Help to deconvolve

[María Victoria Pepe]

Hi!



I´m trying to deconvolve an image, the idea is study the characteristic of
the membrane of apoptotic cells in different stages. So, I read that it´s
possible to do this using two sequential plugins (Diffraction PSF 3D and
Iterative Deconvolve 3D), but I´m not sure how to complete the input
parameters.

I´m sending you an example image, the Images I am working with, are 3D
images obtained with a Confocal Laser Scanning Microscope. Parameters to
obtain the image were calculated using the NyquistCalculator



Thanks for your help


 MDCKlgfpPAKmChAN647ZOOM4 7.oib
<https://drive.google.com/file/d/1P87NPMnWLOnMdgclaB95YS-U950wAY0S/view?usp=drive_web>

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[bnorthan]

Hi Maria

Diffraction PSF should be relatively straightforward.  It does not seem to
have an option for confocal PSF.  As an aproximation you could square the
output.

The only output that is non-standard is "Longitudinal Spherical
Aberration".  I am not sure of the units of this parameter, however you can
probably still get a reasonable result keeping it at zero, unless you have
reason to believe your image has severe SA.

You will have to create a PSF for each channel in your image using the
appropriate wavelength, split the channels from the original image then
deconvolve each separately (I don't think Iterative Deconvolve 3D is able
to handle multiple channels at once).

Currently the ImageJ2 team is working on a new library called ops, which
has functions for PSF generation and deconvolution, (including an
experimental GPU version).  Ops is not a plugin but a library and requires
a bit of scripting.  If you are interested in this approach I recommend
posting a question to the Image.sc forum (https://forum.image.sc/).

Note that Diffraction PSF and Iterative Deconvolution 3D is a perfectly
good solution, especially if you are only going to be deconvolving a few
images.   The ops solution is more complicated but could be worth it if you
will be doing deconvolution long term, and it makes sense to invest up
front time to develop customized scripts.

Brian

On Tue, Mar 26, 2019 at 8:23 AM María Victoria Pepe <
[hidden email]> wrote:

> Hi!
>
>
>
> I´m trying to deconvolve an image, the idea is study the characteristic of
> the membrane of apoptotic cells in different stages. So, I read that it´s
> possible to do this using two sequential plugins (Diffraction PSF 3D and
> Iterative Deconvolve 3D), but I´m not sure how to complete the input
> parameters.
>
> I´m sending you an example image, the Images I am working with, are 3D
> images obtained with a Confocal Laser Scanning Microscope. Parameters to
> obtain the image were calculated using the NyquistCalculator
>
>
>
> Thanks for your help
>
>
>  MDCKlgfpPAKmChAN647ZOOM4 7.oib
> <
> https://drive.google.com/file/d/1P87NPMnWLOnMdgclaB95YS-U950wAY0S/view?usp=drive_web
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[María Victoria Pepe]

Hi Brian!!

Thank you very much for answering,  you are very kind.

Victoria




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El jue., 28 mar. 2019 a las 8:55, Brian Northan (<[hidden email]>)
escribió:

> Hi Maria
>
> Diffraction PSF should be relatively straightforward.  It does not seem to
> have an option for confocal PSF.  As an aproximation you could square the
> output.
>
> The only output that is non-standard is "Longitudinal Spherical
> Aberration".  I am not sure of the units of this parameter, however you can
> probably still get a reasonable result keeping it at zero, unless you have
> reason to believe your image has severe SA.
>
> You will have to create a PSF for each channel in your image using the
> appropriate wavelength, split the channels from the original image then
> deconvolve each separately (I don't think Iterative Deconvolve 3D is able
> to handle multiple channels at once).
>
> Currently the ImageJ2 team is working on a new library called ops, which
> has functions for PSF generation and deconvolution, (including an
> experimental GPU version).  Ops is not a plugin but a library and requires
> a bit of scripting.  If you are interested in this approach I recommend
> posting a question to the Image.sc forum (https://forum.image.sc/).
>
> Note that Diffraction PSF and Iterative Deconvolution 3D is a perfectly
> good solution, especially if you are only going to be deconvolving a few
> images.   The ops solution is more complicated but could be worth it if you
> will be doing deconvolution long term, and it makes sense to invest up
> front time to develop customized scripts.
>
> Brian
>
> On Tue, Mar 26, 2019 at 8:23 AM María Victoria Pepe <
> [hidden email]> wrote:
>
> > Hi!
> >
> >
> >
> > I´m trying to deconvolve an image, the idea is study the characteristic
> of
> > the membrane of apoptotic cells in different stages. So, I read that it´s
> > possible to do this using two sequential plugins (Diffraction PSF 3D and
> > Iterative Deconvolve 3D), but I´m not sure how to complete the input
> > parameters.
> >
> > I´m sending you an example image, the Images I am working with, are 3D
> > images obtained with a Confocal Laser Scanning Microscope. Parameters to
> > obtain the image were calculated using the NyquistCalculator
> >
> >
> >
> > Thanks for your help
> >
> >
> >  MDCKlgfpPAKmChAN647ZOOM4 7.oib
> > <
> >
> https://drive.google.com/file/d/1P87NPMnWLOnMdgclaB95YS-U950wAY0S/view?usp=drive_web
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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