combineZ

[Eric BADEL-2]

Hello everyone,
Did anyone write a macro or plugin that deals with depth of field ?
I know the combineZ freeware that uses several images and combine them
to generate a very good quality image (large field of view) but I did
not find the theory that would help me to write the corresponding macro
with ImageJ.
Thank you
Eric

[Eric BADEL-2]

Sorry. I did not explain enough.
You can record several pictures with a very low depth of field. Each
picture is in focus at a different depth of field. Some algorithm, like
CombineZ freeware
(http://www.hadleyweb.pwp.blueyonder.co.uk/CZ5/Reference/introduction_and_acknowledgement.htm)
are able to combien these images and to generate an image that is in
focus for each pixel. It means that the program is able to choose , for
each pixel location (x,y), what z slice is the good one.. Or something
like that...(but I can be wrong !)

This looks very powerful to restore a image.
It my question more clearer ?

Eric

>
> Do you just mean a Z-axis projection?  Try Image>Stacks>ZProject
>
>> Hello everyone,
>> Did anyone write a macro or plugin that deals with depth of field ?
>> I know the combineZ freeware that uses several images and combine
>> them to generate a very good quality image (large field of view) but
>> I did not find the theory that would help me to write the
>> corresponding macro with ImageJ.
>> Thank you
>> Eric
>

--
Eric BADEL

Attention: new details !

******  [hidden email]  ***********
BADEL Eric
PIAF
INRA Site de Crouel
234, avenue du Brezet
63100 Clermont-Ferrand - France
tel: [phone]

[hidden email]
************************************************
other e-mail addresses are not available any more

[jmutterer]

Eric,

The EPFL Biomedical Imaging Group's "Extended Depth of Field" plugins can do
that with different advanced methods.
You'll find them at http://bigwww.epfl.ch/demo/edf/

Jerome

On Wed, Feb 25, 2009 at 5:55 PM, Eric Badel <[hidden email]>wrote:

> Sorry. I did not explain enough.
> You can record several pictures with a very low depth of field. Each
> picture is in focus at a different depth of field. Some algorithm, like
> CombineZ freeware (
> http://www.hadleyweb.pwp.blueyonder.co.uk/CZ5/Reference/introduction_and_acknowledgement.htm)
> are able to combien these images and to generate an image that is in focus
> for each pixel. It means that the program is able to choose , for each pixel
> location (x,y), what z slice is the good one.. Or something like that...(but
> I can be wrong !)
>
> This looks very powerful to restore a image.
> It my question more clearer ?
>
> Eric
>
>
>> Do you just mean a Z-axis projection?  Try Image>Stacks>ZProject
>>
>>
>>  Hello everyone,
>>> Did anyone write a macro or plugin that deals with depth of field ?
>>> I know the combineZ freeware that uses several images and combine them to
>>> generate a very good quality image (large field of view) but I did not find
>>> the theory that would help me to write the corresponding macro with ImageJ.
>>> Thank you
>>> Eric
>>>
>>
>>
> --
> Eric BADEL
> Attention: new details !
>
> ******  [hidden email]  ***********
> BADEL Eric PIAF
> INRA Site de Crouel
> 234, avenue du Brezet
> 63100 Clermont-Ferrand - France
> tel: [phone]
>
> [hidden email]
> ************************************************
> other e-mail addresses are not available any more
>

[Joel Sheffield]

In addition to the Extended Depth of Field plugins, there is also one
called "Stack Focusser" that uses a simpler approach.

Joel

> Sorry. I did not explain enough.
> You can record several pictures with a very low depth of field. Each
> picture is in focus at a different depth of field. Some algorithm, like
> CombineZ freeware
> (http://www.hadleyweb.pwp.blueyonder.co.uk/CZ5/Reference/introduction_and_acknowledgement.htm)
> are able to combien these images and to generate an image that is in
> focus for each pixel. It means that the program is able to choose , for
> each pixel location (x,y), what z slice is the good one.. Or something
> like that...(but I can be wrong !)
>
> This looks very powerful to restore a image.
> It my question more clearer ?
>
> Eric
>
> >
> > Do you just mean a Z-axis projection?  Try Image>Stacks>ZProject
> >
> >> Hello everyone,
> >> Did anyone write a macro or plugin that deals with depth of field ?
> >> I know the combineZ freeware that uses several images and combine
> >> them to generate a very good quality image (large field of view) but
> >> I did not find the theory that would help me to write the
> >> corresponding macro with ImageJ.
> >> Thank you
> >> Eric
> >
>
> --
> Eric BADEL
>
> Attention: new details !
>
> ******  [hidden email]  ***********
> BADEL Eric
> PIAF
> INRA Site de Crouel
> 234, avenue du Brezet
> 63100 Clermont-Ferrand - France
> tel: [phone]
>
> [hidden email]
> ************************************************
> other e-mail addresses are not available any more

--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]  
[phone], fax [phone]
http://astro.temple.edu/~jbs