref),g.locData.loc.ynm(inref),'.',g.locData.loc.xnm(~inref),g.locData.loc.ynm(~inref),'.')
+figure(92)
+plot(g.locData.loc.xnm(inref),g.locData.loc.ynm(inref),'.',cn(:,1),cn(:,2),'.',xav,yav,'.')
+
+
+ind=true(size(g.locData.loc.xnm));
+ind(iA)=false;
+g.locData.removelocs(ind)
+g.locData.loc.xnm=xav; 
+g.locData.loc.ynm=yav;
+
+g.locData.regroup;
diff --git a/settings/cameras.mat b/settings/cameras.mat
index 9dee023961b3b7ceab8d83f3980674d9a8c884f5..60f284e153d707ad41139f77029724646a43ff7d 100644
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VFJ8TWW3_F&chrgB{{^2ptB$AE*8>0m


From cbb639d2851856a74551176cf25990c94ec16c1f Mon Sep 17 00:00:00 2001
From: Jonas Ries <jonas.ries@gmail.com>
Date: Sat, 5 Dec 2020 16:30:52 +0100
Subject: [PATCH 2/4] implement proper weighting

---
 other/BP_Gauss_analysis.m                     | 68 +++++++------------
 plugins/+Analyze/+sr3D/Biplane_getPSFxy.m     | 61 +++++++++++++----
 plugins/+Process/+Register/CombineChannels.m  |  8 +--
 .../+Fitters/MLE_global_spline.m              |  4 +-
 4 files changed, 79 insertions(+), 62 deletions(-)

diff --git a/other/BP_Gauss_analysis.m b/other/BP_Gauss_analysis.m
index 08f6db30..74837cc0 100644
--- a/other/BP_Gauss_analysis.m
+++ b/other/BP_Gauss_analysis.m
@@ -1,21 +1,26 @@
 
-pixs=100;
+% pixs=100;
 dz=10;
+zoff=750;
 
 %% BEADS: calibrate sx
-figure(88);
+pixs=g.locData.files.file(1).info.cam_pixelsize_um(1)*1000;
+loc=g.locData.getloc({'PSFxnm','PSFynm','frame'},'layer',1,'position','roi');
+indg=loc.PSFxnm>0.1&loc.PSFynm>0.1;
+sx=loc.PSFxnm(indg)/pixs;
+sy=loc.PSFynm(indg)/pixs;
 
-sx=g.locData.loc.PSFxnm/pixs;
-sy=g.locData.loc.PSFynm/pixs;
-frame=g.locData.loc.frame;
-z=frame*dz;
-plot(frame,sx,'.',frame,sy,'.')
+
+frame=loc.frame(indg);
+z=frame*dz-zoff;
+figure(88);
+plot(frame,sx,'+',frame,sy,'.')
 
 ds=sx.^2-sy.^2;
 figure(89)
 plot(frame,ds,'.')
 
-range=[45,95];
+range=[44,100];
 
 inr=frame>range(1)&frame<range(2);
 
@@ -23,52 +28,29 @@
 hold off
 plot(ds(inr),z(inr),'.')
 
-calbead=fit(ds(inr),z(inr),'poly4');
+calbead=fit(ds(inr),z(inr),'smoothingspline','SmoothingParam',.1);
 hold on
-plot(ds(inr),calbead(ds(inr)))
+nds=min(ds(inr)):0.1:max(ds(inr));
+plot(nds,calbead(nds))
 
 maxrangeds=[min(ds(inr)) max(ds(inr))];
+%%
+pfad=[fileparts(g.locData.files.file(1).name) filesep 'beadcal_Gauss_smoothingspline'];
+save(pfad,'calbead','maxrangeds')
 
 %% data: calculate z
+pixs=g.locData.files.file(1).info.cam_pixelsize_um(1)*1000;
 outz=1000;
 sx=g.locData.loc.PSFxnm/pixs;
 sy=g.locData.loc.PSFynm/pixs;
 ds=sx.^2-sy.^2;
 z=calbead(ds);
-g.locData.loc.znm=z-750;
+g.locData.loc.znm=z;
 
