Make compatible with DeltaVision files

Cytoo/colonyColorPointPlot.m

@@ -1,4 +1,4 @@
-function colonyColorPointPlot(col,dcols,ps,climits,newfig,rescale_fac,centerpos)
+function colonyColorPointPlot(col,dcols,ps,climits,newfig,rescale_fac,centerpos,dofilter)
 %function colonyColorPointPlot(col,dcols)
 %---------------------------------------
 %Colony scatter plot with points colored by data
@@ -7,6 +7,7 @@ function colonyColorPointPlot(col,dcols,ps,climits,newfig,rescale_fac,centerpos)
 %           if length==2, use 2nd one for norm
 %ps = pointsize (default 12);
 
+
 xdat=col.data(:,1);
 ydat=col.data(:,2);
 
@@ -37,21 +38,29 @@ function colonyColorPointPlot(col,dcols,ps,climits,newfig,rescale_fac,centerpos)
     centerpos=1;
 end
 
+if ~exist('dofilter','var')
+    dofilter=1;
+end
+
 if newfig
-figure; 
+    figure;
 end
 
 if centerpos
     xdat=bsxfun(@minus,xdat,mean(xdat));
     ydat=bsxfun(@minus,ydat,mean(ydat));
 end
 
-includeinds=sqrt(xdat.*xdat+ydat.*ydat) < 30*50+5;
+if dofilter
+    includeinds=sqrt(xdat.*xdat+ydat.*ydat) < 30*50+5;
+else
+    includeinds=1:length(xdat);
+end
 xdat=xdat(includeinds); ydat=ydat(includeinds);
 coldat=coldat(includeinds);
 
 colormap('jet');
-scatter(rescale_fac*xdat,rescale_fac*ydat,ps,coldat);
+scatter(rescale_fac*xdat,rescale_fac*ydat,ps,coldat,'filled');
 minx=min(xdat); maxx=max(xdat);
 miny=min(ydat); maxy=max(ydat);
 

Cytoo/getDimsFromLogFile.m

@@ -0,0 +1,82 @@
+function [dims, wavenames]=getDimsFromLogFile(direc)
+%[dims wavenames]=getDimsFromLogFile(direc)
+%-----------------------------------------------
+%Function to find dimensions of the tiling and
+%the names of the wavelengths from the .dv.log file outputted by
+%deltavision
+%direc = output directory containing the .dv.log file
+%   assumes only one .dv.log file in that directory.
+%dims = 2 component vector containing dimension
+%wavenames = cell array containing wavelength names
+
+verbose = 0;
+
+fnames=dir([direc filesep '*log']);
+scanfile=[direc filesep fnames(1).name];
+ff=fopen(scanfile);
+
+strtofind1='DO ';
+strtofind2='CHANNEL';
+strtofind3='Stage coordinates:';
+strtofind4='Image ';
+
+tline=fgetl(ff);
+q=1;
+Y=1;
+
+while ischar(tline)
+
+    k1=strfind(tline,strtofind1);
+    k2=strfind(tline,strtofind2);
+    k4=strfind(tline,strtofind3);
+    n=strfind(tline,strtofind4);
+
+    if k1
+        if verbose
+            disp(tline);
+        end
+        panels=str2double(tline(k1+3:end));
+    end
+
+    if k2
+        if verbose
+            disp(tline);
+        end
+
+        k3=strfind(tline,',');
+        wavenames{q}=tline(k3(1)+1:k3(2)-1);
+        q=q+1;
+    end
+
+    if n
+        n1=strfind(tline,'.');
+        imageNum=str2double(tline(n+6:n1-1));
+    end
+
+    if k4
+        if verbose
+            disp(tline);
+        end
+
+        k5=strfind(tline,',');
+        y=str2double(tline(k5(1)+1:k5(2)-1));
+
+        if Y==1
+            y1=y;
+            Y=2;
+        end
+
+        if Y==2 && y~=y1
+            cols = (imageNum-1)./length(wavenames);
+            Y=3;
+        end
+
+    end
+
+    tline=fgetl(ff);
+
+end
+
+rows = floor(panels./cols);
+
+dims = [rows,cols];

