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revised dotfinding scripts to export connected paths between associat…

…ed dots.
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1 parent f026d15 commit 859d1562f2e7b5b21d719fca5e3d2d61c0acfede @AlistairMobile AlistairMobile committed Nov 29, 2011
Showing with 382 additions and 257 deletions.
  1. +29 −14 CheckDotUpDown.m
  2. +53 −35 CheckDotUpDown.m~
  3. +5 −4 Unsupervised_DotFinding.m
  4. +5 −5 Unsupervised_DotFinding.m~
  5. +101 −64 Unsupervised_DotFinding2.m
  6. +101 −64 Unsupervised_DotFinding2.m~
  7. +81 −63 Unsupervised_DotFinding3.m
  8. +1 −1 imviewer_lsm.m
  9. +6 −7 imviewer_lsm.m~
View
@@ -10,7 +10,7 @@
% if getpreciseZ is off, the first layer in which the dot occurs is used as
% the z postion, rather than the brightest layer
-function New_dotC = CheckDotUpDown(DotLabels,DotData,Inds,Ints,plotdata,getpreciseZ,consec_layers,ovlap,xp1,xp2,yp1,yp2,intype)
+function [New_dotC,Linx,Liny] = CheckDotUpDown(DotLabels,DotData,Inds,Ints,plotdata,getpreciseZ,consec_layers,ovlap,xp1,xp2,yp1,yp2,intype,watershedZ)
%% Updates
% Rewritten 03/07/11 to convert more things to uint16 / uint8 to save
@@ -44,7 +44,7 @@
dotzpos{z} = z*ones(dotsinlayer(z),1);
end
dotC = [cell2mat(DotData'), cell2mat(dotzpos)];
-clear DotData;
+%clear DotData;
NDots = length(dotC); % total number of dots;
@@ -149,8 +149,8 @@
% liny = dotC(nonzeros(DotConn(n,:)),2) ;
% plot(linx,liny,'w');
% end
-
-
+%
+%
%%
@@ -202,6 +202,7 @@
mask = bwareaopen(mask,consec_layers); % figure(3); clf; imagesc(mask);
% bwareaopen is very expensive for big images
+ if watershedZ == 1
% Watershed to split dots
% W = ConnInt_T.*uint16(mask.*longDots); figure(4); clf; imagesc(W);
W = immultiply(ConnInt_T,cast(mask,intype));
@@ -210,7 +211,8 @@
% figure(3); clf; imagesc(W); colormap lines;
mask(W==0) = 0;
% figure(4); clf; imagesc(mask);
-
+ end
+
if getpreciseZ == 1
labeled = bwlabel(mask);
R = regionprops(labeled,ConnInt_T,'WeightedCentroid');
@@ -248,17 +250,27 @@
toc
- %% Troubleshooting
+ %% Troubleshooting
% figure(2); clf;
-% imagesc(Imax_dots); hold on;
+% imagesc(Imax_dots); colormap hot; hold on;
% plot(dotC(:,1),dotC(:,2),'c+');
% for n=1:2:2*NDots
% linx = dotC(nonzeros(masked_inds(n,:)),1); % trailing zero prevents cellfun error
