basics steps for deconvolution of microscopic images

[Kolb, Thorsten]

Dear all and a happy new year!

I am working with deltavision files that I want to deconvolve with ImageJ.
Is there some easy to understand step by step tutorial? I searched a bit
with google but had no success ... Maybe someone of you can provide me
the necessary informations.

Thanks a lot in advance,

Thorsten

[Piotr Wendykier-2]

Dear Thorsten,

If you already have a point spread function (or you can generate one),
then my plugins should work:

http://sites.google.com/site/piotrwendykier/software/deconvolution/parallelspectraldeconvolution
http://sites.google.com/site/piotrwendykier/software/deconvolution/paralleliterativedeconvolution

User guides are also available.

Piotr

On Thu, Jan 7, 2010 at 8:59 AM, Thorsten Kolb <[hidden email]> wrote:

> Dear all and a happy new year!
>
> I am working with deltavision files that I want to deconvolve with ImageJ.
> Is there some easy to understand step by step tutorial? I searched a bit
> with google but had no success ... Maybe someone of you can provide me the
> necessary informations.
>
> Thanks a lot in advance,
>
> Thorsten
>

[Kolb, Thorsten]

I do not have a point spread function, but have optical transfer
funcions from the deltavision software.
Is it possible for a non mathematician  like me to convert them to a
PSF, or can I use the OTFs
somehow directly?


Thorsten

> Dear Thorsten,
>
> If you already have a point spread function (or you can generate one),
> then my plugins should work:
>
> http://sites.google.com/site/piotrwendykier/software/deconvolution/parallelspectraldeconvolution
> http://sites.google.com/site/piotrwendykier/software/deconvolution/paralleliterativedeconvolution
>
> User guides are also available.
>
> Piotr
>
> On Thu, Jan 7, 2010 at 8:59 AM, Thorsten Kolb <[hidden email]> wrote:
>  
>> Dear all and a happy new year!
>>
>> I am working with deltavision files that I want to deconvolve with ImageJ.
>> Is there some easy to understand step by step tutorial? I searched a bit
>> with google but had no success ... Maybe someone of you can provide me the
>> necessary informations.
>>
>> Thanks a lot in advance,
>>
>> Thorsten
>>
>>    

--
Thorsten Kolb
Functional Architecture of the Cell (B065)
German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 580 (TP3)
69120 Heidelberg
Germany
 
Fon: [phone] or 3517
Email: [hidden email]

[Gluender-3]

Thorsten,

just a short note on your issue.

First I assume that you deal with 2D-deconvolution (image
enhancement/sharpening) and not with depth reconstruction (3D).

OTF: optical transfer function
PSF: point spread function

In fact the OTF is related to the PSF, but the latter is commonly not
fully determined by the former. Commonly published OTFs represent
(grosso modo) the modulus of the Fourier-transform of the PSF. In
general however the complete transfer function is complex-valued
(modulus and phase) and therefore the OTF doesn't provide enough
information.

As the name suggests, the PSF is the response of your optical system
to a point in the object plane, i.e. the image of the point. You may
experimentally approximate an ideal point by a tiny small object,
i.e. a colour bead or the like. Depending on your optics and
especially your illumination (coherent, partially coherent,
incoherent) the image of a point-like object may actually show
negative values that can't be recognized as such in the detected
image and must indirectly be reconstructed.

If the phase component of the transfer function is negligible, then
you may Fourier-transform the OTF in order to gain the PSF.

>I do not have a point spread function, but have optical transfer
>funcions from the deltavision software.
>Is it possible for a non mathematician  like me to convert them to a
>PSF, or can I use the OTFs
>somehow directly?
>
>Thorsten
>>Dear Thorsten,
>>
>>If you already have a point spread function (or you can generate one),
>>then my plugins should work:
>>
>>http://sites.google.com/site/piotrwendykier/software/deconvolution/parallelspectraldeconvolution
>>http://sites.google.com/site/piotrwendykier/software/deconvolution/paralleliterativedeconvolution
>>
>>User guides are also available.
>>
>>Piotr
>>
>>On Thu, Jan 7, 2010 at 8:59 AM, Thorsten Kolb
>><[hidden email]> wrote:
>>
>>>Dear all and a happy new year!
>>>
>>>I am working with deltavision files that I want to deconvolve with ImageJ.
>>>Is there some easy to understand step by step tutorial? I searched a bit
>>>with google but had no success ... Maybe someone of you can provide me the
>>>necessary informations.
>>>
>>>Thanks a lot in advance,
>>>
>>>Thorsten
>--
>Thorsten Kolb
>Functional Architecture of the Cell (B065)
>German Cancer Research Center (DKFZ)
>Im Neuenheimer Feld 580 (TP3)
>69120 Heidelberg
>Germany
>
>Fon: [phone] or 3517
>Email: [hidden email]

HTH
--

                   Herbie

          ------------------------
          <http://www.gluender.de>

[Joel Sheffield]

