diff --git a/workflow/script-run-workflow b/workflow/script-run-workflow
index 05581f03..6c9ca1e4 100755
--- a/workflow/script-run-workflow
+++ b/workflow/script-run-workflow
@@ -538,11 +538,11 @@ easy() {
     export SCANS_DIR PROJECT_DATE EASY_DIR PROJECT_USER PROJECT_PREFIX EASY_SUFFIX EASY_RESULTS_DIR MASTER_PLATE_FILE DRUG_MEDIA_FILE
     echo "Hit enter to use the default EASY results directory $SCANS_DIR/Results_${PROJECT_PREFIX}_($PROJECT_SUFFIX)"
     (( YES )) || read -r -p "Or enter a custom suffix: " suffix
-    EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${Ssuffix:-$PROJECT_SUFFIX}"
+    EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${suffix:-$PROJECT_SUFFIX}"
     while [[ -d $EASY_RESULTS_DIR ]]; do
       count=1
       if [[ $count -eq 1 ]] && ask "$EASY_RESULTS_DIR already exists, increment dir name (y) or overwrite (N)?"; then
-        EASY_SUFFIX="${Ssuffix:-$PROJECT_SUFFIX}.$((count++))"
+        EASY_SUFFIX="${suffix:-$PROJECT_SUFFIX}.$((count++))"
         EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${EASY_SUFFIX}"
       else
         EASY_SUFFIX=${suffix:-$PROJECT_SUFFIX}
diff --git a/workflow/templates/easy/DMPexcel2mat.m b/workflow/templates/easy/DMPexcel2mat.m
index 14213a2e..a1c834b5 100755
--- a/workflow/templates/easy/DMPexcel2mat.m
+++ b/workflow/templates/easy/DMPexcel2mat.m
@@ -253,13 +253,13 @@ if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinat
   if ispc
     while (~isequal(txt{excLnNum,2},'###'))
       numb=numb+1;    
-      DM.drug(numb) = {raw(excLnNum,2)};
-      DM.conc(numb) = {raw(excLnNum,3)};
-      DM.media(numb) = {raw(excLnNum,4)};
-      DM.mod1(numb) = {raw(excLnNum,5)};
-      DM.conc1(numb) = {raw(excLnNum,6)};
-      DM.mod2(numb) = {raw(excLnNum,7)};
-      DM.conc2(numb) = {raw(excLnNum,8)};
+      DM.drug(numb)={raw(excLnNum,2)};
+      DM.conc(numb)={raw(excLnNum,3)};
+      DM.media(numb)={raw(excLnNum,4)};
+      DM.mod1(numb)={raw(excLnNum,5)};
+      DM.conc1(numb)={raw(excLnNum,6)};
+      DM.mod2(numb)={raw(excLnNum,7)};
+      DM.conc2(numb)={raw(excLnNum,8)};
       excLnNum=excLnNum+1;
       msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
     end
@@ -268,20 +268,20 @@ if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinat
     excLnNum=1;
     while (~isequal(DMcell{excLnNum+1,2},'###'))
       numb=numb+1;    
-      DM.drug(numb) = {DMtbl(excLnNum,2)};
-      DM.drug(numb)= table2cell(DM.drug{numb});
-      DM.conc(numb) = {DMtbl(excLnNum,3)};
-      DM.conc(numb)= table2cell(DM.conc{numb});
-      DM.media(numb) = {DMtbl(excLnNum,4)};
-      DM.media(numb)= table2cell(DM.media{numb});
-      DM.mod1(numb) = {DMtbl(excLnNum,5)};
-      DM.mod1(numb)= table2cell(DM.mod1{numb});
-      DM.conc1(numb) = {DMtbl(excLnNum,6)};
-      DM.conc1(numb)= table2cell(DM.conc1{numb});
-      DM.mod2(numb) = {DMtbl(excLnNum,7)};
-      DM.mod2(numb)= table2cell(DM.mod2{numb});
-      DM.conc2(numb) = {DMtbl(excLnNum,8)};
-      DM.conc2(numb)= table2cell(DM.conc2{numb});
+      DM.drug(numb)={DMtbl(excLnNum,2)};
+      DM.drug(numb)=table2cell(DM.drug{numb});
+      DM.conc(numb)={DMtbl(excLnNum,3)};
+      DM.conc(numb)=table2cell(DM.conc{numb});
+      DM.media(numb)={DMtbl(excLnNum,4)};
+      DM.media(numb)=table2cell(DM.media{numb});
+      DM.mod1(numb)={DMtbl(excLnNum,5)};
+      DM.mod1(numb)=table2cell(DM.mod1{numb});
+      DM.conc1(numb)={DMtbl(excLnNum,6)};
+      DM.conc1(numb)=table2cell(DM.conc1{numb});
+      DM.mod2(numb)={DMtbl(excLnNum,7)};
+      DM.mod2(numb)=table2cell(DM.mod2{numb});
+      DM.conc2(numb)={DMtbl(excLnNum,8)};
+      DM.conc2(numb)=table2cell(DM.conc2{numb});
       excLnNum=excLnNum+1;
       msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
     end
@@ -296,28 +296,28 @@ if isequal(Linked,0) % 0 indicates Drugs and Media are combinatorial
   if ispc
     while (~isequal(txt{excLnNum,2},'###'))
       drgCnt=drgCnt+1;    
-      DM.drug(drgCnt) = {raw(excLnNum,2)};
-      DM.conc(drgCnt) = {raw(excLnNum,3)};
+      DM.drug(drgCnt)={raw(excLnNum,2)};
+      DM.conc(drgCnt)={raw(excLnNum,3)};
       excLnNum=excLnNum+1;
     end
 
     while (~isequal(txt{excLnNum,4},'###'))
       medCnt=medCnt+1;    
-      DM.media(medCnt) = {raw(excLnNum,4)};
+      DM.media(medCnt)={raw(excLnNum,4)};
       excLnNum=excLnNum+1;
     end
   else
     excLnNum=1;
     while (~isequal(DMcell{excLnNum+1,2},'###'))
       drgCnt=drgCnt+1;    
-      DM.drug(drgCnt) = {DMtbl(excLnNum,2)};
-      DM.conc(drgCnt) = {DMtbl(excLnNum,3)};
+      DM.drug(drgCnt)={DMtbl(excLnNum,2)};
+      DM.conc(drgCnt)={DMtbl(excLnNum,3)};
       excLnNum=excLnNum+1;
     end
 
     while (~isequal(DMcel{excLnNum+1,4},'###'))
       medCnt=medCnt+1;    
-      DM.media(medCnt) = {DMtbl(excLnNum,4)};
+      DM.media(medCnt)={DMtbl(excLnNum,4)};
       excLnNum=excLnNum+1;
     end
   end
diff --git a/workflow/templates/easy/DgenResults.m b/workflow/templates/easy/DgenResults.m
index 8247fcfc..1c2d83d1 100755
--- a/workflow/templates/easy/DgenResults.m
+++ b/workflow/templates/easy/DgenResults.m
@@ -2,12 +2,12 @@
 % Updated 240724 Bryan C Roessler to improve file operations and portability
 %
 global scansDir
-global easyResultsDir
 global matFile
 global defImParMat
 global printResultsDir
 global fotosResultsDir
 global pointMapsFile
+global pointMapsResultsDir
 
 ln=1;
 
@@ -52,6 +52,7 @@ end
 %   localscansDir=scansDir;
 % end
 
+% TODO this seems weird
 expNm=scansDir(max(strfind(scansDir,'/'))+1:end);
 drivePos=min(strfind(scansDir,'/'));
 drive=scansDir(1:(drivePos-1));
@@ -85,9 +86,9 @@ drgCnt=0;
 medCnt=0;
 
 try
-  load(fullfile(easyResultsDir,'Fotos','Nbdg')) % Convolute scan array data into plates
+  load(fullfile(fotosResultsDir,'Nbdg')) % Convolute scan array data into plates
 catch
-  load(fullfile(easyResultsDir,'PTmats','Nbdg')) % Convolute scan array data into plates
+  load(fullfile(pointMapsResultsDir,'Nbdg')) % Convolute scan array data into plates
 end
 
 for s=1:size(scan,2)
@@ -102,14 +103,14 @@ for s=1:size(scan,2)
   for p=1:size((scan(s).plate),2)
     totPlCnt=totPlCnt+1;
     if destPerMP>1 && rem(totPlCnt,destPerMP)==1
-      mpCnt=mpCnt+1
+      mpCnt=mpCnt+1;
     end
     if destPerMP==1
-      mpCnt=mpCnt+1
+      mpCnt=mpCnt+1;
     end
     pertCnt=rem(totPlCnt,destPerMP);
     if pertCnt==0
-      pertCnt=destPerMP
+      pertCnt=destPerMP;
     end
     pert=strcat('Perturb_',num2str(pertCnt));
     s % TODO seems wrong
@@ -365,9 +366,9 @@ if isequal(opt,'DB')||isequal(opt,'Both')
   try
     copyfile(DBfilename,DBupload)
   catch ME
-    rep = getReport(ME, 'basic');
+    rep=getReport(ME, 'basic');
     rep=strcat('Failed copyfile to ',DBupload,' -', rep);
-      errordlg(rep)
+    errordlg(rep)
   end
 end
 