% liny = dotC(nonzeros(masked_inds(n,:)),2);
% plot(linx,liny,'c');
% text(dotC((n+1)/2,1)+1,dotC((n+1)/2,2),[' ', num2str(dotC((n+1)/2,3) )],'color','c','FontSize',8);
% end
-%
+%
+%
+% figure(1); clf;
+% imagesc(Imax_dots(:,:,mRNAchn)); colormap hot; hold on;
+% for n=1:2:2*NDots
+% linx = dotC(nonzeros(masked_inds(n,:)),1); % trailing zero prevents cellfun error
+% liny = dotC(nonzeros(masked_inds(n,:)),2);
+% plot(linx,liny,'c');
+% % text(dotC((n+1)/2,1)+1,dotC((n+1)/2,2),[' ', num2str(dotC((n+1)/2,3) )],'color','c','FontSize',8);
+% end
+
%% Free up some Memory
%clear ConnInt_T DotConn LayerJoin mask ConnInt
@@ -288,9 +300,10 @@
UL = cellfun(@(x,y,z) [x(1:3),y(1:3),z(1)],Linx,Liny,Lind,'UniformOutput',0); % Add index to
UL = cell2mat(UL); % this is infact uniform output, not sure why matlab insists we do it this way
UL = UL(UL(:,1)>0,:); % remove all empty values
- unique_inds = UL(:,7);
- [~,ui] = unique(sum(UL(:,1:6),2));
- unique_inds = UL(ui,7);
+ % unique_inds = UL(:,7);
+ [~,ui] = unique([UL(:,1);UL(:,2);UL(:,3)]);
+ ULi = [UL(:,7);UL(:,7);UL(:,7)];
+ unique_inds = ULi(ui);
unique_dotX = Linx(unique_inds);
unique_dotY = Liny(unique_inds);
@@ -314,14 +327,16 @@
disp([num2str(Ndots),' total spheres found']);
toc
-
+%
%
% figure(4); clf;
% imagesc(Imax_dots); hold on;
% plot(New_dotC(:,1),New_dotC(:,2),'w.','MarkerSize',30);
-% plot(dotC(:,1),dotC(:,2),'c+');
+% plot(dotC(:,1),dotC(:,2),'m+');
%
-
+% for k=1:length(Linx)
+% plot(Linx{k}(1:end-3),Liny{k}(1:end-3),'c');
+% end
View
@@ -10,7 +10,7 @@
% if getpreciseZ is off, the first layer in which the dot occurs is used as
% the z postion, rather than the brightest layer
-function New_dotC = CheckDotUpDown(DotLabels,DotData,Inds,Ints,plotdata,getpreciseZ,consec_layers,ovlap,xp1,xp2,yp1,yp2,intype)
+function [New_dotC,Linx,Liny] = CheckDotUpDown(DotLabels,DotData,Inds,Ints,plotdata,getpreciseZ,consec_layers,ovlap,xp1,xp2,yp1,yp2,intype,watershedZ)
%% Updates
% Rewritten 03/07/11 to convert more things to uint16 / uint8 to save
@@ -44,7 +44,7 @@ for z = 1:Zs
dotzpos{z} = z*ones(dotsinlayer(z),1);
end
dotC = [cell2mat(DotData'), cell2mat(dotzpos)];
-clear DotData;
+%clear DotData;
NDots = length(dotC); % total number of dots;
@@ -138,19 +138,19 @@ toc
%% Trouble-shooting: Draw lines between connected dots
