Posted by
Daniel James White on
Mar 10, 2011; 2:43pm
URL: http://imagej.273.s1.nabble.com/Deconvolution-on-MacBook-tp3685439p3685443.html
Hi Elizabeth,
>>
>> which plugin exactly do you mean?
>> Indeed there are 2 RIs to take care of, and you correctly query which it asks for... better ask them or look for clarification in the docs.
>>
>>
> I am referring to the PSF generator plugin at
http://bigwww.epfl.ch/deconvolution//?p=plugins> The documentation amounts to: Select the parameters and click on "Generate PSF". I am not joking! So I contacted the author with my specific questions.
OK, so there is that one, and also Bob's Diffraction PSD 3D plugin.
They give similar but slightly different PSFs for the same input parameters,
as they must use a different model to generate the image....?
>>
>>> I also have stacks of subresolution size beads that I would like to use to measure my PSF. How can I obtain this measurement?
>>>
>> the image of 1 bead is pretty much almost-ish the PSF. So long as its really a sub resolution bead. You can align multiple images of beads and average them.
>> But if you get a single good bead with very good signal : noise, that will work.
>>
>>
> This is a strange concept for me, that a "function" could be equated to an image stack! But I suppose the mathematical function itself is calculated from the image stack by the software? After all the information I have read, PSF still remains a vague term for me, sometimes used to describe an image, sometimes used to describe the diffraction pattern of light around an object, sometimes used to describe the mathematical function that will be applied to the raw image to deconvolve it.
you are right, it is odd to talk about a discretized image ( a set of point values) as a function... its just the jargon of the field.
Physically, it is a smooth function, but we have to deal with a discrete representation of it... an "image", in order to do the deconvolution.
I understand your confusion, and it is well grounded
>
>> Huygens software has a tool to make a psf from a bead image by removing the size of the bead and cleaning up the psf image.
>> API softWoRx does it too (OTF in this case)
>> Not sure i saw a tool like this for imageJ... if you did then please let me know!
>>
> Yes, it is the plugin by Janick Cardinale from the Mosaic lab. You can find the pdf manual at www.mosaic.ethz.ch/Downloads/ParticleTracker/PSF_measurement_3D.pdf
> But I cannot find the plugin anywhere! I wrote to the author.
I has a quick look... this is not what you need, as you want to measure the PSF in 3D,
but this one takes bead images and averaved them axially, to make a 2D PSF that is a rotational projection around the axis. You dont want that,
What you want is a gadget likje the Huygens PSF distiller that makes 3D PSFs from real bead images....
but you can use an image of a bead that is 100nm AS the PSF.
cheers
Dan
>
> To be continued... thanks again,
> Elizabeth
>
>
>
>> For use as a psf, the bead image must be centered on the centre of the bead for it to work as a psf.
>>
>>
>>
>>> I found information on a PSF 3D measurement plugin by Janick Cardinale, but it does not appear to be available for download in the list of ImageJ plugins, and I find no similar plugins.
>>>
>>>
>>
>> can you share that info?
>> Also see the mosaic plugins from ETH (i haven't tested them yet though)
>> feel free to ask more on the imagej list...
>>
>> cheers
>>
>>
>> Dan
>>
>>
>>
>>
>
Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
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