Matt:LabNotes/2013-10-17

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Using PISA[edit]

ATTO488 ACTB Targets[edit]

 img_raw=imread('Oct42013/Series021_20xobj-Zstack-2kx2k_MaxProject_ATTO488.tif','tiff');
 img_flt=medfilt2(img_raw,[3 3]);
 [xsize ysize] = size(img_raw);
 hi=prctile(double(reshape(img_flt,1,xsize*ysize)),99.9);
 img_flt_doub = double(img_flt);
 img_double=img_flt_doub/hi;
 mask=ones(xsize,ysize);
 [bw_img imgsegdata]=PISA7(img_double,mask);
 [bw_count dummy]=size(imgsegdata);
 comp_img=zeros(2048,2048,3);
 comp_img(:,:,1)=img_double;
 comp_img(:,:,3)=bw_img;
 imwrite(comp_img,'Series021_20xobj-Zstack-2kx2k_MaxProject_ATTO488_PISA.png','png');
  • All parameters were default except "area lower" was set to 4
  • bw_count = 228

File:Series021 20xobj-Zstack-2kx2k MaxProject ATTO488 PISA.png

Cy5 Primary Rolonies[edit]

 img_raw=imread('Oct42013/Series021_20xobj-Zstack-2kx2k_MaxProject_Cy5.tif','tiff');
 img_flt=medfilt2(img_raw,[3 3]);
 [xsize ysize] = size(img_raw);
 hi=prctile(double(reshape(img_flt,1,xsize*ysize)),99.9);
 img_double=double(img_flt)/hi;
 mask=ones(xsize,ysize);
 [bw_img imgsegdata]=PISA7(img_double,mask);
 [bw_count dummy]=size(imgsegdata);
 comp_img=zeros(2048,2048,3);
 comp_img(:,:,1)=img_double;
 comp_img(:,:,3)=bw_img;
 imwrite(comp_img,'Series021_20xobj-Zstack-2kx2k_MaxProject_Cy5_PISA.png','png');
  • bw_count = 31,147

File:Series021 20xobj-Zstack-2kx2k MaxProject Cy5 PISA.png