%
%
-figure(1); clf;
- Imax = imread([rawfolder,stackfolder,'max_',fname,'_',emb,'.tif']);
- Imax_dots = 3*Imax(xp1:xp2,yp1:yp2,1:3);
- Imax_dots(:,:,3) = .1*Imax_dots(:,:,3);
- imagesc(Imax_dots); hold on;
-plot(dotC(:,1),dotC(:,2),'c+');
-for n=1:2*NDots
- linx = dotC(nonzeros(DotConn(n,:)),1);
- liny = dotC(nonzeros(DotConn(n,:)),2) ;
- plot(linx,liny,'w');
-end
-
-
+% figure(1); clf;
+% Imax = imread([rawfolder,stackfolder,'max_',fname,'_',emb,'.tif']);
+% Imax_dots = 3*Imax(xp1:xp2,yp1:yp2,1:3);
+% Imax_dots(:,:,3) = .1*Imax_dots(:,:,3);
+% imagesc(Imax_dots); hold on;
+% plot(dotC(:,1),dotC(:,2),'c+');
+% for n=1:2*NDots
+% linx = dotC(nonzeros(DotConn(n,:)),1);
+% liny = dotC(nonzeros(DotConn(n,:)),2) ;
+% plot(linx,liny,'w');
+% end
+%
+%
%%
@@ -202,6 +202,7 @@ for k=1:Nsects
mask = bwareaopen(mask,consec_layers); % figure(3); clf; imagesc(mask);
% bwareaopen is very expensive for big images
+ if watershedZ == 1
% Watershed to split dots
% W = ConnInt_T.*uint16(mask.*longDots); figure(4); clf; imagesc(W);
W = immultiply(ConnInt_T,cast(mask,intype));
@@ -210,7 +211,8 @@ for k=1:Nsects
% figure(3); clf; imagesc(W); colormap lines;
mask(W==0) = 0;
% figure(4); clf; imagesc(mask);
-
+ end
+
if getpreciseZ == 1
labeled = bwlabel(mask);
R = regionprops(labeled,ConnInt_T,'WeightedCentroid');
@@ -248,17 +250,27 @@ end
toc
- %% Troubleshooting
- figure(2); clf;
- imagesc(Imax_dots); hold on;
- plot(dotC(:,1),dotC(:,2),'c+');
-for n=1:2:2*NDots
- linx = dotC(nonzeros(masked_inds(n,:)),1); % trailing zero prevents cellfun error
- liny = dotC(nonzeros(masked_inds(n,:)),2);
- plot(linx,liny,'c');
- text(dotC((n+1)/2,1)+1,dotC((n+1)/2,2),[' ', num2str(dotC((n+1)/2,3) )],'color','c','FontSize',8);
-end
-%%
+ %% Troubleshooting
+% figure(2); clf;
+% imagesc(Imax_dots); colormap hot; hold on;
+% plot(dotC(:,1),dotC(:,2),'c+');
+% for n=1:2:2*NDots
+% linx = dotC(nonzeros(masked_inds(n,:)),1); % trailing zero prevents cellfun error
+% liny = dotC(nonzeros(masked_inds(n,:)),2);
+% plot(linx,liny,'c');
+% text(dotC((n+1)/2,1)+1,dotC((n+1)/2,2),[' ', num2str(dotC((n+1)/2,3) )],'color','c','FontSize',8);
+% end
+%
+%
+% figure(1); clf;
+% imagesc(Imax_dots(:,:,mRNAchn)); colormap hot; hold on;
+% for n=1:2:2*NDots