@@ -424,8 +425,8 @@ try
           asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
           aucEndPt=  strcat('AUC',num2str(asd(9)));
         end
-        fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene')
-        fprintf(fid, '\t %s',aucEndPt)
+        fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene');
+        fprintf(fid, '\t %s',aucEndPt);
         fprintf(fid, '\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd'); %17_0629 MinBaseIntens update for MedianBase label
       end     
       clear outTseries
@@ -438,7 +439,7 @@ try
       outIntens=[];
       RawIntens=[];
       RawIntens=scan(s).plate(p).intens;
-      RawIntensSize= size(RawIntens,2)
+      RawIntensSize=size(RawIntens,2);
       clear Ag;  %Ag is Growth Area
       Ag=scan(s).plate(p).Ag;
       AgSize= size(Ag);
diff --git a/workflow/templates/easy/EASYconsole.m b/workflow/templates/easy/EASYconsole.m
index 4353468f..3257376a 100644
--- a/workflow/templates/easy/EASYconsole.m
+++ b/workflow/templates/easy/EASYconsole.m
@@ -20,6 +20,7 @@ function varargout = EASYconsole(varargin)
   global mpdmFile
   global userName
   global srchRange
+  global searchRangeFile
 
   % Initialize some variables from matlab
   easyPath=which(mfilename);
@@ -115,7 +116,7 @@ function varargout = EASYconsole(varargin)
   else
     % Try to find MasterPlate_ file on our own
     mp=fullfile(scansDir,'MasterPlateFiles',strcat('MasterPlate_', easySuffix,'.xlsx'));
-    if exist(mp, 'file'))
+    if exist(mp, 'file')
       masterPlateFile=mp;
       disp(strcat('Using drug media file: ', masterPlateFile, ' from internal logic'))
     else
@@ -129,7 +130,7 @@ function varargout = EASYconsole(varargin)
   else
     % Try to find MasterPlate_ file on our own
     dm=fullfile(scansDir,'MasterPlateFiles',strcat('DrugMedia_', easySuffix,'.xlsx'));
-    if exist(mp, 'file'))
+    if exist(mp, 'file')
       drugMediaFile=dm;
       disp(strcat('Using drug media file: ', drugMediaFile, ' from internal logic'))
     else
@@ -147,16 +148,16 @@ function varargout = EASYconsole(varargin)
   fotosResultsDir=fullfile(easyResultsDir,'Fotos');
   figsResultsDir=fullfile(easyResultsDir,'figs');
   pointMapsResultsDir=fullfile(easyResultsDir,'PTmats');
-  pointMapsFile=fullfile(pointMapsResultsDir,'NImParameters.mat')
-  oldPointMapsFile=fullfile(pointMapsResultsDir,'ImParameters.mat')
-  CSearchRangeFile=fullfile(fotosResultsDir,'CSearchRange.mat');
+  pointMapsFile=fullfile(pointMapsResultsDir,'NImParameters.mat');
+  oldPointMapsFile=fullfile(pointMapsResultsDir,'ImParameters.mat');
+  searchRangeFile=fullfile(fotosResultsDir,'CSearchRange.mat');
   mpdmFile=fullfile(matDir,'MPDM.mat');
 
   % This can be removed, I think it should add the previous search range?
   % Might be nice feature but can remove if it causes issues
   % We are using searchRangeNum to hold old CSrchRange value(s)
-  if exist(CSearchRangeFile, 'file')
-    searchRangeNum=load(CSearchRangeFile);
+  if exist(searchRangeFile, 'file')
+    searchRangeNum=load(searchRangeFile);
   end
   % Add easyDir to the MATLAB path
   % I have not idea if this is necessary or works but theoretically should
@@ -212,7 +213,6 @@ end
 % varargin--input arguments to EASYconsole (see VARARGIN)
 function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
   global fhconsole
-  global easyResultsDir
 
   % Choose default command line output for EASYconsole
   handles.output=hObject;
@@ -371,7 +371,7 @@ function LoadDatFile_Callback(~, ~, ~)
     end
 
     % Create supporting dirs
-    dirs={'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'}
+    dirs={'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'};
     for i=1:length(dirs)
       d=dirs{i};
       if ~exist(fullfile(easyResultsDir, d), 'dir')
diff --git a/workflow/templates/easy/NCfitImCFparforFailGbl2.m b/workflow/templates/easy/NCfitImCFparforFailGbl2.m
index 1e81b5fa..0952b7b6 100755
--- a/workflow/templates/easy/NCfitImCFparforFailGbl2.m
+++ b/workflow/templates/easy/NCfitImCFparforFailGbl2.m
@@ -20,18 +20,18 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
   par4resMat=zeros(384,27);
   par4resMatStd=zeros(384,27);
 
-  % Spot(cultures) loop
-  for ii=1:384   %startSpot:numCultures
-    ii;  %%%db print out the culture number 
+  % Spot (cultures) loop
+  for ii=1:384   % startSpot:numCultures
+    ii; % db print out the culture number 
     timepts=[];
     currValues=[];
     currSpotAreas=[];
     currSpotArea=[];
     dataMatrix=[];
-    selTimesStd=[];  %191024 parfor
-    selIntensStd=[]; %191024 parfor
-    FiltTimesELr=[]; %191024 parfor
-    NormIntensELr=[]; %191024 parfor
+    selTimesStd=[]; % 191024 parfor
+    selIntensStd=[]; % 191024 parfor
+    FiltTimesELr=[]; % 191024 parfor
+    NormIntensELr=[]; % 191024 parfor
     
     % add offset...1 offset PER PLATE
     timepts=times + timeOffsets;  % (floor((ii-1)/arrayFormat) + 1);    
@@ -48,7 +48,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
     currNormIntens=currValues/currSpotArea;
     tmpx=find(currNormIntens>5); %15jh % 2.3);
     validSpot=true;
-    if(isempty(tmpx) || (length(tmpx)<3)) 
+    if(isempty(tmpx) || length(tmpx)<3)
         validSpot=false;
         normIntens=currNormIntens;
         filterTimes=timepts; %filterTimes; %currTimes;
@@ -63,9 +63,9 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
       resMat=zeros(1,27);
       hold off;
       dataMatrix=[];
-      K=0;r=0;l=0;Klow=0;Kup=0;rlow=0;rup=0;llow=0;lup=0;AUC=0;MSR=0; rsquare=0; 
+      K=0;r=0;l=0;Klow=0;Kup=0;rlow=0;rup=0;llow=0;lup=0;AUC=0;MSR=0;rsquare=0; 
       bl=0;
-      Tpt1=0; numFitTpts =0;thresGT2=0;minTime=0;fitbl=0; %diagnostic outputs only 
+      Tpt1=0;numFitTpts=0;thresGT2=0;minTime=0;fitbl=0; % diagnostic outputs only 
       
       timepts=timepts; % timepts=currTimes; parfor
       normIntens=currNormIntens;
@@ -82,7 +82,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
         threshold=0;
       end
 
-      dropThreshold=-0.0001* max(normIntens);
+      dropThreshold=-0.0001*max(normIntens);
 
       % Initialize dataMatrix
       dataMatrix(1,:)=timepts;
@@ -102,7 +102,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
       % NCLoIntstdTrim
       % NCLoSstdTrim.m called by NCfilImCF and NCfil.m
       flg1=0;
-      loScurvLim=stdLoIntLim;  %
+      loScurvLim=stdLoIntLim;
       loStimeN=1;
       last2n=1;
       stdDev=[];
@@ -110,26 +110,27 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
       for n=1:meanIntIndPt
         if nrmIntens0(n)<=0
           nrmIntens0(n)=0;
-        end      
+        end    
         if(nrmIntens0(n)<threshold)
           if (loStimeN-2)>0
             dataMatrix(3,1:(n-2))=2; % add to lowIntensity cull flags, the pre S cull data
           else 
-            dataMatrix(3,1:n)=2;end
-            dataMatrix(3,1:(n-2))=2;
-            last2n=n; 
+            dataMatrix(3,1:n)=2;
+          end
+          dataMatrix(3,1:(n-2))=2;
+          last2n=n; 
+        end
+        if n<(length(nrmIntens0)-3)
+          x=nrmIntens0(n:(n+3));
+          stdDev(n)=std(x);
+          if (stdDev(n)<loScurvLim && flg1~=1)
+            loStime=timepts(n); 
+            loStimeN=n;
           end
-          if n<(length(nrmIntens0)-3)
-            x=nrmIntens0(n:(n+3));
-            stdDev(n)=std(x);
-            if (stdDev(n)<loScurvLim && flg1~=1)
-              loStime=timepts(n); 
-              loStimeN=n;
-            end
           if stdDev(n)>6
-            flg1=1
-          end % detect S curve rise->stop stdLoInt detection
-        end  
+            flg1=1;
+          end
+        end
       end
 