Cytoo/mkFullCytooPlotPeaks.m

@@ -13,25 +13,41 @@
 pp=load(matfile);
 peaks=pp.peaks;
 ac=pp.acoords;
+col=pp.plate1.colonies;
+
+totcells = 0;
+for ii=1:length(peaks)
+    totcells=totcells+size(peaks{ii},1);
+end
+
+ncolumn=size(col(1).data,2);
+alldat=zeros(totcells,ncolumn);
+
+
 
 cc=colorcube(19);
 figure; hold on;
+q=1;
+
 for ii=1:length(peaks)
     if ~isempty(peaks{ii})
-    toadd=[ac(ii).absinds(2) ac(ii).absinds(1)];
-    %toadd=[0 0];
-    dtoplot=bsxfun(@plus,peaks{ii}(:,1:2),toadd);
-    if returndat
-        alldat(q:(q+col(ii).ncells-1),:)=[dtoplot col(ii).data(:,3:end)];
-        q=q+col(ii).ncells;
-    end
-    plot(dtoplot(:,2),dtoplot(:,1),'.','Color',cc(mod(ii,19)+1,:));
-%   txtcolor=cc(mod(ii+10,19)+1,:);
-%     cen=[col(ii).center(2)+toadd(2) col(ii).center(1)+toadd(1)];
-%     if printnum && col(ii).ncells > 200
-%         text(cen(1),cen(2),int2str(ii),'Color','m');
-%     end
-    %disp(int2str(ii));
+        toadd=[ac(ii).absinds(2) ac(ii).absinds(1)];
+        %toadd=[0 0];
+        dtoplot=bsxfun(@plus,peaks{ii}(:,1:2),toadd);
+        if returndat
+            alldat(q:(q+size(peaks{ii},1)-1),:)=[dtoplot peaks{ii}(:,3:end)];
+            q=q+size(peaks{ii},1);
+
+        end
+
+        text(mean(dtoplot(:,2)),mean(dtoplot(:,1)),int2str(ii),'Color','k');
+        plot(dtoplot(:,2),dtoplot(:,1),'.','Color',cc(mod(ii,19)+1,:));
+        %   txtcolor=cc(mod(ii+10,19)+1,:);
+        %     cen=[col(ii).center(2)+toadd(2) col(ii).center(1)+toadd(1)];
+        %     if printnum && col(ii).ncells > 200
+        %         text(cen(1),cen(2),int2str(ii),'Color','m');
+        %     end
+        %disp(int2str(ii));
     end
 end
 

Cytoo/peaksToColonies.m

@@ -1,9 +1,10 @@
-function [colonies peaks]=peaksToColonies(matfile)
+function [colonies, peaks]=peaksToColonies(matfile)
 
-pp=load(matfile,'peaks','acoords','imgfiles','dims');
+pp=load(matfile,'peaks','acoords','imgfiles','dims','si');
 peaks=pp.peaks;
 ac=pp.acoords;
 dims=pp.dims;
+si=pp.si;
 
 peaks=removeDuplicateCells(peaks,ac);
 
@@ -40,7 +41,7 @@
 %Make colony structure
 for ii=1:length(groups)
     cellstouse=allinds==ii;
-    colonies(ii)=colony(alldat(cellstouse,:),ac,dims,[],pp.imgfiles);
+    colonies(ii)=colony(alldat(cellstouse,:),ac,dims,si,pp.imgfiles);
 end
 