You might take a look at Robert Dougherty's deconvolution programs

On Fri, Jan 8, 2010 at 5:13 AM, Thorsten Kolb <[hidden email]>wrote:

> I do not have a point spread function, but have optical transfer funcions
> from the deltavision software.
> Is it possible for a non mathematician  like me to convert them to a PSF,
> or can I use the OTFs
> somehow directly?
>
>
> Thorsten
>
>  Dear Thorsten,
>>
>> If you already have a point spread function (or you can generate one),
>> then my plugins should work:
>>
>>
>> http://sites.google.com/site/piotrwendykier/software/deconvolution/parallelspectraldeconvolution
>>
>> http://sites.google.com/site/piotrwendykier/software/deconvolution/paralleliterativedeconvolution
>>
>> User guides are also available.
>>
>> Piotr
>>
>> On Thu, Jan 7, 2010 at 8:59 AM, Thorsten Kolb <[hidden email]>
>> wrote:
>>
>>
>>> Dear all and a happy new year!
>>>
>>> I am working with deltavision files that I want to deconvolve with
>>> ImageJ.
>>> Is there some easy to understand step by step tutorial? I searched a bit
>>> with google but had no success ... Maybe someone of you can provide me
>>> the
>>> necessary informations.
>>>
>>> Thanks a lot in advance,
>>>
>>> Thorsten
>>>
>>>
>>>
>>
>
> --
> Thorsten Kolb
> Functional Architecture of the Cell (B065)
> German Cancer Research Center (DKFZ)
> Im Neuenheimer Feld 580 (TP3)
> 69120 Heidelberg
> Germany
>
> Fon: [phone] or 3517
> Email: [hidden email]
>

--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs <http://astro.temple.edu/%7Ejbs>

[Joachim Wesner]

Hi,

I second that. If your OTF only has modulus information, but misses phase
information, it will not give enough info about the most important
aberrations in cell microscopy,
that are caused by index mismatches in the environment and the cell and
residual lense aberrations. Modulus errors (apodisation) instead only have
a slight effect on the results
and are usually small, if they become large, phase effects will be "active"
too!

However, I looked around a bit on the net about that Deltavision software
but could not find too much details. How does it derive that OTF? Only by
theoretical grounds?

Mit freundlichen Grüßen / Best regards

Joachim Wesner
Projektleiter Optik Technologiesysteme



                                                                           
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                                        of microscopic images              
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Thorsten,

just a short note on your issue.

First I assume that you deal with 2D-deconvolution (image
enhancement/sharpening) and not with depth reconstruction (3D).

OTF: optical transfer function
PSF: point spread function

In fact the OTF is related to the PSF, but the latter is commonly not
fully determined by the former. Commonly published OTFs represent
(grosso modo) the modulus of the Fourier-transform of the PSF. In
general however the complete transfer function is complex-valued
(modulus and phase) and therefore the OTF doesn't provide enough
information.

As the name suggests, the PSF is the response of your optical system
to a point in the object plane, i.e. the image of the point. You may
experimentally approximate an ideal point by a tiny small object,
i.e. a colour bead or the like. Depending on your optics and
especially your illumination (coherent, partially coherent,
incoherent) the image of a point-like object may actually show
negative values that can't be recognized as such in the detected
image and must indirectly be reconstructed.

If the phase component of the transfer function is negligible, then
you may Fourier-transform the OTF in order to gain the PSF.

>I do not have a point spread function, but have optical transfer
>funcions from the deltavision software.
>Is it possible for a non mathematician  like me to convert them to a
>PSF, or can I use the OTFs
>somehow directly?
>
>Thorsten
>>Dear Thorsten,
>>
>>If you already have a point spread function (or you can generate one),
>>then my plugins should work:
>>
>>http://sites.google.com/site/piotrwendykier/software/deconvolution/parallelspectraldeconvolution

>>http://sites.google.com/site/piotrwendykier/software/deconvolution/paralleliterativedeconvolution

>>
>>User guides are also available.
>>
>>Piotr
>>
>>On Thu, Jan 7, 2010 at 8:59 AM, Thorsten Kolb
>><[hidden email]> wrote:
>>
>>>Dear all and a happy new year!
>>>
>>>I am working with deltavision files that I want to deconvolve with

ImageJ.
>>>Is there some easy to understand step by step tutorial? I searched a bit
>>>with google but had no success ... Maybe someone of you can provide me
the

>>>necessary informations.
>>>
>>>Thanks a lot in advance,
>>>
>>>Thorsten
>--
>Thorsten Kolb
>Functional Architecture of the Cell (B065)
>German Cancer Research Center (DKFZ)
>Im Neuenheimer Feld 580 (TP3)
>69120 Heidelberg
>Germany
>
>Fon: [phone] or 3517
>Email: [hidden email]

HTH
--

                   Herbie

          ------------------------
          <http://www.gluender.de>



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