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====Image 1: Hybridized 3 Probes==== *Strict settings: Area 4-21 pixels, Bkgmult_lower 9 img1_raw=imread('Oct292013/S2_20131022_3Dye_DetachTest_2After_ACTB.tif','tiff'); img1_flt=medfilt2(img1_raw,[3 3]); [xsize ysize] = size(img1_raw); hi1=prctile(double(reshape(img1_flt,1,xsize*ysize)),99.9); img1_flt_doub = double(img1_flt); img1_double=img1_flt_doub/hi1; mask=ones(xsize,ysize); [bw_img1 img1segdata]=PISA7(img1_double,mask); area upper: 21 area lower: 4 axratio lower: .7 circ upper: 1.5 circ lower: .8 perim conn: 8 bkgmult lower: 9 [bw1_count dummy1]=size(img1segdata); (bw1_count = 24) comp_img1=zeros(2048,2048,3); comp_img1(:,:,1)=img1_double; comp_img1(:,:,3)=bw_img1; imwrite(comp_img1,'Oct292013/S2_20131022_3Dye_DetachTest_2After_ACTB_PISA7_area4-21_bkgmult9_Overlay.png','png'); *Lenient settings: Area 4-199 pixels, Bkgmult_lower 7 [bw_img1 img1segdata]=PISA7(img1_double,mask); area upper: 199 area lower: 4 axratio lower: .7 circ upper: 1.5 circ lower: .8 perim conn: 8 bkgmult lower: 7 [bw1_count dummy1]=size(img1segdata); (bw1_count = 129) comp_img1=zeros(2048,2048,3); comp_img1(:,:,1)=img1_double; comp_img1(:,:,3)=bw_img1; imwrite(comp_img1,'Oct292013/S2_20131022_3Dye_DetachTest_2After_ACTB_PISA7_area4-199_bkgmult7_Overlay.png','png'); *Best settings?: Area 4-40 pixels, Bkgmult_lower 9 [bw_img1 img1segdata]=PISA7(img1_double,mask); area upper: 40 area lower: 4 axratio lower: .7 circ upper: 1.5 circ lower: .8 perim conn: 8 bkgmult lower: 9 [bw1_count dummy1]=size(img1segdata); (bw1_count = 50) comp_img1=zeros(2048,2048,3); comp_img1(:,:,1)=img1_double; comp_img1(:,:,3)=bw_img1; imwrite(comp_img1,'Oct292013/S2_20131022_3Dye_DetachTest_2After_ACTB_PISA7_area4-40_bkgmult9_Overlay.png','png'); {| {{table}} | Strict Settings (Area 4-21, Bkg_mult 9) || | Lenient Settings (Area 4-199, Bkg_mult 7) || | Best Settings? (Area 4-40, Bkg_mult 9) |- | 24 Counted || | 129 Counted || | 50 Counted |- | [[File:S2_20131022_3Dye_DetachTest_2After_ACTB_PISA7_area4-21_bkgmult9_Overlay.png|450px]] || | [[File:S2_20131022_3Dye_DetachTest_2After_ACTB_PISA7_area4-199_bkgmult7_Overlay.png|450px]] || | [[File:S2_20131022_3Dye_DetachTest_2After_ACTB_PISA7_area4-40_bkgmult9_Overlay.png|450px]] | |} *Strict settings seems to have missed many bright spots but not sure if it's because they are larger than max_area or other reasons *Lenient settings is able to identify all the bright spots previously left out but also highlights some small spots that could be just noise *"Best" settings captures most of the small bright spots. Bright spots not identified are obviously too large and about 3 microns in diameter
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