 %put data back into peaks

runFiles/runDeltaVisionTile.m

@@ -0,0 +1,136 @@
+function runDeltaVisionTile(direc,outfile,paramfile,step,tiffs,prefix)
+%runDeltaVisionTile(direc,outfile,paramfile,step,tiffs,prefix)
+%---------------------
+%Version of runFullTile for DeltaVision (.dv) files
+%Requries MATLAB Bio-Formats files
+%Run from directory containing .dv.log file
+%For a set of tiled images, runs segmentCells (uses parfor for this), runs
+%alignment program for images, outputs in matfile -- peaks -- cell by cells
+%list by image, colonies -- colonies data structure
+%direc -- image directory 
+%prefix -- prefix for TIFF images
+%outfile -- matfile for output
+%step = step to begin at. See code. allows for skipping finding cells etc.
+%tiffs = 1 (0) means extract tiff images and save to direc (0 to skip,
+%default = 1)
+
+if ~exist('tiffs','var')
+    tiffs = 1;
+end
+
+if ~exist('step','var')
+    step=1;
+end
+
+if ~exist('paramfile','var')
+    paramfile='setUserParamSC20xIFEDS';
+end
+
+reader=bfGetReader('path/to/data/file');
+omeMeta=reader.getMetadataStore();
+numChans=omeMeta.getChannelCount(0);
+[dims, wavenames]=getDimsFromLogFile('.');
+
+for ii = 1:numChans
+    chanstemp{ii}=['w' char(omeMeta.getChannelEmissionWavelength(0,ii-1))];
+end
+
+if tiffs == 1
+    dvToTiffs(direc,prefix,chanstemp,reader,dims)
+end
+
+chans=orderchans(chanstemp,wavenames);
+
+ff=folderFilesFromKeyword(direc,chans{1});
+maxims=ff(end-1);
+
+nloop=12;
+imgsperprocessor=ceil(maxims/12);
+%generate background image for each channel
+if step < 2
+    for ii=1:length(chans)
+        [minI meanI]=mkBackgroundImage(direc,chans{ii},min(500,maxims));
+        bIms{ii}=uint16(2^16*minI);
+        normIm=(meanI-minI);
+        normIm=normIm.^-1;
+        normIm=normIm/min(min(normIm));
+        nIms{ii}=normIm;
+    end
+
+    si=size(bIms{1});
+    save([direc filesep outfile],'bIms','nIms','dims','si');
+end
+%runTileLoop--runs segmentCells in parfor loop,
+%send imgsperprocessor to each, nloop = total number necessary
+%Assemble Mat Files--puts together matfiles, all data stored as peaks in
+%outfile
+if step < 3
+    load([direc filesep outfile],'bIms','nIms');
+    runTileLoop(direc,chans,imgsperprocessor,nloop,maxims,bIms,nIms,paramfile);
+end
+
+%performs a series of pairwise alignments,
+%each img is aligned img on top and to the left, pixel overlap
+%stored in accords, can also return fully aligned image, but not
+%recommended for large numbers of files.
+if step < 4
+    [acoords]=alignManyPanels(direc,chans{1},1,4,dims,85:150,maxims);
+    save([direc filesep outfile],'acoords','-append');
+end
+
+if step < 5
+    assembleMatFiles(direc,imgsperprocessor,nloop,outfile);
+end
+%peaksToColonies generates the colony structure from peaks and accords
+%computes alpha volume and then finds all connected components.
+if step < 6
+    load([direc filesep outfile],'bIms','nIms');
+    [colonies, peaks]=peaksToColonies([direc filesep outfile]);
+    plate1=plate(colonies,dims,direc,chans,bIms,nIms);
+    save([direc filesep outfile],'plate1','peaks','-append');
+end
+
+function chans=orderchans(chanstemp,wavenames,nucname)
+
+if ~exist('nucname','var')
+    nucname='DAPI';
+end
+
+kk=strfind(wavenames,nucname);
+ii=~cellfun(@isempty,kk);
+nuc_ind=find(ii);
+
+allchans=1:length(wavenames);
+nonnucchans=setdiff(allchans,nuc_ind);
+chans{1}=chanstemp{nuc_ind};
+for jj=1:length(nonnucchans)
+    chans{jj+1}=chanstemp{nonnucchans(jj)};
+end
+
+function dvToTiffs(direc,prefix,chans,reader,dims)
+
+if ~exist(direc,'file')
+    mkdir(direc);
+end
+
+for kk=1:length(chans)
+    for ii=1:dims(1)
+        for jj=1:dims(2)
+            if ~mod(ii,2) %even
+                oldnum=(ii-1)*dims(2)+dims(2)-jj+1;
+            else
+                oldnum=(ii-1)*dims(2)+jj;
+            end
+
+            newnum=(jj-1)*dims(1)+ii;
+
+            reader.setSeries(oldnum-1);
+
+            series_plane = bfGetPlane(reader, kk);
+
+            %t1=imread(fnames(rr==oldnum).name);
+            newname= [direc filesep prefix '_' chans{kk} '_s' int2str(newnum) '_t1.TIF'];
+            imwrite(series_plane,newname);
+        end
+    end
+end

runFiles/runFullTile.m

@@ -34,7 +34,8 @@ function runFullTile(direc,outfile,paramfile,step)
         normIm=normIm/min(min(normIm));
         nIms{ii}=normIm;
     end
-    save([direc filesep outfile],'bIms','nIms','dims');
+    si=size(bIms{1});
+    save([direc filesep outfile],'bIms','nIms','dims','si');
 end
 %runTileLoop--runs segmentCells in parfor loop,
 %send imgsperprocessor to each, nloop = total number necessary