+% linx = dotC(nonzeros(masked_inds(n,:)),1); % trailing zero prevents cellfun error
+% liny = dotC(nonzeros(masked_inds(n,:)),2);
+% plot(linx,liny,'c');
+% % text(dotC((n+1)/2,1)+1,dotC((n+1)/2,2),[' ', num2str(dotC((n+1)/2,3) )],'color','c','FontSize',8);
+% end
+
%% Free up some Memory
%clear ConnInt_T DotConn LayerJoin mask ConnInt
@@ -288,18 +300,22 @@ end
UL = cellfun(@(x,y,z) [x(1:3),y(1:3),z(1)],Linx,Liny,Lind,'UniformOutput',0); % Add index to
UL = cell2mat(UL); % this is infact uniform output, not sure why matlab insists we do it this way
UL = UL(UL(:,1)>0,:); % remove all empty values
- unique_inds = UL(:,7);
-% [~,unique_inds] = unique(sum(UL(:,1:6),2));
-
+ unique_inds = UL(:,7);
+ [~,ui] = unique([UL(:,1);UL(:,2);UL(:,3)]);
+ ULi = [UL(:,7);UL(:,7);UL(:,7)];
+ unique_inds = ULi(ui,7);
unique_dotX = Linx(unique_inds);
unique_dotY = Liny(unique_inds);
Ndots = length(unique_dotX);
New_dotC = zeros(Ndots,3);
for k =1:Ndots
phalf = round(length((unique_dotX{k})-3)/2);
- [New_dotC(k,1)] = unique_dotX{k}(phalf); % median(unique_dotX{k}); %
- New_dotC(k,2) = unique_dotY{k}(phalf); %median(unique_dotY{k}); %
+ %New_dotC(k,1) = unique_dotX{k}(phalf); % median(unique_dotX{k}); %
+ %New_dotC(k,2) = unique_dotY{k}(phalf); %median(unique_dotY{k}); %
+
+ New_dotC(k,1) = median(unique_dotX{k}(1:end-3)); %
+ New_dotC(k,2) = median(unique_dotY{k}(1:end-3)); %
if plotdata == 1 && getpreciseZ == 1
New_dotC(k,3) = cent(cent(:,2) == 2*unique_inds(k)-1,1);
@@ -312,13 +328,15 @@ disp([num2str(Ndots),' total spheres found']);
toc
-%
+
figure(4); clf;
imagesc(Imax_dots); hold on;
plot(New_dotC(:,1),New_dotC(:,2),'w.','MarkerSize',30);
-plot(dotC(:,1),dotC(:,2),'c+');
-
+plot(dotC(:,1),dotC(:,2),'m+');
+ for k=1:length(Linx)
+ plot(Linx{k}(1:end-3),Liny{k}(1:end-3),'c');
+ end
@@ -13,7 +13,7 @@
rawfolder = '/home/alistair/Documents/Research/Raw_Data_Temp/2011-05-22/'; %2011-06-20/'; % 2011-04_and_earlier/'; %'; % 2011-06-20/'; % '/Volumes/Data/Lab Data/Raw_Data/02-17-11/'; %% %
%rawfolder = '/media/GRAID/Raw_Data/2011-05-22/'
stackfolder = 's05_MP06/';% 's07_MP08/'; % 's07_MP05Hz/';% 's04_MP10/';% 'MP07Hz/'; % 'MP12Hz/'; % 's02_MP01/';% 's01_MP09/';% 'sna2.8Hz/' ;%'s06_MP10_sna18/'; %'s21_MP07/';% 'MP07Hz/';% 's11_G4B/' % 's06_MP10_sna18/'; % %'s10_bcd1x/';% 's11_bcd6x/'; %'s14_comp_cntrl/'; % 's12_cntrl_2label/'; %'MP02_22C/'; %'MP01_22C/'; % 'MGa1x/'; % 'MP10_22C/'; %'MP05_22C/'; %'YW_ths_sog/'; % 'MP10_22C/'; % % 'MP09_22C/'; % 'MGa2x/'; % 'MGa1x/'; % 'MGa2x/'; % 'MP10_22C_sna_y_c/'; %
