Hosuk:LabNotes/2014-7-23: Difference between revisions

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*[[Hosuk:Lab_Notes|LabNote]]
*[[Hosuk:Lab_Notes|LabNote]]


===Deconvolution and PSF images - Update2===
===Deconvolution test - Update===


====Better PSF Functions====
====PSF Functions====
*Generated by '''PSF Generator''' plug-in
*[[Media:PSF_20x_4096x4096_best1st_256x256.tif|PSF_20x_4096x4096_best1st_256x256.tif]]
*[[Media:PSF_20x_4096x4096_best1st_256x256.tif|PSF_20x_4096x4096_best1st_256x256.tif]]
*[[Media:PSF Richards and Wolf_63x_Sqrt_Stack21_z10.tif|PSF Richards and Wolf_63x_Sqrt_Stack21_z10.tif]]
*[[Media:PSF_63x_2048x2048_best1st_40x40.tif|PSF_63x_2048x2048_best1st_40x40.tif]]
*[[Media:PSF Richards and Wolf_63xZoom4_Sqrt_Stack21_z10.tif|PSF Richards and Wolf_63xZoom4_Sqrt_Stack21_z10.tif]]
*[[Media:PSF_63xZoom4_2048x2048_best1st_128x128.tif|PSF_63xZoom4_2048x2048_best1st_128x128.tif.tif]]




**20x PSF is the same as previous one.
====Procedure for PISA====
**PSF for 63x and 63x Zoom=4 are used 'Richard and Wolf' instead of 'Gibson and Lani'.
*Don't do medfilt2 when deconvoluted images are used.
**Choose middle image (11th) after creating 21 stacks, which means use the smallest size of intensity distribution
*deconvblind Image --> mat2gray (for normalize the image for PISA run)




====Matlab code (latest version====
*[[Media:PISA7_Shield_Core_v5.m|PISA7_Shield_Core_v5.m]]
*[[Media:Rolony_Counting_Batch_7.m|Rolony_Counting_Batch_7.m]]


====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=====
====PISA Parameters (same as 07/18)====
*deconvblind Image --> medfilt2
*PISA Param for 20x, 2048 x 2048
*#img_raw = imread(ImgFileName, 'tif');
**Gaussian Std : 2
*#PSFimg = imread(PSFFileName, 'tif');
**Gaussian Upper : -2e-4
*#[img_decv, PSF] = deconvblind(img_raw, PSFimg);
**area upper: 16
*#img_flt = medfilt2(img_decv, [3 3]);
**area lower: 3
*#hi = prctile( double( reshape(img_flt, 1, xsize*ysize) ), 99.9);
**axratio lower: 0.5
*#img_decv_double = double(img_flt)/hi;
**circ upper: 1.6
**circ lower: 0.8
**perim conn: 8
**bkgmult lower: 4




=====For 63x and 63x Zoom=4, 2048x2048=====
 
*deconvblind Image --> mat2gray
*PISA Param for 20x, 4096 x 4096
*#img_raw = imread(ImgFileName, 'tif');
**Gaussian Std : 2
*#PSFimg = imread(PSFFileName, 'tif');
**Gaussian Upper : -5e-4
*#[img_decv, PSF] = deconvblind(img_raw, PSFimg);
**area upper: 50
*#img_decv_double = mat2gray(img_decv);
**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

Latest revision as of 06:24, 24 July 2014

Deconvolution test - Update[edit]

PSF Functions[edit]


Procedure for PISA[edit]

  • Don't do medfilt2 when deconvoluted images are used.
  • deconvblind Image --> mat2gray (for normalize the image for PISA run)


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