-outofrange=ds<maxrangeds(1) | ds>maxrange(2);
+outofrange=ds<maxrangeds(1) | ds>maxrangeds(2) | sx==0 | sy==0;
 g.locData.loc.znm(outofrange)=outz;
+g.locData.regroup;
 
-%% data: average x,y
-trafo=g.locData.files.file.transformation;
-inref=trafo.getRef(g.locData.loc.xnm,g.locData.loc.ynm);
-cr=[g.locData.loc.xnm(inref),g.locData.loc.ynm(inref)];
-ct=[g.locData.loc.xnm(~inref),g.locData.loc.ynm(~inref)];
-ctt=trafo.transformToReference(2,ct/pixs)*pixs;
-lr.x=g.locData.loc.xnm;lr.y=g.locData.loc.ynm;lr.frame=g.locData.loc.frame;
-ft=g.locData.loc.frame(~inref);
-locpt=g.locData.loc.locprecnm(~inref);
-lt.x=ctt(:,1);lt.y=ctt(:,2);lt.frame=ft;
-[iA,iB]=matchlocsall(lr,lt,0,0,500);
-
-normw=1./g.locData.loc.locprecnm(iA).^2+1./locpt(iB).^2;
-xav=(lr.x(iA)./g.locData.loc.locprecnm(iA).^2+lt.x(iB)./locpt(iB).^2)./normw;
-yav=(lr.y(iA)./g.locData.loc.locprecnm(iA).^2+lt.y(iB)./locpt(iB).^2)./normw;
-
-figure(91)
-plot(lr.y(iA),lt.y(iB),'.')
-
-
-% plot(g.locData.loc.xnm(inref),g.locData.loc.ynm(inref),'.',g.locData.loc.xnm(~inref),g.locData.loc.ynm(~inref),'.')
-figure(92)
-plot(g.locData.loc.xnm(inref),g.locData.loc.ynm(inref),'.',cn(:,1),cn(:,2),'.',xav,yav,'.')
-
-
-ind=true(size(g.locData.loc.xnm));
-ind(iA)=false;
-g.locData.removelocs(ind)
-g.locData.loc.xnm=xav; 
-g.locData.loc.ynm=yav;
 
-g.locData.regroup;
+%% data: average x,y
+%use combine channels plugin 
\ No newline at end of file
diff --git a/plugins/+Analyze/+sr3D/Biplane_getPSFxy.m b/plugins/+Analyze/+sr3D/Biplane_getPSFxy.m
index 574a4147..9f3abb23 100644
--- a/plugins/+Analyze/+sr3D/Biplane_getPSFxy.m
+++ b/plugins/+Analyze/+sr3D/Biplane_getPSFxy.m
@@ -17,9 +17,20 @@
                 out.error='selected transformation file does not have a valid transformation';
                 return
             end
-            file=obj.locData.files.file(p.dataselect.Value);
+            
              p.datapart.selection='all';
-            loc=get2ClocPSF(obj.locData.loc,tload.transformation,file,p);
+             if p.allfiles
+                 loc=obj.locData.loc;
+                 keepold=true;
+                 for k=1:length(obj.locData.files.file)
+                     k
+                     loc=get2ClocPSF(loc,tload.transformation,obj.locData.files.file(k),p,keepold);
+                 end
+             else
+                 file=obj.locData.files.file(p.dataselect.Value);
+                 keepold=false;
+                loc=get2ClocPSF(obj.locData.loc,tload.transformation,file,p,keepold);
+             end
             obj.locData.loc=copyfields(obj.locData.loc,loc);
             obj.locData.regroup;
              obj.setPar('locFields',fieldnames(obj.locData.loc))
@@ -53,21 +64,43 @@ function loadbutton(obj,a,b)
 end
 
 
-function loco=get2ClocPSF(loc,transform,file,p)
+function loco=get2ClocPSF(loc,transform,file,p,keepold)
 