       % TODO repetitive code
@@ -142,14 +143,14 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
       qcutoff=2;
       qind=find(normIntens>2);  %,:,'first');
       if ~isempty(qind(3))
-        qcutoff=qind(3)
+        qcutoff=qind(3);
       end
       [minInt,I]=min(normIntens(2:qcutoff));
       bl=minInt;
-      minTime=dataMatrix(1,I);  %diagnostic output only
+      minTime=dataMatrix(1,I);
 
       if (length(qind)>5)&&I>1
-        dataMatrix(3,1:(I-1))=5
+        dataMatrix(3,1:(I-1))=5;
       end
 
       tGT2Flg=0;
@@ -157,7 +158,7 @@ function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanInte
         dataMatrix(4,n)=normIntens(n)-bl; 
         if n>I && dataMatrix(4,n)>=2 && tGT2Flg==0
           thresGT2=n;thresGT2Tm=dataMatrix(1,n);tGT2Flg=1;
-        end %diagnostic output only    
+        end   
       end
 
       resMat(18)=bl;
diff --git a/workflow/templates/easy/NCscurImCF_3parfor.m b/workflow/templates/easy/NCscurImCF_3parfor.m
index f557671b..d7f5ea45 100755
--- a/workflow/templates/easy/NCscurImCF_3parfor.m
+++ b/workflow/templates/easy/NCscurImCF_3parfor.m
@@ -86,7 +86,7 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
     if(isnan(Klow)||isnan(Kup)||isnan(llow)||isnan(lup)||isnan(rlow)||isnan(rup))
       NANcond=1; stdNANcond=1; % stdNANcond added to relay not to attempt ELr as there is no curve to find critical point
     end  
-  catch ME
+  catch
     % if no data is given, return zeros
     AUC=0;MSR=0;K=0;r=0;l=0;rsquare=0;Klow=0;Kup=0;
     rlow=0;rup=0;lup=0;llow=0; 
@@ -222,7 +222,7 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
         GrowthELr=K ./ (1 +  exp(-r.* (t - l )));
         fitblELr=min(GrowthELr);   %jh diag
       end
-    catch ME
+    catch
       % if no data is given, return zeros
       AUC=0;MSR=0;K=0;r=0;l=0;rsquare=0;Klow=0;Kup=0;
       rlow=0;rup=0;lup=0;llow=0; %normIntens=[];
@@ -290,7 +290,7 @@ function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntens
       resMat(19)=fitblStd; % only applicable to Std curve Fit; ELr superceeds and makes meaningless
       resMat(20)=minTime; % only applicable to Std curve Fit; ELr superceeds and makes meaningless
     end  % if r3>r1
-  catch ME
+  catch
     % if no data is given, return zeros
     AUC=0;MSR=0;K=0;r=0;l=0;rsquare=0;Klow=0;Kup=0;
     rlow=0;rup=0;lup=0;llow=0; % normIntens=[];
diff --git a/workflow/templates/easy/NImParamRadiusGui.m b/workflow/templates/easy/NImParamRadiusGui.m
index d9976c07..09a79b0a 100755
--- a/workflow/templates/easy/NImParamRadiusGui.m
+++ b/workflow/templates/easy/NImParamRadiusGui.m
@@ -21,6 +21,7 @@ function NImParamRadiusGui(scansDir)
   global numCols
   global scanSize
   global scanMax
+  global searchRangeFile
 
   % Ncode ImRobot adaptation
   % TODO this code block and variables needs explanation
@@ -38,17 +39,17 @@ function NImParamRadiusGui(scansDir)
   selScan=1;
   SWgrowthArea=1;
 
-  if exist(pointMapsFile)
+  if exist(pointMapsFile, 'file')
     load(pointMapsFile);
   else
     load(fullfile(PTmats,'NImParameters')) % hardcoded default
     disp('WARNING: Using hardcoded NImParameters.mat')
   end
-  ImParMat
+  ImParMat;
   % if ~exist('searchRangeNum','var') || isempty(searchRangeNum)
-  if exist(CSearchRangeFile), 'file')
-    load(CSearchRangeFile);
-    CSearchRange;
+  if exist(searchRangeFile, 'file')
+    load(searchRangeFile);
+    CSearchRange; % TODO, might be an issue, figure out what this is doing
   end
       
   % yInitPos=0.30;
@@ -117,6 +118,8 @@ function NImParamRadiusGui(scansDir)
   btnNumber=7;
   yPos=0.85-(btnNumber-1)*(btnHt+spacing);
   btnPos=[xPos yPos-spacing btnWid btnHt];
+
+  % TODO, I don't think these are defined?
   try
     srchRange=ImParMat(12);
   catch  % Legacy default value was 18 before being made a user input variable (ImParMat(12)). A preferable value now might be 12 or 14.
@@ -164,7 +167,6 @@ function NImParamRadiusGui(scansDir)
     'callback',{@load_listbox});  %'uiresume(gcbf)'); 'Position', [5 100 60 20])
   
   function load_listbox(source,~)
-    global 
     userIndx=(get(source,'value'));
     userStr=(get(source,'string'));
     %scLstIndx=str2num(char(strrep(userStr(userIndx), 'Scan', '')))
@@ -239,7 +241,7 @@ function NImParamRadiusGui(scansDir)
   searchRangeNum;
 
   save(pointMapsFile, 'ImParMat');
-  save(CSearchRangeFile,'searchRangeNum');
+  save(searchRangeFile,'searchRangeNum');
 
   close
   return
diff --git a/workflow/templates/easy/NIscanIntensBGpar4GblFnc.m b/workflow/templates/easy/NIscanIntensBGpar4GblFnc.m
index 0d6ad8dc..16fa386c 100755
--- a/workflow/templates/easy/NIscanIntensBGpar4GblFnc.m
+++ b/workflow/templates/easy/NIscanIntensBGpar4GblFnc.m
@@ -1,15 +1,16 @@
 %% CALLED BY par4GblFnc8c.m %%
 function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ...
-    NIscanIntensBGpar4GblFnc(Fflg, tifFileLst, ImParMat,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
-    tptLength,selScan,Empsc,~, ~, ~, ~,easyResultsDir, Tmpsbdg1)    
+  NIscanIntensBGpar4GblFnc(Fflg, tifFileLst, ImParMat,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
+  tptLength,selScan,Empsc,~, ~, ~, ~,easyResultsDir, Tmpsbdg1)    
 
   global matFile
   global CSrchRng
   global figsResultsDir
   global fotosResultsDir
 
-  searchIntens=[]; intensMax=[]; detMaxPos=[]; scIntens=[]; areaOfIntensAboveBG=[]; BkgrdMat=[];
+  searchIntens=[];intensMax=[];detMaxPos=[];scIntens=[];areaOfIntensAboveBG=[];BkgrdMat=[];
 
+  % TODO needs explanation
   if Fflg==1
     % Preallocation
     tPtLength=length(tifFileLst);
@@ -133,7 +134,7 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
     MaxANDVal=0; % sum(sum(BWimage(:,:)));  %seed MaxANDVal from the BWimage 
     regDith=4;
     TestmapOnesDbl=zeros(2075,1400);
-  
+
     % Create a Search Range centered on C==1 and R==1 of the PinTool map
     RtopBndry=96; RbotBndry=176;
     ClfBndry=96; CrtBndry=154;
@@ -169,7 +170,7 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
             testPosC=PTrefPt(2) + shiftPosC;         
             a=[testPosR,testPosC];   %testPos(r,c)={testPosR,testPosC};
             testPos(r,c)={a};
-            doCircle
+            doCircle;
             TestmapOnesDbl(testPosR:(testPosR+(diaExt-1)),testPosC:(testPosC+(diaExt-1)))=cirMask;  %optCirMask;
           end
         end
@@ -222,7 +223,7 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
           MaxPosSkDbl=TestmapSkDbl;
         end
       end
-    end   
+    end
 
     if MaxANDValSk> MaxANDVal 
       MaxANDVal=MaxANDValSk;
@@ -299,11 +300,11 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
     if ANDValCent>=MaxANDVal 
       MaxPosDbl=lastDetMaxCentDbl; 
       MaxPos=lastDetMaxPos;
-      %detPos=lastDetMaxPos;
+      % detPos=lastDetMaxPos;
     end
-    %detPos=lastDetMaxPos;
+    % detPos=lastDetMaxPos;
     detPos=MaxPos;
-  end  %if length(tifFileLst) >2
+  end
 
