Matt:LabNotes/2013-10-30

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Revision as of 21:24, 31 October 2013 by >Mzcai (→‎Image 1: Hybridized 3 Probes)
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PISA7 Analysis on ACTB Targets of Primary Rolonies

Images

  1. Hybridized 3 Probes (1st Rolonies, ACTB Target, RAB7A Target) and Imaging ATTO488: S2_20131022_3Dye_DetachTest_2After_ACTB.tif
  2. Stripped all dyes and Imaging ATTO488: S2_20131022_Add1ProbeOnlyTest_1Strip_ACTB.tif
  3. Hybridized ACTB Probe and Imaging ATTO488: S2_20131022_Add1ProbeOnlyTest_2AddACTBOnly_ACTB.tif

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');
Strict Settings (Area 4-21, Bkg_mult 9) Lenient Settings (Area 4-199, Bkg_mult 7) Best Settings? (Area 4-40, Bkg_mult 9)
File:S2 20131022 3Dye DetachTest 2After ACTB PISA7 area4-21 bkgmult9 Overlay.png File:S2 20131022 3Dye DetachTest 2After ACTB PISA7 area4-199 bkgmult7 Overlay.png File:S2 20131022 3Dye DetachTest 2After ACTB PISA7 area4-40 bkgmult9 Overlay.png