PSF Generator in headless or macro

[pen]

Hi,

I was using the PSF generator from here:

http://bigwww.epfl.ch/algorithms/psfgenerator/

and was wondering if anyone knew if batch or macro is supported. If not, does anyone have any suggestions for a PSF generator that does support it since I have image stacks (3D) of different size which will need an individual PSF for each image.

Thanks!

[Daniel Sage]

Pen,

You can prepare a configuration file (.txt) that contains all the parameters of your PSF and run the following commands:

from the terminal: java -cp PSFGenerator.jar PSFGenerator config.txt
from the Matlab console: psf = PSFGenerator.compute('config.txt');

See the example below:

dsage:PSF dsage$ ls -l
-rw-r--r--   2532894 18 jul  2014 PSFGenerator.jar
-rw-r--r--       141  5 mar 23:29 config.txt

dsage:PSF dsage$ more config.txt
Lambda=610.0
LUT=Fire
NA=1.4
NX=256
NY=256
NZ=32
ResAxial=250.0
ResLateral=100.0
Scale=Linear
Type=double
psf-BW-accuracy=Good
psf-BW-NI=1.5

dsage:PSF dsage$ java -cp PSFGenerator.jar PSFGenerator config.txt
Computing BW
Save PSF BW

dsage:PSF dsage$ ls -l
-rw-r--r--    8393128  5 mar 23:30 PSF BW.tif
-rw-r--r--   2532894 18 jul  2014 PSFGenerator.jar
-rw-r--r--       141  5 mar 23:29 config.txt

At the end of the computation you get a PSF_BW.tif file containing the required PSF.

Best,

Daniel

> Hi,
>
> I was using the PSF generator from here:
>
> http://bigwww.epfl.ch/algorithms/psfgenerator/
>
> and was wondering if anyone knew if batch or macro is supported. If not,
> does anyone have any suggestions for a PSF generator that does support it
> since I have image stacks (3D) of different size which will need an
> individual PSF for each image.
>
> Thanks!
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/PSF-Generator-in-headless-or-macro-tp5011899.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[pen]

Hi Daniel,

Thank you for the reply, this should work!

 Just wondering though, would it be possible to feed the configuration inputs in as arguments instead of having to modify or generate a config.txt every time and have everything run within ImageJ, example flow of what I was hoping to do:

Open Image
Grab Image properties (x,y,z)
Set arguments to account for different x,y,z
Generate PSF
Run Deconvolution
Save deconvolved image
Close all

[Daniel Sage]

The settings of PSFGenerator dialog box (on ImageJ) are stored in the PSFGeneraor.txt into plugins when you click on the button "Close".

Best,

Daniel

> Hi Daniel,
>
> Thank you for the reply, this should work!
>
> Just wondering though, would it be possible to feed the configuration
> inputs in as arguments instead of having to modify or generate a config.txt
> every time and have everything run within ImageJ, example flow of what I was
> hoping to do:
>
> Open Image
> Grab Image properties (x,y,z)
> Set arguments to account for different x,y,z
> Generate PSF
> Run Deconvolution
> Save deconvolved image
> Close all
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/PSF-Generator-in-headless-or-macro-tp5011899p5011902.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Akeem38]

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