-fname = 's05_MP06Hz_b', ver = '_v3'% 'MP08Hz_snaD_22C_b'; % 's07_MP05Hz_22C'; ver = '_v2'; % 'MP10Hz_c'; %'MP07Hz_snaD_22C_b' ; ver = '_v3';% 'MP12Hz_snaD_22C_b'; % 's04_MP10Hz'; % 's02_MP01_Hz_22C_b'; % 's01_MP09_Hz_22C_c'; %'sna2.8Hz_snaD_22C'; % 's06_MP10_sna18_b'; % 'MP07het_snaD_22C'; % 'MP07Hz_snaD_22C';%'s11_G4B_LacZ';% 's06_MP10_sna18_b'; % 's05_MP06Hz'; % %'s10_bcd1x';% 's11_bcd6x'; % 's14_comp_cntrl'; Es =1; % 's12_cntrl_2label'; Es = 1; % 'MP09_22C_hb_y_f'; Es = 7; % 'MP02_22C_hb_y'; Es = 9; % 'MP02_22C_hb_y_b'; Es = 10; % % 'MP01_22C_hb_y_f'; Es = 12; % 'MP01_22C_hb_y_c'; Es = 10; % 'MP01_22C_hb_y'; Es = 13; % 'MGa1x_LacZ_b'; Es = 12; % 'MP10_22C_sna_y_e'; Es = 12; % 'MP05_22C_sna_y_c'; Es =7; % 'MP10_22C_sna_y_d3'; Es = 1; %'YW_ths_sog'; Es = 12; % % 'MP09_22C_hb_y_e'; Es = 10; % 'MP09_22C_hb_y_d'; Es=11; % 'MGa2x_LacZ_sna_b'; Es = 10; % 'MP10_22C_sna_y_d'; % 'MGa_LacZ'; %'MGa2x_LacZ_sna'; %'MP10_22C_sna_y_c'; old_lab = 1; % 'MP05_22C_sna_y'; old_lab = 1; %
+fname = 's05_MP06Hz', ver = '_vN2'% 'MP08Hz_snaD_22C_b'; % 's07_MP05Hz_22C'; ver = '_v2'; % 'MP10Hz_c'; %'MP07Hz_snaD_22C_b' ; ver = '_v3';% 'MP12Hz_snaD_22C_b'; % 's04_MP10Hz'; % 's02_MP01_Hz_22C_b'; % 's01_MP09_Hz_22C_c'; %'sna2.8Hz_snaD_22C'; % 's06_MP10_sna18_b'; % 'MP07het_snaD_22C'; % 'MP07Hz_snaD_22C';%'s11_G4B_LacZ';% 's06_MP10_sna18_b'; % 's05_MP06Hz'; % %'s10_bcd1x';% 's11_bcd6x'; % 's14_comp_cntrl'; Es =1; % 's12_cntrl_2label'; Es = 1; % 'MP09_22C_hb_y_f'; Es = 7; % 'MP02_22C_hb_y'; Es = 9; % 'MP02_22C_hb_y_b'; Es = 10; % % 'MP01_22C_hb_y_f'; Es = 12; % 'MP01_22C_hb_y_c'; Es = 10; % 'MP01_22C_hb_y'; Es = 13; % 'MGa1x_LacZ_b'; Es = 12; % 'MP10_22C_sna_y_e'; Es = 12; % 'MP05_22C_sna_y_c'; Es =7; % 'MP10_22C_sna_y_d3'; Es = 1; %'YW_ths_sog'; Es = 12; % % 'MP09_22C_hb_y_e'; Es = 10; % 'MP09_22C_hb_y_d'; Es=11; % 'MGa2x_LacZ_sna_b'; Es = 10; % 'MP10_22C_sna_y_d'; % 'MGa_LacZ'; %'MGa2x_LacZ_sna'; %'MP10_22C_sna_y_c'; old_lab = 1; % 'MP05_22C_sna_y'; old_lab = 1; %
mRNA_channels = 2;% 2; % 3; % 1; % total mRNA channels
sname = fname; % 'MP07het_snaD_22C_1';% '_1'; % additional label on slide.
