Hosuk:LabNotes/2014-7-23: Difference between revisions
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*[[Hosuk:Lab_Notes|LabNote]] | |||
===Deconvolution test - Update=== | |||
====PSF Functions==== | |||
*Generated by '''PSF Generator''' plug-in | |||
*[[Media:PSF_20x_4096x4096_best1st_256x256.tif|PSF_20x_4096x4096_best1st_256x256.tif]] | |||
*[[Media:PSF_63x_2048x2048_best1st_40x40.tif|PSF_63x_2048x2048_best1st_40x40.tif]] | |||
*[[Media:PSF_63xZoom4_2048x2048_best1st_128x128.tif|PSF_63xZoom4_2048x2048_best1st_128x128.tif.tif]] | |||
====Procedure for PISA==== | |||
*Don't do medfilt2 when deconvoluted images are used. | |||
*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]] | |||
====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 |
Latest revision as of 06:24, 24 July 2014
Deconvolution test - Update[edit]
PSF Functions[edit]
- Generated by PSF Generator plug-in
- PSF_20x_4096x4096_best1st_256x256.tif
- PSF_63x_2048x2048_best1st_40x40.tif
- PSF_63xZoom4_2048x2048_best1st_128x128.tif.tif
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