Hosuk:LabNotes/2014-7-23

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Deconvolution and PSF images - Update2

Better PSF Functions


    • 20x PSF is the same as previous one.
    • PSF for 63x and 63x Zoom=4 are used 'Richard and Wolf' instead of 'Gibson and Lani'.
    • Choose middle image (11th) after creating 21 stacks, which means use the smallest size of intensity distribution


Procedure

  • deconvblind function can perform deconvolution with uint16 class images.
  • deconvoluted result need to be double, normalized [0 1] for PISA run or other post rolony detection algorithm


For 20x, 4096x4096
  • deconvblind Image --> medfilt2
    1. img_raw = imread(ImgFileName, 'tif');
    2. PSFimg = imread(PSFFileName, 'tif');
    3. [img_decv, PSF] = deconvblind(img_raw, PSFimg);
    4. img_flt = medfilt2(img_decv, [3 3]);
    5. hi = prctile( double( reshape(img_flt, 1, xsize*ysize) ), 99.9);
    6. img_decv_double = double(img_flt)/hi;


For 63x and 63x Zoom=4, 2048x2048
  • deconvblind Image --> mat2gray
    1. img_raw = imread(ImgFileName, 'tif');
    2. PSFimg = imread(PSFFileName, 'tif');
    3. [img_decv, PSF] = deconvblind(img_raw, PSFimg);
    4. img_decv_double = mat2gray(img_decv);