   % Preallocation for speed on 2019_1121 ***
   scIntens=zeros(24,16,length(tifFileLst));
@@ -361,9 +362,9 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
         else % standard square analysis area
           refPtRExt=refPtR+widthEx;
           if (refPtRExt)> size(fIntsc,1), refPtRExt=size(fIntsc,1); end
-            refPtCExt=refPtC+widthEx;
+          refPtCExt=refPtC+widthEx;
           if (refPtCExt)> size(fIntsc,2), refPtCExt=size(fIntsc,2); end
-            zeroSearchIntens=sum(sum(fIntsc(refPtR:(refPtRExt),refPtC:(refPtCExt))));
+          zeroSearchIntens=sum(sum(fIntsc(refPtR:(refPtRExt),refPtC:(refPtCExt))));
         end
         % clear ('searchIntens')
         searchIntens=[];
@@ -514,678 +515,711 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
       end
     end
 
-  % [F_spots,bmtp, BGthres,bmm,rwm,lstTpt,BGsc,totBkgrd]=... 
-  % NIgenBkGrdDataPar4Fnc(ImParMat, tifFileLst, lastDetMaxPos, numRows, numCols, fullsc, tPt,BGthres, doCircle, cirPixA,diaExt, cirMask, BGTav);
-  % NIgenBkGrdDataPar4Fnc
-  % function [F_spots,bmtp, BGthres,bmm,rwm,lstTpt,BGsc,totBkgrd ]=... 
-  % NIgenBkGrdDataPar4Fnc(ImParMat, tifFileLst, lastDetMaxPos, numRows, numCols, fullsc, tPt, BGthres, doCircle, cirPixA, diaExt, cirMask, BGTav)
-  % Called by NIscanIntensBG.m
-  
-  % global easyResultsDir
-  global matFile
-  % global pixsAboveBG
-  MPnum=ImParMat(1);
-  destPerMP=ImParMat(2);
-  spotThres=ImParMat(4)/100;  %selScan=ImParMat(4);
-  width=ImParMat(5);
-  dither=ImParMat(6);
-  BGthresInput=ImParMat(3); % a value of percent to be added (20=>1.20*BGTav)
-  lstTpt=length(tifFileLst);
-  LfOffset=65;   %lf;   %Ncode
-  TopOffset=65;  %tp;
-  rtLim=1350;  %1400;  %1350;
-  rtNotchOffset=10;
-  cushion=20;
-  % close2edgeTol=90;
-  botLim=2003;
-  botNotchOffset=60;
-
-  % Initialize
-  % clear('totBkgrd')
-  % clear('pixsAboveBG')
-  % clear('lineV','pixCnt','lineSum,meanBkgrd')
-  % clear('rw','rwm')
-  totBkgrd=0;
-  pixsAboveBG=0;
-  lineV=0; pixCnt=0; lineSum=0; meanBkgrd=85;
-  rw=0; rwm=0;
-  % Start Generation of BackGround data after the 2nd Row (&& 2nd Col)
-  % Optimized spot positions determined
-  %if r>=2 && c>=2,
-  BGsc=zeros(2075,1400);  %Empsc;
-  widthEx=width-1;  %width extention from reference point
-  for r=1:numRows      
-    for c=1:numCols
-      refP=lastDetMaxPos{r,c};
-      if r<numRows,refNxR=lastDetMaxPos{r+1,c}; end
-      if c<numCols,refNxC=lastDetMaxPos{r,c+1}; end
-      if r>1, refPrR=lastDetMaxPos{r-1,c}; end    
-      if c>1, refPrC=lastDetMaxPos{r,c-1}; end
-
-      % At least NINE conditions which must be treated differently
-      % Condition 0: most spots fall in this central category
-      if r>1 && r<numRows && c>1 && c<numCols 
-        if rem(r,numRows)==1
-          refBG(1)=refP(1)-floor(0.5*(plateBotSpace));    
-        else    
-          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx))); 
-        end
-        if rem(c,numCols)==1
-          refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));
-        else
-          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));
-        end
-        if rem(r,numRows)==0
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));    
-        else
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
-        end
-        if rem(c,numCols)==0
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));
-        else
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
-        end
-        %refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-refP(2)+widthEx));
-        detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
-        % clear('lineV','pixCnt','lineSum')          
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-        pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
-        meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-        if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-        if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end
-        %{
-        lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
-        lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
-        lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
-        lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
-        meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-        totBkgrd(r,c)=meanBkgrd* width^2;
-        %}             
-      end
-  
-      % Condition 1
-      if r==1 && c==1
-        % if (size(refP(1)-4)>0    
-        refBG(1)=refP(1)- floor(0.5*(refP(1) - TopOffset));             
-        refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset)); % Icode -0
-        refBG(3)=refP(1)+widthEx+ floor(0.5*((refNxR(1)-(refP(1)+widthEx))));
-        refBG(4)=refP(2)+widthEx+ floor(0.5*((refNxC(2)-(refP(2)+widthEx))));
-        detBG(r,c)={uint8(refBG)}; % Store Background Reference pt data in a Cell
-        % clear('lineV','pixCnt','lineSum')          
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); %mean across top rt
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-        pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));          
-        meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
-        if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-        % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-        if doCircle==1
-          totBkgrd(r,c)=meanBkgrd* cirPixA;
-        else
-          totBkgrd(r,c)=meanBkgrd* width^2;
-        end
-        %{
-        lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
-        lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
-        lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
-        lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
-        meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-        totBkgrd(r,c)=round(meanBkgrd* width^2);
-        %}
-      end
-
-      % Condition 1a
-      if r==1 && c>1 && c<numCols
-        refBG=zeros(1,4); 
-        refBG(1)=refP(1)-floor(0.5*(refP(1)-TopOffset));
-        if rem(c,numCols)==1
-          refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));
-        else
-          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));
-        end
-        refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
-        if rem(c,numCols)==0
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));
-        else
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
-        end
-        detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
-        % clear('lineV','pixCnt','lineSum')          
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-        pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
-        if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-        if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end    
-        %{          
-        lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
-        lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
-        lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
-        lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
-        meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-        totBkgrd(r,c)=meanBkgrd* width^2;
-        %}
-      end
-
-      % Condition 2
-      if r==1 && c==numCols
-        % close2edgeTol=14;
-        refBGcExt=refP(2)+ widthEx;
-        refBG(1)=refP(1)-floor(0.5*(refP(1)-TopOffset));  %vertical (row)          
-        refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  %horizontal(col)
-        refBG(3)=refP(1)+widthEx+ floor(0.5*((refNxR(1)-(refP(1)+widthEx))));
-        % if refBGcExt>(size(fullsc,2)-close2edgeTol)%if intens area too close to edge
-        if refBGcExt>(rtLim-cushion)%if intens area too close to edge
-          refBG(4)=rtLim-rtNotchOffset;
-        else
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));    
-        end
-        detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell             
-        % clear('lineV','pixCnt','lineSum')          
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')
-        lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-        pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % if refBGcExt>(size(fullsc,2)-close2edgeTol) %if intens area too close to edge
-        if refBGcExt>(rtLim-cushion) %if intens area too close to edge
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
-          % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  %divby 2*across+1*down
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end   
-        else
-          % clear('lineV')  %3
-          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
-          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end   
-        end
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
-      end
-          
-      % Condition 2a: down rows 2->47  farRight col edge
-      if r>1 && r<numRows && c==numCols
-        % close2edgeTol=14;  %Icode=4
-        refBGcExt=refP(2)+widthEx;
-        if rem(r,numRows)==1
-          refBG(1)=refP(1)-floor(0.5*(plateBotSpace));                 
-        else
-          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));             
-        end
-        refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx))); % return from lunch fix start here!!!!!
-        if rem(r,numRows)==0
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));          
-        else
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));      
-        end
-        if refBGcExt<(rtLim-cushion) %if intens area too close to edge
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));
-        else
-          refBG(4)=rtLim-cushion;
-        end
-        detBG(r,c)={uint8(refBG)};  % store Background Reference pt data in a Cell          
-        % clear('lineV','pixCnt','lineSum')  %1        
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %2
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %4
-        lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-        pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        %if refBGcExt<(size(fullsc,2)-close2edgeTol) % if intens area too close to edge
-        if refBGcExt<(rtLim-cushion) % if intens area too close to edge
-          % clear('lineV')  %3
-          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
-          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end
-        else
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end   
-          % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
-          % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  %divby 2*across+1*down
-          if doCircle==1
-            totBkgrd(r,c)=meanBkgrd* cirPixA
-          else 
-            totBkgrd(r,c)=meanBkgrd* width^2
-          end  
-        end 
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
-      end
+    % [F_spots,bmtp, BGthres,bmm,rwm,lstTpt,BGsc,totBkgrd]=... 
+    % NIgenBkGrdDataPar4Fnc(ImParMat, tifFileLst, lastDetMaxPos, numRows, numCols, fullsc, tPt,BGthres, doCircle, cirPixA,diaExt, cirMask, BGTav);
+    % NIgenBkGrdDataPar4Fnc
+    % function [F_spots,bmtp, BGthres,bmm,rwm,lstTpt,BGsc,totBkgrd ]=... 
+    % NIgenBkGrdDataPar4Fnc(ImParMat, tifFileLst, lastDetMaxPos, numRows, numCols, fullsc, tPt, BGthres, doCircle, cirPixA, diaExt, cirMask, BGTav)
+    % Called by NIscanIntensBG.m
     