- p.datapart.selection='all (T->R)';
-loct=apply_transform_locs(loc,transform,file,p);
+p.datapart.selection='all (T->R)';
+% p.datapart.selection='target';
+infi=file.number==loc.filenumber;
+
+inref=transform.getRef(loc.xnm,loc.ynm);
+locref=copystructReduce(loc,infi&inref);
+locth=copystructReduce(loc,infi&~inref);
+loct=apply_transform_locs(locth,transform,file,p);
 
 % only valid parts?
-[iA,iB,uiA,uiB]=matchlocsall(renamefields(loc),renamefields(loct),0,0,1000);
+[iA,iB,uiA,uiB]=matchlocsall(renamefields(locref),renamefields(loct),0,0,1000);
 length(iA)/(length(uiA)+length(uiB))
-loco.PSFxnm_old=loc.PSFxnm;
-loco.PSFxnm=zeros(size(loc.xnm),'single');
-loco.PSFynm=zeros(size(loc.xnm),'single');
-loco.PSFxnm(iA)=loc.PSFxnm(iA);
-loco.PSFynm(iA)=loc.PSFxnm(iB);
-loco.PSFxnm(iB)=loc.PSFxnm(iA);
-loco.PSFynm(iB)=loc.PSFxnm(iB);
+inffr=find(infi&inref);
+infft=find(infi&~inref);
+
+
+if ~keepold
+    loco.PSFxnm_old=loc.PSFxnm;
+    loco.PSFxnm=zeros(size(loc.xnm),'single');
+    loco.PSFynm=zeros(size(loc.xnm),'single');
+else
+    loco=loc;
+    if ~isfield(loco,'PSFxnm')
+        loco.PSFxnm=zeros(size(loc.xnm),'single');
+    end
+    if ~isfield(loco,'PSFynm')
+        loco.PSFynm=zeros(size(loc.xnm),'single');
+    end
+end
+
+
+loco.PSFxnm(inffr(iA))=loc.PSFxnm(inffr(iA));
+loco.PSFynm(inffr(iA))=loc.PSFxnm(infft(iB));
+loco.PSFxnm(infft(iB))=loc.PSFxnm(inffr(iA));
+loco.PSFynm(infft(iB))=loc.PSFxnm(infft(iB));
 end
 
 function loco=renamefields(loci)
@@ -84,6 +117,8 @@ function loadbutton(obj,a,b)
 pard.dataselect.object=struct('Style','popupmenu','String','File');
 pard.dataselect.position=[2,1];
 
+pard.allfiles.object=struct('Style','checkbox','String','all files');
+pard.allfiles.position=[2,2];
 % pard.datapart.object=struct('Style','popupmenu','String','all|left|right|top|bottom');
 % pard.datapart.position=[3,1];
 
diff --git a/plugins/+Process/+Register/CombineChannels.m b/plugins/+Process/+Register/CombineChannels.m
index ba5293e3..e607b7a3 100644
--- a/plugins/+Process/+Register/CombineChannels.m
+++ b/plugins/+Process/+Register/CombineChannels.m
@@ -45,13 +45,13 @@
                 unmatchedB=copystructReduce(loctt,uiB);
                 fn=fieldnames(loc);
                 if isfield(matchedA,'locprecnm')
-                    wA=1./matchedA.locprecnm;
-                    wB=1./matchedB.locprecnm;
+                    wA=1./matchedA.locprecnm.^2;
+                    wB=1./matchedB.locprecnm.^2;
                 else
                     photA=matchedA.phot;
                     photB=matchedB.phot;
-                    wA=sqrt(photA);
-                    wB=sqrt(photB);
+                    wA=(photA);
+                    wB=(photB);
                 end
                 for k=1:length(fn)
                     switch fn{k}
diff --git a/plugins/+WorkflowModules/+Fitters/MLE_global_spline.m b/plugins/+WorkflowModules/+Fitters/MLE_global_spline.m
index 2349761a..5d389676 100644
--- a/plugins/+WorkflowModules/+Fitters/MLE_global_spline.m
+++ b/plugins/+WorkflowModules/+Fitters/MLE_global_spline.m
@@ -253,8 +253,8 @@ function loadscmos_callback(a,b,obj)
             switch fitpar.mainchannel
                 case 1
                     locs.([names{k} 'err'])=1./sqrt(1./ve(:,1).^2+1./ve(:,2).^2)*sqrt(2);
-                    ve(:,1)=ve(:,1)/errfactor(1);
-                    ve(:,2)=ve(:,2)/errfactor(2);
+                    ve(:,1)=(ve(:,1)/errfactor(1)).^2; %use as weights the correct 1/sigma^2
+                    ve(:,2)=(ve(:,2)/errfactor(2)).^2;
                     locs.(names{k})=sum(v./ve,2)./sum(1./ve,2); %average based on CRLB before weighting
                 case 2
                     locs.(names{k})=v(:,1);

