Hosuk:LabNotes/2014-7-20

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Deconvolution and PSF images - Update[edit]

PSF Functions[edit]

  • Generated by PSF Generator plug-in
    • Settings

File:PSFGeneratorSettings 2014-07-20.png.png



Procedure for PISA[edit]

  • Pre-processing before an actual identification algorithm
    1. img_raw = imread(ImgFileName);
    2. img_double1 = mat2gray(img_raw);
    3. [img_decv, PSF] = deconvblind(img_double1, PSFimg, 10);
    4. img_flt = medfilt2(img_decv, [3 3]);
    5. [xsize, ysize]=size(img_raw);
    6. hi = prctile( double( reshape(img_flt, 1, xsize*ysize) ), 99.9);
    7. img_decv_filt = double(img_flt)/hi;
    8. imwrite(uint16(img_decv_filt*65535), strcat(DecovPath, 'Decv_', ImgFileName), 'tiff');
    9. img_raw = imread(strcat(DecovPath, 'Decv_', ImgFileName), 'tiff');
    10. [bw_img, bw_count, img_masking, seg_data, elapse_time, img_filtered_uint16] = PISA7_Shield_Core_v4(img_raw, PISAParam, RunBackgroundSubtraction);
    • (RunBackgroundSubtraction=0)


  • Need to test the result between doing medfilt2 or not for 20x 4096x4096
    • medfilt2 (of 20x 4096x4096 image) seems to make more blurred image…
    • So don't medfilt2 after deconvolution of 20x 4096x4096 image


Matlab code (latest version[edit]


PISA Parameters (same as 07/18)[edit]

  • PISA Param for 20x, 2048 x 2048
    • Gaussian Std : 2
    • Gaussian Upper : -2e-4
    • area upper: 16
    • area lower: 3
    • axratio lower: 0.5
    • circ upper: 1.6
    • circ lower: 0.8
    • perim conn: 8
    • bkgmult lower: 4


  • PISA Param for 20x, 4096 x 4096
    • Gaussian Std : 2
    • Gaussian Upper : -5e-4
    • area upper: 50
    • area lower: 6
    • axratio lower: 0.5
    • circ upper: 1.6
    • circ lower: 0.8
    • perim conn: 8
    • bkgmult lower: 3


  • PISA Param for 63x, 2048 x 2048
    • Gaussian Std : 3
    • Gaussian Upper : -2e-4
    • area upper: 81
    • area lower: 9
    • axratio lower: 0.6
    • circ upper: 1.6
    • circ lower: 0.8
    • perim conn: 8
    • bkgmult lower: 4


  • PISA Param for 63x Zoom 4, 2048 x 2048
    • Gaussian Std : 5
    • Gaussian Upper : -2e-5
    • area upper: 1296
    • area lower: 81
    • axratio lower: 0.5
    • circ upper: 1.6
    • circ lower: 0.8
    • perim conn: 8
    • bkgmult lower: 4


Rolony Count:Compare prev. vs. new code[edit]

  • Data : 07/15

File:RolonyCountTable withlatestPISACode 2014-07-21.png