-      % Condition 3: Lower right corner
-      if r==numRows && c==numCols
-        %close2edgeTol=14;
-        refBGrExt=refP(1)+ widthEx;
-        refBGcExt=refP(2)+ widthEx;
-        refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  %vertical (row)          
-        refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  %horizontal(col)
-        if refBGrExt>(botLim-botNotchOffset)%if intens area not too close to bot edge else
-          refBG(3)=botLim + cushion;
-        else
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt));
-        end
-        if refBGcExt>(rtLim- cushion)%if intens area not too close to edge else
-          refBG(4)=rtLim -cushion;
-        else
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));    
-        end
-        detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
-                      
-        % clear('lineV','pixCnt','lineSum')  %1        
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %2
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+    MPnum=ImParMat(1);
+    destPerMP=ImParMat(2);
+    spotThres=ImParMat(4)/100;  %selScan=ImParMat(4);
+    width=ImParMat(5);
+    dither=ImParMat(6);
+    BGthresInput=ImParMat(3); % a value of percent to be added (20=>1.20*BGTav)
+    lstTpt=length(tifFileLst);
+    LfOffset=65;   %lf;   %Ncode
+    TopOffset=65;  %tp;
+    rtLim=1350;  %1400;  %1350;
+    rtNotchOffset=10;
+    cushion=20;
+    % close2edgeTol=90;
+    botLim=2003;
+    botNotchOffset=60;
 
