Hosuk:LabNotes/2014-7-20: Difference between revisions
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>Hosuki78 (Created page with "*LabNote ===Deconvolution and PSF images - Update=== ====PSF Functions==== *Generated by '''PSF Generator''' plug-in **Settings [[File:PSFGeneratorSettin...") |
>Hosuki78 No edit summary |
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(6 intermediate revisions by the same user not shown) | |||
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*Generated by '''PSF Generator''' plug-in | *Generated by '''PSF Generator''' plug-in | ||
**Settings | **Settings | ||
[[File:PSFGeneratorSettings_2014-07-20.png.png| | [[File:PSFGeneratorSettings_2014-07-20.png.png|900px]] | ||
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====Procedure for PISA==== | ====Procedure for PISA==== | ||
*Pre-processing before an actual identification algorithm | |||
*#img_raw = imread(ImgFileName); | *#img_raw = imread(ImgFileName); | ||
*#img_double1 = mat2gray(img_raw); | *#img_double1 = mat2gray(img_raw); | ||
Line 21: | Line 22: | ||
*#[xsize, ysize]=size(img_raw); | *#[xsize, ysize]=size(img_raw); | ||
*#hi = prctile( double( reshape(img_flt, 1, xsize*ysize) ), 99.9); | *#hi = prctile( double( reshape(img_flt, 1, xsize*ysize) ), 99.9); | ||
*# | *#img_decv_filt = double(img_flt)/hi; | ||
*#imwrite(uint16(img_decv_filt*65535), strcat(DecovPath, 'Decv_', ImgFileName), 'tiff'); | |||
*#img_raw = imread(strcat(DecovPath, 'Decv_', ImgFileName), 'tiff'); | |||
*#[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''' | *Need to test the result between doing medfilt2 or not for '''20x 4096x4096''' | ||
**medfilt2 (of 20x 4096x4096 image) seems to make more blurred image… | **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==== | |||
*[[Media:PISA7_Shield_Core_v4.m|'''PISA7_Shield_Core_v4.m''']] | |||
*[[Media:Rolony_Counting_Batch_6.m|'''Rolony_Counting_Batch_6.m''']] | |||
**Those codes were fixed the bug about over-counting with singlet and doublet as well as included deconvolution. | |||
====PISA Parameters (same as 07/18)==== | |||
*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==== | |||
*Data : 07/15 | |||
[[File:RolonyCountTable_withlatestPISACode_2014-07-21.png|900px]] |
Latest revision as of 19:29, 21 July 2014
Deconvolution and PSF images - Update[edit]
PSF Functions[edit]
- Generated by PSF Generator plug-in
- Settings
File:PSFGeneratorSettings 2014-07-20.png.png
- PSF_20x_4096x4096_best1st_40x40.tif
- PSF_63x_2048x2048_best1st_40x40.tif
- PSF_63xZoom4_2048x2048_best1st_128x128.tif.tif
Procedure for PISA[edit]
- Pre-processing before an actual identification algorithm
- img_raw = imread(ImgFileName);
- img_double1 = mat2gray(img_raw);
- [img_decv, PSF] = deconvblind(img_double1, PSFimg, 10);
- img_flt = medfilt2(img_decv, [3 3]);
- [xsize, ysize]=size(img_raw);
- hi = prctile( double( reshape(img_flt, 1, xsize*ysize) ), 99.9);
- img_decv_filt = double(img_flt)/hi;
- imwrite(uint16(img_decv_filt*65535), strcat(DecovPath, 'Decv_', ImgFileName), 'tiff');
- img_raw = imread(strcat(DecovPath, 'Decv_', ImgFileName), 'tiff');
- [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]
- PISA7_Shield_Core_v4.m
- Rolony_Counting_Batch_6.m
- Those codes were fixed the bug about over-counting with singlet and doublet as well as included deconvolution.
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