@@ -36,7 +36,7 @@
Es = length(fields(Datas)) - 3; % Number of Stacks
end
% ------- Option: Focus on subset of image: ------------------- %
- m = .95;% 1/2048; % .7; % .5; .7; % 1/2048; %
+ m = 1/2048; % .7; % .5; .7; % 1/2048; %
xp1= floor(h/2*m)+1; xp2 = floor(h/2*(2-m))+1; yp1 = floor(w/2*m)+1; yp2 = floor(w/2*(2-m))+1;
hs = yp2-yp1+1; ws = xp2-xp1+1;
@@ -69,8 +69,9 @@
% sphere finding parameters
getpreciseZ = 0;
- consec_layers = 3;
+ consec_layers = 2;
ovlap = 2;
+ watershedZ = 1;
% large ovlap yields confusing dots and then watershed splits these up
% in weird dot-distructive ways
%---------------------------------%
@@ -152,7 +153,7 @@
%%
intype = class(Iin_z);
- dotC = CheckDotUpDown(DotLabels,DotData,Inds,Ints,plotdata,getpreciseZ,consec_layers,ovlap,xp1,xp2,yp1,yp2,intype);
+ dotC = CheckDotUpDown(DotLabels,DotData,Inds,Ints,plotdata,getpreciseZ,consec_layers,ovlap,xp1,xp2,yp1,yp2,intype,watershedZ);
Cents = cell2mat(DotData');
% Project all layers
View
@@ -9,11 +9,11 @@ clear all;
tot_time = tic;
% Input options
old_lab = 0; Es = 0; ver = '';
-folder = '/home/alistair/Documents/Research/Projects/mRNA_counting/Data/2011-05-22/'; %2011-06-20/'; % 2011-04_and_earlier/'; % % 2011-05-22/'; % 2011-06-20/'; % '/Users/alistair/Documents/Berkeley/Levine_Lab/Projects/Enhancer_Modeling/Data/';
-rawfolder = '/home/alistair/Documents/Research/Raw_Data_Temp/2011-05-22/'; %2011-06-20/'; % 2011-04_and_earlier/'; %'; % 2011-06-20/'; % '/Volumes/Data/Lab Data/Raw_Data/02-17-11/'; %% %
-%rawfolder = '/media/GRAID/Raw_Data/2011-05-22/'
+folder = '/home/alistair/Documents/Research/Projects/mRNA_counting/Data/2011-06-20/'; % 2011-05-22/'; %2011-06-20/'; % 2011-04_and_earlier/'; % % 2011-05-22/'; % 2011-06-20/'; % '/Users/alistair/Documents/Berkeley/Levine_Lab/Projects/Enhancer_Modeling/Data/';
+rawfolder = '/home/alistair/Documents/Research/Raw_Data_Temp/2011-06-20/'; % 2011-05-22/'; % 2011-04_and_earlier/'; %'; % 2011-06-20/'; % '/Volumes/Data/Lab Data/Raw_Data/02-17-11/'; %% %
+%rawfolder = '/media/GRAID/Raw_Data/2011-05-22/';
stackfolder = 's05_MP06/';% 's07_MP08/'; % 's07_MP05Hz/';% 's04_MP10/';% 'MP07Hz/'; % 'MP12Hz/'; % 's02_MP01/';% 's01_MP09/';% 'sna2.8Hz/' ;%'s06_MP10_sna18/'; %'s21_MP07/';% 'MP07Hz/';% 's11_G4B/' % 's06_MP10_sna18/'; % %'s10_bcd1x/';% 's11_bcd6x/'; %'s14_comp_cntrl/'; % 's12_cntrl_2label/'; %'MP02_22C/'; %'MP01_22C/'; % 'MGa1x/'; % 'MP10_22C/'; %'MP05_22C/'; %'YW_ths_sog/'; % 'MP10_22C/'; % % 'MP09_22C/'; % 'MGa2x/'; % 'MGa1x/'; % 'MGa2x/'; % 'MP10_22C_sna_y_c/'; %