-        % if refBGcExt>(size(fullsc,2)-close2edgeTol)&&...
-        if refBGcExt>(rtLim-cushion)&&...
-          refBGrExt<(botLim-botNotchOffset) % if intens area too close to right edge only
-          % clear('lineV')  %4
-          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
-          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
-          % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  % divby 2*across+1*down
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end   
-        elseif refBGrExt>(botLim-botNotchOffset) && ...
-          refBGcExt>(rtLim-cushion)%if intens area too close to bottom edge only
-          % clear('lineV')  %3
-          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
-          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(3))./ ...
-          %((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  % divby 1*across+2*down
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end  
-        % elseif refBGcExt>(size(fullsc,2)-close2edgeTol)&& ...    
-        elseif refBGcExt>(rtLim-cushion)&& ...
-          refBGrExt>(botLim-botNotchOffset) % if intens area too close to both right edge and bottom edge
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(lineSum(1)+lineSum(2))./ ...
-          % ((refBG(4)-refBG(2)+(refBG(3)-refBG(1))));  %divby 1across+1*down
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end  
-        else
-          % clear('lineV')  %3
-          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
-          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-          % clear('lineV')  %4
-          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
-          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-            % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end   
-        end
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
-      end
-              
-      % Condition 3a: Bottom across row48 col2-79
-      if r==numRows && c>1 && c<numCols
-        refBG=zeros(1,4);
-        % close2edgeTol=14; % Icode=4
-        refBGrExt=refP(1)+ widthEx;  
-        refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  % vertical (row)          
-        if rem(c,numCols)==1
-          refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));  % horizontal(col)    
-        else
-          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  % horizontal(col)
-        end             
-        if refBGrExt>(botLim-botNotchOffset) % if intens area not too close to bot edge else
-          refBG(3)=botLim + cushion;
-        else
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt)); 
-        end
-        if rem(c,numCols)==0
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));   
-        else
-          refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));    
-          %refBG(4)=refP(2)+widthEx+ floor(0.5*(size(fullsc,2)-refBGcExt));
-        end
-        detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell       
-        % clear('lineV','pixCnt','lineSum')  %1        
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %2
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %3
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        if refBGrExt>(botLim-botNotchOffset) % if intens area too close to bottom edge
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
-          % ((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  %divby 1*across+2*down
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
-        else
-          % clear('lineV')  %4
-          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
-          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(sum(lineSum(1:4)))./ ((2*(refBG(4)-refBG(2))+ 2*(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
-        end
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end          
-      end
-
-      % Condition 4: Bottom Left Corner row48 col1
-      if r==numRows && c==1
-        %close2edgeTol=14;   %Icode=4
-        refBGrExt=refP(1)+ widthEx;              
-        refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx))); % vertical (row)          
-        refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset)); % horizontal(col)  Icode -0 instead of LfOffset
-        if refBGrExt>(botLim-botNotchOffset) % if intens area not too close to bot edge else
-          refBG(3)=botLim + cushion; 
-        else
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt));
-        end
-        refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
-        detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell
-        % clear('lineV','pixCnt','lineSum')  %1        
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %2
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %3
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        if refBGrExt>(botLim-botNotchOffset) % if intens area too close to bottom edge
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(3))./ ...
-          % ((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  % divby 1*across+2*down
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
-        else
-          % clear('lineV')  %4
-          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
-          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));    
-          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-          % meanBkgrd=(sum(lineSum(1:4)))./ ((2*(refBG(4)-refBG(2))+ 2*(refBG(3)-refBG(1))));
-          if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
-        end 
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
-      end
-
-      % Condition 4a:  Left edge center area  rows2-47 col1
-      if r>1  && r<numRows && c==1
-        % close2edgeTol=14; %Icode=4
-        refBGrExt=refP(1)+ widthEx;
-        if rem(r,numRows)==1
-          refBG(1)=refP(1)-floor(0.5*(plateBotSpace));  % vertical (row)          
-        else    
-          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  % vertical (row)          
-        end
-        refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset));  % horizontal(col) %Icode=0
-        if rem(r,numRows)==0
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));
-        else
-          refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
-        end
-        refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
-        detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell              
-        % clear('lineV','pixCnt','lineSum')  %1        
-        lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
-        if tPt==1 || tPt==lstTpt,rw=lineV';end
-        pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %2
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %3
-        lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
-        pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        % clear('lineV')  %4
-        lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
-        if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
-        pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
-        lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
-        meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
-        if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
-        if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
-        if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end
-      end
-
-      % Determine the actual number of pixels(area) of growth above the  background
-      % Intensity
-      BG=meanBkgrd;
-      [refPtPxAbove]=lastDetMaxPos{r,c};
-      refPtRx=refPtPxAbove(1);
-      refPtCx=refPtPxAbove(2);
-      if doCircle==1
-        cutout=(fullsc(refPtRx:(refPtRx+ (diaExt-1)),refPtCx:(refPtCx+ (diaExt-1)))); 
-        Imcir=cutout .* uint8(cirMask);
-        pixsAboveBG(r,c)=nnz(Imcir>BG);  %calc non-background within circular analysis area  
-        % pixsAboveBG(r,c)=nnz(fullsc(refPtRx:(refPtRx+ (diaExt-1)),refPtCx:(refPtCx+ (diaExt-1)))>BG);  %BG);
-      else % standard square analysis area
-        pixsAboveBG(r,c)=nnz(fullsc(refPtRx:(refPtRx+widthEx),refPtCx:(refPtCx+widthEx))>BG); % calc non-background within square analysis area 
-      end
-        
-      % TimePT average
-      % meanBGTsum(r,c)=meanBGTsum(r,c)+meanBkgrd;
-      % meanBGTav(r,c)=meanBGTsum(r,c) /tPt;
-      bmm(r,c)=uint8(floor(meanBkgrd));
-
-      % For FOTOS only
-      F_spots(r,c,tPt)={refBG}; % Foto spot coordinates
-      bmtp(r,c,tPt)=bmm(r,c); % Added/used for FOTOS 11_0830
-
-      % TimePT Average BG intensity calc method
-      BGTav(r,c)=uint8(round((BGTav(r,c)*(tPt-1))+meanBkgrd)/tPt);
-      % BGTav(r,c)=((BGTav(r,c)*(tPt-1))+meanBkgrd)/tPt;
-
-      % sliding BG average
-      % if r==1 && c==1, slavg(1:5)=BG;end % slavg(1:5)=50; %120620 Epsonvalue is 33; end
-      % slavg(5)=slavg(4);
-      % slavg(4)=slavg(3);
-      % slavg(3)=slavg(2);
-      % slavg(2)=slavg(1);
-      % slavg(1)=BG;
-      % slidingAvg=mean(slavg);
-    
-      % For Visualization Purposes only
-      %1->2  across rt 1, 2-4
-      BGsc(refBG(1),refBG(2):refBG(4))=1;
-      %1->4 down lf 1-3, 2
-      BGsc(refBG(1):refBG(3),refBG(2))=1;
-      %2->3 down rt 1-3, 4
-      BGsc(refBG(1):refBG(3),refBG(4))=1;
-      %4->3 Bot Across rt 1, 2-4
-      BGsc(refBG(3),refBG(2):refBG(4))=1;
-      % BGsc(refBG(1):refBG(3),refBG(2):refBG(4)) %just displays matrices
-    end
-  end
-
-  BGthres=uint8(double(BGTav) * (1+(BGthresInput/100)));
-  optomizedPos(:,:,tPt)=lastDetMaxPos;
-  % if(isequal(SWsingleSc,1))|| ((~isequal(SWsingleSc,1))&&tPt==tptLength)   %190731 change to capture last timePt PTmap if(isequal(SWsingleSc,1))
-  % if(isequal(SWsingleSc,1))&& (tPt==1 || tPt==guesTpt || tPt==tptLength)|| ((~isequal(SWsingleSc,1))&&tPt==tptLength)   %190919 Option for observation
-  % if (tPt==1 || tPt==guesTpt || tPt==tptLength)  %190919 Option for observation
-  if (tPt==tptLength) % 190919 change to capture ONLY last timePt PTmap
-    % clear OptmapOnes;
-    OptmapOnes=[];
-    % OptmapOnes=Empsc+ 1.4;
-    OptmapOnesDbl=double(Empsc)+ .8;
-    for r=1:numRows
+    % Initialize
+    % clear('totBkgrd')
+    % clear('pixsAboveBG')
+    % clear('lineV','pixCnt','lineSum,meanBkgrd')
+    % clear('rw','rwm')
+    totBkgrd=0;
+    pixsAboveBG=0;
+    lineV=0; pixCnt=0; lineSum=0; meanBkgrd=85;
+    rw=0; rwm=0;
+    % Start Generation of BackGround data after the 2nd Row (&& 2nd Col)
+    % Optimized spot positions determined
+    %if r>=2 && c>=2,
+    BGsc=zeros(2075,1400);  %Empsc;
+    widthEx=width-1;  %width extention from reference point
+    for r=1:numRows      
       for c=1:numCols
-        [refPt]=lastDetMaxPos{r,c};
-        refPtR=refPt(1);
-        refPtC=refPt(2);
-        if doCircle==1
-          %OptmapOnesDbl(refPtR:(refPtR+diaExt),refPtC:(refPtC+diaExt))=cirMask;
-          OptmapOnesDbl(refPtR:(refPtR+(diaExt-1)),refPtC:(refPtC+(diaExt-1)))=optCirMask;   
-        else
-          refPtRExt=refPtR+widthEx; 
-          if (refPtRExt)> size(fullsc,1), refPtRExt=size(fullsc,1); end
-          refPtCExt=refPtC+widthEx;
-          if (refPtCExt)> size(fullsc,2), refPtCExt=size(fullsc,2); end
-          OptmapOnesDbl(refPtR:(refPtRExt),refPtC:(refPtCExt))=1;%255;
+        refP=lastDetMaxPos{r,c};
+        if r<numRows,refNxR=lastDetMaxPos{r+1,c}; end
+        if c<numCols,refNxC=lastDetMaxPos{r,c+1}; end
+        if r>1, refPrR=lastDetMaxPos{r-1,c}; end    
+        if c>1, refPrC=lastDetMaxPos{r,c-1}; end
+
+        % At least NINE conditions which must be treated differently
+        % Condition 0: most spots fall in this central category
+        if r>1 && r<numRows && c>1 && c<numCols 
+          if rem(r,numRows)==1
+            refBG(1)=refP(1)-floor(0.5*(plateBotSpace));    
+          else    
+            refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx))); 
+          end
+          if rem(c,numCols)==1
+            refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));
+          else
+            refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));
+          end
+          if rem(r,numRows)==0
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));    
+          else
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
+          end
+          if rem(c,numCols)==0
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));
+          else
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
+          end
+          %refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-refP(2)+widthEx));
+          detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
+          % clear('lineV','pixCnt','lineSum')          
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
+          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+          if doCircle==1
+            totBkgrd(r,c)=meanBkgrd* cirPixA;
+          else 
+            totBkgrd(r,c)=meanBkgrd* width^2;
+          end
+          %{
+          lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
+          lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
+          lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
+          lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
+          meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
+          totBkgrd(r,c)=meanBkgrd* width^2;
+          %}             
         end
+    
+        % Condition 1
+        if r==1 && c==1
+          % if (size(refP(1)-4)>0    
+          refBG(1)=refP(1)- floor(0.5*(refP(1) - TopOffset));             
+          refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset)); % Icode -0
+          refBG(3)=refP(1)+widthEx+ floor(0.5*((refNxR(1)-(refP(1)+widthEx))));
+          refBG(4)=refP(2)+widthEx+ floor(0.5*((refNxC(2)-(refP(2)+widthEx))));
+          detBG(r,c)={uint8(refBG)}; % Store Background Reference pt data in a Cell
+          % clear('lineV','pixCnt','lineSum')          
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); %mean across top rt
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));          
+          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
+          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+          % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
+          if doCircle==1
+            totBkgrd(r,c)=meanBkgrd* cirPixA;
+          else
+            totBkgrd(r,c)=meanBkgrd* width^2;
+          end
+          %{
+          lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
+          lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
+          lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
+          lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
+          meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
+          totBkgrd(r,c)=round(meanBkgrd* width^2);
+          %}
+        end
+
+        % Condition 1a
+        if r==1 && c>1 && c<numCols
+          refBG=zeros(1,4); 
+          refBG(1)=refP(1)-floor(0.5*(refP(1)-TopOffset));
+          if rem(c,numCols)==1
+            refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));
+          else
+            refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));
+          end
+          refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
+          if rem(c,numCols)==0
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));
+          else
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
+          end
+          detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
+          % clear('lineV','pixCnt','lineSum')          
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
+          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+          if doCircle==1
+            totBkgrd(r,c)=meanBkgrd* cirPixA;
+          else 
+            totBkgrd(r,c)=meanBkgrd* width^2;
+          end    
+          %{          
+          lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
+          lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
+          lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
+          lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
+          meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
+          totBkgrd(r,c)=meanBkgrd* width^2;
+          %}
+        end
+
+        % Condition 2
+        if r==1 && c==numCols
+          % close2edgeTol=14;
+          refBGcExt=refP(2)+ widthEx;
+          refBG(1)=refP(1)-floor(0.5*(refP(1)-TopOffset));  %vertical (row)          
+          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  %horizontal(col)
+          refBG(3)=refP(1)+widthEx+ floor(0.5*((refNxR(1)-(refP(1)+widthEx))));
+          % if refBGcExt>(size(fullsc,2)-close2edgeTol)%if intens area too close to edge
+          if refBGcExt>(rtLim-cushion)%if intens area too close to edge
+            refBG(4)=rtLim-rtNotchOffset;
+          else
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));    
+          end
+          detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell             
+          % clear('lineV','pixCnt','lineSum')          
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')
+          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % if refBGcExt>(size(fullsc,2)-close2edgeTol) %if intens area too close to edge
+          if refBGcExt>(rtLim-cushion) %if intens area too close to edge
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
+            % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  %divby 2*across+1*down
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end   
+          else
+            % clear('lineV')  %3
+            lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
+            if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+            pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+            lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end   
+          end
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
+        end
+            
+        % Condition 2a: down rows 2->47  farRight col edge
+        if r>1 && r<numRows && c==numCols
+          % close2edgeTol=14;  %Icode=4
+          refBGcExt=refP(2)+widthEx;
+          if rem(r,numRows)==1
+            refBG(1)=refP(1)-floor(0.5*(plateBotSpace));                 
+          else
+            refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));             
+          end
+          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx))); % return from lunch fix start here!!!!!
+          if rem(r,numRows)==0
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));          
+          else
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));      
+          end
+          if refBGcExt<(rtLim-cushion) %if intens area too close to edge
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));
+          else
+            refBG(4)=rtLim-cushion;
+          end
+          detBG(r,c)={uint8(refBG)};  % store Background Reference pt data in a Cell          
+          % clear('lineV','pixCnt','lineSum')  %1        
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %2
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %4
+          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          %if refBGcExt<(size(fullsc,2)-close2edgeTol) % if intens area too close to edge
+          if refBGcExt<(rtLim-cushion) % if intens area too close to edge
+            % clear('lineV')  %3
+            lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
+            if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+            pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+            lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end
+          else
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end   
+            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
+            % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  %divby 2*across+1*down
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2
+            end  
+          end 
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
+        end
+      
+        % Condition 3: Lower right corner
+        if r==numRows && c==numCols
+          %close2edgeTol=14;
+          refBGrExt=refP(1)+ widthEx;
+          refBGcExt=refP(2)+ widthEx;
+          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  %vertical (row)          
+          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  %horizontal(col)
+          if refBGrExt>(botLim-botNotchOffset)%if intens area not too close to bot edge else
+            refBG(3)=botLim + cushion;
+          else
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt));
+          end
+          if refBGcExt>(rtLim- cushion)%if intens area not too close to edge else
+            refBG(4)=rtLim -cushion;
+          else
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));    
+          end
+          detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
+                        
+          % clear('lineV','pixCnt','lineSum')  %1        
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %2
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+
+          % if refBGcExt>(size(fullsc,2)-close2edgeTol)&&...
+          if refBGcExt>(rtLim-cushion)&&...
+            refBGrExt<(botLim-botNotchOffset) % if intens area too close to right edge only
+            % clear('lineV')  %4
+            lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
+            if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+            pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+            lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
+            % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  % divby 2*across+1*down
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end   
+          elseif refBGrExt>(botLim-botNotchOffset) && ...
+            refBGcExt>(rtLim-cushion)%if intens area too close to bottom edge only
+            % clear('lineV')  %3
+            lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
+            if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+            pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+            lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(3))./ ...
+            %((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  % divby 1*across+2*down
+            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end  
+          % elseif refBGcExt>(size(fullsc,2)-close2edgeTol)&& ...    
+          elseif refBGcExt>(rtLim-cushion)&& ...
+            refBGrExt>(botLim-botNotchOffset) % if intens area too close to both right edge and bottom edge
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(lineSum(1)+lineSum(2))./ ...
+            % ((refBG(4)-refBG(2)+(refBG(3)-refBG(1))));  %divby 1across+1*down
+            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end  
+          else
+            % clear('lineV')  %3
+            lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
+            if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+            pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+            lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+            % clear('lineV')  %4
+            lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
+            if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+            pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+            lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+              % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end   
+          end
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
+        end
+                
+        % Condition 3a: Bottom across row48 col2-79
+        if r==numRows && c>1 && c<numCols
+          refBG=zeros(1,4);
+          % close2edgeTol=14; % Icode=4
+          refBGrExt=refP(1)+ widthEx;  
+          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  % vertical (row)          
+          if rem(c,numCols)==1
+            refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));  % horizontal(col)    
+          else
+            refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  % horizontal(col)
+          end             
+          if refBGrExt>(botLim-botNotchOffset) % if intens area not too close to bot edge else
+            refBG(3)=botLim + cushion;
+          else
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt)); 
+          end
+          if rem(c,numCols)==0
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));   
+          else
+            refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));    
+            %refBG(4)=refP(2)+widthEx+ floor(0.5*(size(fullsc,2)-refBGcExt));
+          end
+          detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell       
+          % clear('lineV','pixCnt','lineSum')  %1        
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %2
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %3
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          if refBGrExt>(botLim-botNotchOffset) % if intens area too close to bottom edge
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
+            % ((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  %divby 1*across+2*down
+            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
+          else
+            % clear('lineV')  %4
+            lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
+            if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+            pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+            lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(sum(lineSum(1:4)))./ ((2*(refBG(4)-refBG(2))+ 2*(refBG(3)-refBG(1))));
+            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
+          end
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end          
+        end
+
+        % Condition 4: Bottom Left Corner row48 col1
+        if r==numRows && c==1
+          %close2edgeTol=14;   %Icode=4
+          refBGrExt=refP(1)+ widthEx;              
+          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx))); % vertical (row)          
+          refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset)); % horizontal(col)  Icode -0 instead of LfOffset
+          if refBGrExt>(botLim-botNotchOffset) % if intens area not too close to bot edge else
+            refBG(3)=botLim + cushion; 
+          else
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt));
+          end
+          refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
+          detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell
+          % clear('lineV','pixCnt','lineSum')  %1        
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %2
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %3
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          if refBGrExt>(botLim-botNotchOffset) % if intens area too close to bottom edge
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(3))./ ...
+            % ((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  % divby 1*across+2*down
+            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
+          else
+            % clear('lineV')  %4
+            lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
+            if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+            pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+            lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));    
+            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+            % meanBkgrd=(sum(lineSum(1:4)))./ ((2*(refBG(4)-refBG(2))+ 2*(refBG(3)-refBG(1))));
+            if doCircle==1
+              totBkgrd(r,c)=meanBkgrd* cirPixA;
+            else 
+              totBkgrd(r,c)=meanBkgrd* width^2;
+            end 
+          end 
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
+        end
+
+        % Condition 4a:  Left edge center area  rows2-47 col1
+        if r>1  && r<numRows && c==1
+          % close2edgeTol=14; %Icode=4
+          refBGrExt=refP(1)+ widthEx;
+          if rem(r,numRows)==1
+            refBG(1)=refP(1)-floor(0.5*(plateBotSpace));  % vertical (row)          
+          else    
+            refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  % vertical (row)          
+          end
+          refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset));  % horizontal(col) %Icode=0
+          if rem(r,numRows)==0
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));
+          else
+            refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
+          end
+          refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
+          detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell              
+          % clear('lineV','pixCnt','lineSum')  %1        
+          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
+          if tPt==1 || tPt==lstTpt,rw=lineV';end
+          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %2
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %3
+          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
+          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          % clear('lineV')  %4
+          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
+          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
+          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
+          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
+          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
+          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
+          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
+          if doCircle==1
+            totBkgrd(r,c)=meanBkgrd* cirPixA;
+          else 
+            totBkgrd(r,c)=meanBkgrd* width^2;
+          end
+        end
+      
+        % Determine the actual number of pixels(area) of growth above the  background
+        % Intensity
+        BG=meanBkgrd;
+        [refPtPxAbove]=lastDetMaxPos{r,c};
+        refPtRx=refPtPxAbove(1);
+        refPtCx=refPtPxAbove(2);
+        if doCircle==1
+          cutout=(fullsc(refPtRx:(refPtRx+ (diaExt-1)),refPtCx:(refPtCx+ (diaExt-1)))); 
+          Imcir=cutout .* uint8(cirMask);
+          pixsAboveBG(r,c)=nnz(Imcir>BG);  %calc non-background within circular analysis area  
+          % pixsAboveBG(r,c)=nnz(fullsc(refPtRx:(refPtRx+ (diaExt-1)),refPtCx:(refPtCx+ (diaExt-1)))>BG);  %BG);
+        else % standard square analysis area
+          pixsAboveBG(r,c)=nnz(fullsc(refPtRx:(refPtRx+widthEx),refPtCx:(refPtCx+widthEx))>BG); % calc non-background within square analysis area 
+        end
+          
+        % TimePT average
+        % meanBGTsum(r,c)=meanBGTsum(r,c)+meanBkgrd;
+        % meanBGTav(r,c)=meanBGTsum(r,c) /tPt;
+        bmm(r,c)=uint8(floor(meanBkgrd));
+
+        % For FOTOS only
+        F_spots(r,c,tPt)={refBG}; % Foto spot coordinates
+        bmtp(r,c,tPt)=bmm(r,c); % Added/used for FOTOS 11_0830
+
+        % TimePT Average BG intensity calc method
+        BGTav(r,c)=uint8(round((BGTav(r,c)*(tPt-1))+meanBkgrd)/tPt);
+        % BGTav(r,c)=((BGTav(r,c)*(tPt-1))+meanBkgrd)/tPt;
+
+        % sliding BG average
+        % if r==1 && c==1, slavg(1:5)=BG;end % slavg(1:5)=50; %120620 Epsonvalue is 33; end
+        % slavg(5)=slavg(4);
+        % slavg(4)=slavg(3);
+        % slavg(3)=slavg(2);
+        % slavg(2)=slavg(1);
+        % slavg(1)=BG;
+        % slidingAvg=mean(slavg);
+      
+        % For Visualization Purposes only
+        %1->2  across rt 1, 2-4
+        BGsc(refBG(1),refBG(2):refBG(4))=1;
+        %1->4 down lf 1-3, 2
+        BGsc(refBG(1):refBG(3),refBG(2))=1;
+        %2->3 down rt 1-3, 4
+        BGsc(refBG(1):refBG(3),refBG(4))=1;
+        %4->3 Bot Across rt 1, 2-4
+        BGsc(refBG(3),refBG(2):refBG(4))=1;
+        % BGsc(refBG(1):refBG(3),refBG(2):refBG(4)) %just displays matrices
       end
     end
 