From a6a9a985d02a278c3e5b0e8fa36f3312b903065e Mon Sep 17 00:00:00 2001
From: Jonas Ries <jonas.ries@gmail.com>
Date: Wed, 16 Dec 2020 15:39:43 +0100
Subject: [PATCH 3/4] Cluster analysis added

---
 plugins/+Analyze/+cluster/ClusterStatistics.m | 93 +++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 plugins/+Analyze/+cluster/ClusterStatistics.m

diff --git a/plugins/+Analyze/+cluster/ClusterStatistics.m b/plugins/+Analyze/+cluster/ClusterStatistics.m
new file mode 100644
index 00000000..48799bfc
--- /dev/null
+++ b/plugins/+Analyze/+cluster/ClusterStatistics.m
@@ -0,0 +1,93 @@
+classdef ClusterStatistics<interfaces.DialogProcessor
+%  pair correlation functions calculated according to:
+%  Sengupta, Prabuddha, Tijana Jovanovic-Talisman, Dunja Skoko, Malte Renz, 
+%  Sarah L Veatch, and Jennifer Lippincott-Schwartz. “Probing Protein Heterogeneity 
+%  in the Plasma Membrane Using PALM and Pair Correlation Analysis.” 
+%  Nature Methods 8 (September 18, 2011): 969.
+    properties
+        resultstable
+    end
+    methods
+        function obj=ClusterStatistics(varargin)    
+            obj@interfaces.DialogProcessor(varargin{:}) ;
+            obj.inputParameters={'sr_pixrec','numberOfLayers','sr_pos','sr_size','layers','sr_layerson'};
+%             obj.history=true;    
+            obj.showresults=true;
+        end
+        
+        function out=run(obj,p)
+           out=[];          
+           layers=find(obj.getPar('sr_layerson'));
+           locs=obj.locData.getloc({'xnm','ynm','znm','clusterindex'},'layer',layers,'Position','roi');
+           clusterinds=unique(locs.clusterindex(locs.clusterindex>0));
+           cind=1;
+           ax=obj.initaxis('boundaries');
+           hold(ax,'off')
+           plot(ax,locs.xnm,locs.ynm,'b.');
+           for k=1:length(clusterinds)
+               inc=locs.clusterindex==clusterinds(k);
+               if sum(inc)<p.minloc
+                   continue
+               end
+               xh=double(locs.xnm(inc));yh=double(locs.ynm(inc));zh=double(locs.znm(inc));
+               numlocs(cind,1)=sum(inc);
+               xpos(cind,1)=mean(xh);
+               ypos(cind,1)=mean(yh);
+               zpos(cind,1)=mean(zh);
+               [kc3,volumeCHull(cind,1)]=convhull(xh,yh,zh);
+               [kc2,areaCHull(cind,1)]=convhull(xh,yh);
+               [kb3,volumeB(cind,1)]=boundary(xh,yh,zh);
+               [kb2,areaB(cind,1)]=boundary(xh,yh);
+               cID(cind,1)=clusterinds(k);
+               cind=cind+1;
+               hold(ax,'on')
+               plot(ax,xh,yh,'+')
+               
+               plot(ax,xh(kc2),yh(kc2),'r')
+               plot(ax,xh(kb2),yh(kb2),'m')
+           end
+           obj.resultstable=table(cID,numlocs,areaCHull,volumeCHull,areaB,volumeB,xpos,ypos,zpos);
+           
+        end
+        function pard=guidef(obj)
+            pard=guidef(obj);
+        end
+        function exportbutton(obj,a,b)
+            tableo=obj.resultstable;
+            fn=obj.getPar('lastSMLFile');
+            if ~isempty(fn)
+                fno=strrep(fn,'_sml.mat','_cluster.csv');
+            else
+                fno='*.csv';
+            end
+           [f,p]=uiputfile(fno);
+           if f
+               writetable(tableo,[p f])
+           end
+            
+        end
+
+    end
+end
+
+
+
+
+function pard=guidef(obj)
+pard.minloct.object=struct('String','min number of locs per cluster','Style','text');
+pard.minloct.position=[1,1];
+pard.minloct.Width=2;
+pard.minloc.object=struct('String','10','Style','edit');
+pard.minloc.position=[1,3];
+pard.minloc.Width=0.5;
+
+pard.export.object=struct('String','export','Style','pushbutton','Callback',@obj.exportbutton);
+pard.export.position=[2,1];
+pard.export.Width=1;
+
+
+pard.plugininfo.name='Cluster Statistics';
+pard.plugininfo.description= 'Calculates spatial statistics based on pair correlation and Ripleys K function. pair correlation functions calculated according to: Sengupta, Prabuddha, Tijana Jovanovic-Talisman, Dunja Skoko, Malte Renz, Sarah L Veatch, and Jennifer Lippincott-Schwartz. “Probing Protein Heterogeneity  Nature Methods 8 (September 18, 2011): 969.';
+pard.plugininfo.type='ProcessorPlugin';
+
+end
\ No newline at end of file

