Matt:LabNotes/2013-10-17
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Using PISA[edit]
- Try using PISA to analyze images from Hosuk:LabNotes/2013-10-9
- Compare to Count Nuclei App: Matt:LabNotes/2013-10-15
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