-    % Cross-optimized Map Matrix onto tifFile Matrix
-    % For visualization purposes only
-    if tPt==1,figure;end  
-    resIm=uint8((double(BGsc) + OptmapOnesDbl) .* double(fullsc));
-    % clear('OptmapOnesDbl')
-    OptmapOnesDbl=[];
-    % hres=imagesc(resIm);
-    hfscanIm=imagesc(resIm);
-    hfIm=gcf;
-    haxis=gca;
-    title(strcat('Scan',num2str(selScan),'timePt-',num2str(tPt)));
-    clf(hfscanIm,'reset');
-    set(hfIm,'NumberTitle','off')
-    set(hfIm,'Name', char(matFile)) % strcat('EASYconsole- ',char(easyResultsDir)))
-    if Fflg==1
-      fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))  
-      hgsave(fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))); %F 14_0626 
+    BGthres=uint8(double(BGTav) * (1+(BGthresInput/100)));
+    optomizedPos(:,:,tPt)=lastDetMaxPos;
+    % if(isequal(SWsingleSc,1))|| ((~isequal(SWsingleSc,1))&&tPt==tptLength)   %190731 change to capture last timePt PTmap if(isequal(SWsingleSc,1))
+    % if(isequal(SWsingleSc,1))&& (tPt==1 || tPt==guesTpt || tPt==tptLength)|| ((~isequal(SWsingleSc,1))&&tPt==tptLength)   %190919 Option for observation
+    % if (tPt==1 || tPt==guesTpt || tPt==tptLength)  %190919 Option for observation
+    if (tPt==tptLength) % 190919 change to capture ONLY last timePt PTmap
+      % clear OptmapOnes;
+      OptmapOnes=[];
+      % OptmapOnes=Empsc+ 1.4;
+      OptmapOnesDbl=double(Empsc)+ .8;
+      for r=1:numRows
+        for c=1:numCols
+          [refPt]=lastDetMaxPos{r,c};
+          refPtR=refPt(1);
+          refPtC=refPt(2);
+          if doCircle==1
+            % OptmapOnesDbl(refPtR:(refPtR+diaExt),refPtC:(refPtC+diaExt))=cirMask;
+            OptmapOnesDbl(refPtR:(refPtR+(diaExt-1)),refPtC:(refPtC+(diaExt-1)))=optCirMask;   
+          else
+            refPtRExt=refPtR+widthEx; 
+            if (refPtRExt)> size(fullsc,1), refPtRExt=size(fullsc,1); end
+            refPtCExt=refPtC+widthEx;
+            if (refPtCExt)> size(fullsc,2), refPtCExt=size(fullsc,2); end
+            OptmapOnesDbl(refPtR:(refPtRExt),refPtC:(refPtCExt))=1;%255;
+          end
+        end
+      end
+
+      % Cross-optimized Map Matrix onto tifFile Matrix
+      % For visualization purposes only
+      if tPt==1,figure;end  
+      resIm=uint8((double(BGsc) + OptmapOnesDbl) .* double(fullsc));
+      % clear('OptmapOnesDbl')
+      OptmapOnesDbl=[];
+      % hres=imagesc(resIm);
+      hfscanIm=imagesc(resIm);
+      hfIm=gcf;
+      haxis=gca;
+      title(strcat('Scan',num2str(selScan),'timePt-',num2str(tPt)));
+      clf(hfscanIm,'reset');
+      set(hfIm,'NumberTitle','off')
+      set(hfIm,'Name', char(matFile)) % strcat('EASYconsole- ',char(easyResultsDir)))
+      if Fflg==1
+        fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))  
+        hgsave(fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))); %F 14_0626 
+      else
+        hgsave(fullfile(figsResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt))));
+      end
     else
-      hgsave(fullfile(figsResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt))));
+      selScan;
+      % tifFile
     end
-  else
-    selScan;
-    % tifFile
-  end
 