From c33fad23bd823edf38c27585bbe5fe9c65da6fb0 Mon Sep 17 00:00:00 2001
From: Jonas Ries <jonas.ries@gmail.com>
Date: Wed, 16 Dec 2020 19:01:10 +0100
Subject: [PATCH 4/4] intensity from Gauss

---
 .../+IntensityCalculator/roi2int_fitG.m       | 163 ++++++++++--------
 1 file changed, 92 insertions(+), 71 deletions(-)

diff --git a/plugins/+WorkflowModules/+IntensityCalculator/roi2int_fitG.m b/plugins/+WorkflowModules/+IntensityCalculator/roi2int_fitG.m
index 8bd15aeb..83154314 100644
--- a/plugins/+WorkflowModules/+IntensityCalculator/roi2int_fitG.m
+++ b/plugins/+WorkflowModules/+IntensityCalculator/roi2int_fitG.m
@@ -62,79 +62,96 @@ function prerun(obj,p)
     PSFypix=PSFxpix;
 end
  nrange=-dn:dn;
-if ~p.fitonbg%nargin<7||isempty(bgroi)
+ 
+switch p.fitmode.selection
+ 
+    case 'fit'
+        if ~p.fitonbg%nargin<7||isempty(bgroi)
 
-    for k=1:sim(3)
-        gauss=make2DGaussfast(dx(k),dy(k),PSFxpix(k),PSFypix(k),nrange);
-%         gauss=exp((-(dx(k)-X).^2)/2/PSFxpix(k)^2-((dy(k)-Y).^2)/2/PSFypix(k)^2)/pi/PSFxpix(k)/PSFypix(k)/2;
-%         weights=sqrt(gauss);
-        Xmat=horzcat(gauss(:), gauss(:)*0+1);
-        roih=roi(mp(1)-dn:mp(1)+dn,mp(2)-dn:mp(2)+dn,k);
-        outp(k,1:2)=Xmat\roih(:);
-        
-        imgfit=gauss*outp(k,1)+outp(k,2);
-        resim=imgfit-roih;
-        res=sqrt(resim.^2./max(imgfit,1));
-        outp(k,3)=mean(res(:));
-        if  0% info.phot(k)>2500 %outp(k,1)>300 %any(roih(:))%p(k,1)>2500~
-            outp(k,:)
-            outp(k,1)./info.phot(k)
-            figure(67)
-            subplot(2,2,1)
-            imagesc(-dn:dn,-dn:dn,roih);
-            hold on
-            plot(dx(k),dy(k),'+')
-            hold off
-            subplot(2,2,2);
-            imagesc(-dn:dn,-dn:dn,gauss*outp(k,1)+outp(k,2))
-            hold on
-            plot(dx(k),dy(k),'+')
-            hold off
-            subplot(2,2,3);
-            imagesc(-dn:dn,-dn:dn,gauss*outp(k,1)+outp(k,2)-roih)
-            subplot(2,2,4);
-            imagesc(-dn:dn,-dn:dn,res)
-            waitforbuttonpress
+            for k=1:sim(3)
+                gauss=make2DGaussfast(dx(k),dy(k),PSFxpix(k),PSFypix(k),nrange);
+        %         gauss=exp((-(dx(k)-X).^2)/2/PSFxpix(k)^2-((dy(k)-Y).^2)/2/PSFypix(k)^2)/pi/PSFxpix(k)/PSFypix(k)/2;
+        %         weights=sqrt(gauss);
+                Xmat=horzcat(gauss(:), gauss(:)*0+1);
+                roih=roi(mp(1)-dn:mp(1)+dn,mp(2)-dn:mp(2)+dn,k);
+                outp(k,1:2)=Xmat\roih(:);