-fname = 's05_MP06Hz_b', ver = '_v3'% 'MP08Hz_snaD_22C_b'; % 's07_MP05Hz_22C'; ver = '_v2'; % 'MP10Hz_c'; %'MP07Hz_snaD_22C_b' ; ver = '_v3';% 'MP12Hz_snaD_22C_b'; % 's04_MP10Hz'; % 's02_MP01_Hz_22C_b'; % 's01_MP09_Hz_22C_c'; %'sna2.8Hz_snaD_22C'; % 's06_MP10_sna18_b'; % 'MP07het_snaD_22C'; % 'MP07Hz_snaD_22C';%'s11_G4B_LacZ';% 's06_MP10_sna18_b'; % 's05_MP06Hz'; % %'s10_bcd1x';% 's11_bcd6x'; % 's14_comp_cntrl'; Es =1; % 's12_cntrl_2label'; Es = 1; % 'MP09_22C_hb_y_f'; Es = 7; % 'MP02_22C_hb_y'; Es = 9; % 'MP02_22C_hb_y_b'; Es = 10; % % 'MP01_22C_hb_y_f'; Es = 12; % 'MP01_22C_hb_y_c'; Es = 10; % 'MP01_22C_hb_y'; Es = 13; % 'MGa1x_LacZ_b'; Es = 12; % 'MP10_22C_sna_y_e'; Es = 12; % 'MP05_22C_sna_y_c'; Es =7; % 'MP10_22C_sna_y_d3'; Es = 1; %'YW_ths_sog'; Es = 12; % % 'MP09_22C_hb_y_e'; Es = 10; % 'MP09_22C_hb_y_d'; Es=11; % 'MGa2x_LacZ_sna_b'; Es = 10; % 'MP10_22C_sna_y_d'; % 'MGa_LacZ'; %'MGa2x_LacZ_sna'; %'MP10_22C_sna_y_c'; old_lab = 1; % 'MP05_22C_sna_y'; old_lab = 1; %
+fname = 'MP10_22C_sna_y_e'; ver = '% 's05_MP06Hz', ver = '_vN'% 'MP08Hz_snaD_22C_b'; % 's07_MP05Hz_22C'; ver = '_v2'; % 'MP10Hz_c'; %'MP07Hz_snaD_22C_b' ; ver = '_v3';% 'MP12Hz_snaD_22C_b'; % 's04_MP10Hz'; % 's02_MP01_Hz_22C_b'; % 's01_MP09_Hz_22C_c'; %'sna2.8Hz_snaD_22C'; % 's06_MP10_sna18_b'; % 'MP07het_snaD_22C'; % 'MP07Hz_snaD_22C';%'s11_G4B_LacZ';% 's06_MP10_sna18_b'; % 's05_MP06Hz'; % %'s10_bcd1x';% 's11_bcd6x'; % 's14_comp_cntrl'; Es =1; % 's12_cntrl_2label'; Es = 1; % 'MP09_22C_hb_y_f'; Es = 7; % 'MP02_22C_hb_y'; Es = 9; % 'MP02_22C_hb_y_b'; Es = 10; % % 'MP01_22C_hb_y_f'; Es = 12; % 'MP01_22C_hb_y_c'; Es = 10; % 'MP01_22C_hb_y'; Es = 13; % 'MGa1x_LacZ_b'; Es = 12; % Es = 12; % 'MP05_22C_sna_y_c'; Es =7; % 'MP10_22C_sna_y_d3'; Es = 1; %'YW_ths_sog'; Es = 12; % % 'MP09_22C_hb_y_e'; Es = 10; % 'MP09_22C_hb_y_d'; Es=11; % 'MGa2x_LacZ_sna_b'; Es = 10; % 'MP10_22C_sna_y_d'; % 'MGa_LacZ'; %'MGa2x_LacZ_sna'; %'MP10_22C_sna_y_c'; old_lab = 1; % 'MP05_22C_sna_y'; old_lab = 1; %
mRNA_channels = 2;% 2; % 3; % 1; % total mRNA channels
sname = fname; % 'MP07het_snaD_22C_1';% '_1'; % additional label on slide.
@@ -36,7 +36,7 @@ if Es==0
Es = length(fields(Datas)) - 3; % Number of Stacks
end
% ------- Option: Focus on subset of image: ------------------- %
- m = .95;% 1/2048; % .7; % .5; .7; % 1/2048; %
+ m = 1/2048; % .7; % .5; .7; % 1/2048; %
xp1= floor(h/2*m)+1; xp2 = floor(h/2*(2-m))+1; yp1 = floor(w/2*m)+1; yp2 = floor(w/2*(2-m))+1;
hs = yp2-yp1+1; ws = xp2-xp1+1;
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