-  BkgrdMat=totBkgrd; % BkgrdMat(:,:,tPt)=totBkgrd;  %debug parfor effort
-  areaOfIntensAboveBG(:,:,tPt)=pixsAboveBG; % actual area of growth for each timepoint  (used for printout of grArea ?not used in previous analysis)
-  scanIntens(:,:,tPt)=intens-BkgrdMat;
+    BkgrdMat=totBkgrd; % BkgrdMat(:,:,tPt)=totBkgrd;  %debug parfor effort
+    areaOfIntensAboveBG(:,:,tPt)=pixsAboveBG; % actual area of growth for each timepoint  (used for printout of grArea ?not used in previous analysis)
+    scanIntens(:,:,tPt)=intens-BkgrdMat;
 
-  % Capture first and last background values
-  if tPt==1
-    bdg(:,:,1)=bmm;  
-    bdg(:,:,3)=rwm;
-    Tmpsbdg1={bdg};
-  end
-  if tPt==lstTpt
-    bdg(:,:,2)=bmm;
-    bdg(:,:,4)=rwm;
-    Tmpsbdg1={bdg};
-  end
+    % Capture first and last background values
+    if tPt==1
+      bdg(:,:,1)=bmm;  
+      bdg(:,:,3)=rwm;
+      Tmpsbdg1={bdg};
+    end
+    if tPt==lstTpt
+      bdg(:,:,2)=bmm;
+      bdg(:,:,4)=rwm;
+      Tmpsbdg1={bdg};
+    end
 
-  TmpexpScanIntens1={scanIntens}; % par4Gbl 20_0122
-  TmpFexpScanSpots1={F_spots};
-  TmpFexpScanBMtp1={bmtp};
-  TmpanlZoneRefs1={optomizedPos}; % added to store tPt by tPt positions
-  TmpexpScanIntens2=TmpexpScanIntens1;
-  TmpFexpScanSpots2=TmpFexpScanSpots1;
-  TmpFexpScanBMtp2=TmpFexpScanBMtp1;
-  TmpanlZoneRefs2=TmpanlZoneRefs1;
-  Tmpsbdg2=Tmpsbdg1;
-  
+    TmpexpScanIntens1={scanIntens}; % par4Gbl 20_0122
+    TmpFexpScanSpots1={F_spots};
+    TmpFexpScanBMtp1={bmtp};
+    TmpanlZoneRefs1={optomizedPos}; % added to store tPt by tPt positions
+    TmpexpScanIntens2=TmpexpScanIntens1;
+    TmpFexpScanSpots2=TmpFexpScanSpots1;
+    TmpFexpScanBMtp2=TmpFexpScanBMtp1;
+    TmpanlZoneRefs2=TmpanlZoneRefs1;
+    Tmpsbdg2=Tmpsbdg1;
+  end
 end
\ No newline at end of file
diff --git a/workflow/templates/easy/par4GblFnc8c.m b/workflow/templates/easy/par4GblFnc8c.m
index 63833085..7df84c91 100755
--- a/workflow/templates/easy/par4GblFnc8c.m
+++ b/workflow/templates/easy/par4GblFnc8c.m
@@ -40,7 +40,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
       fFail=((fullfile(printResultsDir,'ImageFileReadFailure.txt')));  
       fid=fopen(fFail,'a'); %create,open and append
       % fprintf(fid,'%s \n',char(tifFile))
-      fclose(fid)
+      fclose(fid);
       nndx=nndx-1;
       swCatch=1;
       rep=getReport(ME, 'basic');
@@ -158,8 +158,8 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
     end
     locIndx=0;
     Ag=zeros(1,384);
-    for m=1:16 %N code change from 16  %Vert back to 16
-      for n=1:24     %Ncode change from  24 %Vert back to 24
+    for m=1:16 % Ncode change from 16  %Vert back to 16
+      for n=1:24 % Ncode change from  24 %Vert back to 24
         growthArea=max(grArea(n,m,:,1));
         if SWprint==1
           fprintf(fid,'%3.f\n',growthArea);
@@ -294,7 +294,7 @@ function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneR
   p4L1{16}=selScan; 
 
   p4L1{17}=cirPixA;
-  p4L1{18}=datestr((now),31);
+  p4L1{18}=datestr((now),31); % TODO this seems bad
 
   p4L2=p4L1;
 end
diff --git a/workflow/templates/easy/par4Gbl_Main8c.m b/workflow/templates/easy/par4Gbl_Main8c.m
index a60015eb..02b5b2a4 100755
--- a/workflow/templates/easy/par4Gbl_Main8c.m
+++ b/workflow/templates/easy/par4Gbl_Main8c.m
@@ -100,9 +100,9 @@ NIcircle
 lastPlateOnLastScan=1; % Ncode
 
 if size(scLst,1)==1
-  SWsingleSc=1
+  SWsingleSc=1;
 else 
-  SWsingleSc=0
+  SWsingleSc=0;
 end
 
 dvec=datevec(datestr(floor(now))); %method to get current offset year '01-Jan-"currentyr"'
@@ -220,10 +220,10 @@ end
 % Save data in .mat files
 save(matFile,'scan');
 % save((fullfile(easyResultsDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time
-save((fullfile(easyResultsDir,'Fotos','Nbdg')), 'sbdg');
-save((fullfile(easyResultsDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt
-save((fullfile(easyResultsDir,'Fotos','BGatTpts')),'FexpScanBMtp')
-save((fullfile(easyResultsDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
+save((fullfile(fotosResultsDir,'Nbdg')), 'sbdg');
+save((fullfile(fotosResultsDir,'Coordinates')),'FexpScanSpots') %Saves frames at each tPt
+save((fullfile(fotosResultsDir,'BGatTpts')),'FexpScanBMtp')
+save((fullfile(fotosResultsDir,'anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
 
 % Print FitResults
 fileExt='.txt';