+
+                imgfit=gauss*outp(k,1)+outp(k,2);
+                resim=imgfit-roih;
+                res=sqrt(resim.^2./max(imgfit,1));
+                outp(k,3)=mean(res(:));
+                if  0% info.phot(k)>2500 %outp(k,1)>300 %any(roih(:))%p(k,1)>2500~
+                    outp(k,:)
+                    outp(k,1)./info.phot(k)
+                    figure(67)
+                    subplot(2,2,1)
+                    imagesc(-dn:dn,-dn:dn,roih);
+                    hold on
+                    plot(dx(k),dy(k),'+')
+                    hold off
+                    subplot(2,2,2);
+                    imagesc(-dn:dn,-dn:dn,gauss*outp(k,1)+outp(k,2))
+                    hold on
+                    plot(dx(k),dy(k),'+')
+                    hold off
+                    subplot(2,2,3);
+                    imagesc(-dn:dn,-dn:dn,gauss*outp(k,1)+outp(k,2)-roih)
+                    subplot(2,2,4);
+                    imagesc(-dn:dn,-dn:dn,res)
+                    waitforbuttonpress
+                end
+            end
+        else %fit bg
+        %     bgnorm=(2*dn+1)^2;
+            nrange=-dn:dn;
+            for k=1:sim(3)
+                bgh=bg(k);
+        %         exponent=(-(dx(k)-X).^2)/2/PSFxpix(k)^2-((dy(k)-Y).^2)/2/PSFypix(k)^2;
+        %         gauss=exp(exponent)/pi/PSFxpix(k)/PSFypix(k)/2;
+                gauss=make2DGaussfast(dx(k),dy(k),PSFxpix(k),PSFypix(k),nrange);
+        %         weights=sqrt(gauss);
+                Xmat=horzcat(gauss(:));
+        %         bgh=bg(mp(1)-dn:mp(1)+dn,mp(2)-dn:mp(2)+dn,k);
+                roih=roi(mp(1)-dn:mp(1)+dn,mp(2)-dn:mp(2)+dn,k)-bgh;
+                outp(k,1)=Xmat\roih(:);
+                outp(k,2)=bgh;
+                imgfit=gauss*outp(k,1)+outp(k,2);
+                resim=imgfit-roih;
+                res=resim.^2./max(imgfit,1);
+                outp(k,3)=mean(res(:));
+        %         p(k,2)=(sum(bgh(:)))/bgnorm;
+                if 0%p(k,1)>2500~
+                    outp(k,:)
+                    figure(67)
+                    subplot(2,2,1)
+                    imagesc(-dn:dn,-dn:dn,roih);
+                    hold on
+                    plot(dx(k),dy(k),'+')
+                    hold off
+                    subplot(2,2,2);
+                    imagesc(-dn:dn,-dn:dn,gauss*outp(k,1)+outp(k,2))
+                    hold on
+                    plot(dx(k),dy(k),'+')
+                    hold off
+                    subplot(2,2,3);
+                    imagesc(-dn:dn,-dn:dn,gauss*outp(k,1)+outp(k,2)-roih)
+                    waitforbuttonpress
+                end
+            end
         end
-    end
-else %fit bg
-%     bgnorm=(2*dn+1)^2;
-    nrange=-dn:dn;
-    for k=1:sim(3)
-        bgh=bg(k);
-%         exponent=(-(dx(k)-X).^2)/2/PSFxpix(k)^2-((dy(k)-Y).^2)/2/PSFypix(k)^2;
-%         gauss=exp(exponent)/pi/PSFxpix(k)/PSFypix(k)/2;
-        gauss=make2DGaussfast(dx(k),dy(k),PSFxpix(k),PSFypix(k),nrange);
-%         weights=sqrt(gauss);
-        Xmat=horzcat(gauss(:));
-%         bgh=bg(mp(1)-dn:mp(1)+dn,mp(2)-dn:mp(2)+dn,k);
-        roih=roi(mp(1)-dn:mp(1)+dn,mp(2)-dn:mp(2)+dn,k)-bgh;
-        outp(k,1)=Xmat\roih(:);
-        outp(k,2)=bgh;
-        imgfit=gauss*outp(k,1)+outp(k,2);
-        resim=imgfit-roih;
-        res=resim.^2./max(imgfit,1);
-        outp(k,3)=mean(res(:));
-%         p(k,2)=(sum(bgh(:)))/bgnorm;
-        if 0%p(k,1)>2500~
-            outp(k,:)
-            figure(67)
-            subplot(2,2,1)
-            imagesc(-dn:dn,-dn:dn,roih);
-            hold on
-            plot(dx(k),dy(k),'+')
-            hold off
-            subplot(2,2,2);
-            imagesc(-dn:dn,-dn:dn,gauss*outp(k,1)+outp(k,2))
-            hold on
-            plot(dx(k),dy(k),'+')
-            hold off
-            subplot(2,2,3);
-            imagesc(-dn:dn,-dn:dn,gauss*outp(k,1)+outp(k,2)-roih)
-            waitforbuttonpress
+    case 'multiply'
+        for k=1:sim(3)
+            if p.fitonbg
+                bgh=bg(k);
+            else
+                bgh=0;
+            end
+            gauss=make2DGaussfast(dx(k),dy(k),PSFxpix(k),PSFypix(k),nrange);
+            roih=roi(mp(1)-dn:mp(1)+dn,mp(2)-dn:mp(2)+dn,k)-bgh;
+            outp(k,1)=sum(roih(:).*gauss(:))/sum(gauss(:));
+            outp(k,2)=bgh;
+            outp(k,3)=0;
         end
-    end
-
 end
 end
 
@@ -158,9 +175,13 @@ function prerun(obj,p)
 
 pard.fitonbg.object=struct('Style','checkbox','String','subtract BG before fitting','Value',0);
 pard.fitonbg.position=[3,1];
-pard.fitonbg.Width=4;
+pard.fitonbg.Width=3;
 pard.fitonbg.TooltipString='If selected, the background is subtracted and the fit is performed with an offset=0. Otherwise the background is a fit parameter.';
 
+pard.fitmode.object=struct('Style','popupmenu','String',{{'fit','multiply'}},'Value',1);
+pard.fitmode.position=[3,4];
+pard.fitmode.Width=1;
+
 info.prefix='fit';
 info.name='fit';
 info.fields={'fit_n','fit_bg','fit_res'};