Removing uneven illuminaiton

[donny008]

Hello

I have been trying to look for methods to remove uneven illumination form
images. I did try  t      he built-in "Subtract Background" command (Process
->
Subtract Background) and from a thread on i      magej  the plugin
"Background Correction"  (http://rsb.info.nih.gov/ij/plugins/background.html
). But none of them provided useful to me. The images are taken from the
production line with a camera and the flash system causes the uneven
illumination. Can someone who has already tried making images homogenous
help me with my task

thank you

--
Donny George

[Johannes-P. Koch]

Donny,

either you have a plain image, just with your background, then you can
perform an a priori shading correction, otherwise you can use an a
posteriori corrector...

check this out:
http://imagejdocu.tudor.lu/doku.php?id=howto:working:how_to_correct_background_illumination_in_brightfield_microscopy 



BTW: I have the mentioned a posteriori shading corrector from the
University of Reims - the Professor there is now retired so he took his
page off the web, unfortunately all the plugins are gone as well; for me
it works extremely well. if you want to test this particular corrector,
let me know and I will mail you the jar file.

Best,
Johannes


Am 11.08.2010 11:33, schrieb Donny George:

> Hello
>
> I have been trying to look for methods to remove uneven illumination form
> images. I did try  t      he built-in "Subtract Background" command (Process
> ->
> Subtract Background) and from a thread on i      magej  the plugin
> "Background Correction"  (http://rsb.info.nih.gov/ij/plugins/background.html
> ). But none of them provided useful to me. The images are taken from the
> production line with a camera and the flash system causes the uneven
> illumination. Can someone who has already tried making images homogenous
> help me with my task
>
> thank you
>
>    

--
Mag. Johannes-P. KOCH
Department of Biochemistry and Cell Biology
MFPL, University of Vienna
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

phone: [phone]
fax: [phone]

mail to: [hidden email]

[amrishchawla]

hi Johannes,

I need the posteriori shading corrector jar file as well. Can you email it
to me

Thanks,
Amrish
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Johannes-P. Koch
Sent: Wednesday, August 11, 2010 5:43 AM
To: [hidden email]
Subject: Re: Removing uneven illuminaiton

Donny,

either you have a plain image, just with your background, then you can
perform an a priori shading correction, otherwise you can use an a
posteriori corrector...

check this out:
http://imagejdocu.tudor.lu/doku.php?id=howto:working:how_to_correct_backgrou
nd_illumination_in_brightfield_microscopy



BTW: I have the mentioned a posteriori shading corrector from the
University of Reims - the Professor there is now retired so he took his
page off the web, unfortunately all the plugins are gone as well; for me
it works extremely well. if you want to test this particular corrector,
let me know and I will mail you the jar file.

Best,
Johannes


Am 11.08.2010 11:33, schrieb Donny George:
> Hello
>
> I have been trying to look for methods to remove uneven illumination form
> images. I did try  t      he built-in "Subtract Background" command
(Process
> ->
> Subtract Background) and from a thread on i      magej  the plugin
> "Background Correction"
(http://rsb.info.nih.gov/ij/plugins/background.html
> ). But none of them provided useful to me. The images are taken from the
> production line with a camera and the flash system causes the uneven
> illumination. Can someone who has already tried making images homogenous
> help me with my task
>
> thank you
>
>    

--
Mag. Johannes-P. KOCH
Department of Biochemistry and Cell Biology
MFPL, University of Vienna
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

phone: [phone]
fax: [phone]

mail to: [hidden email]

[Gabriel Landini]

On Wednesday 11 August 2010, Amrish Chawla wrote:
> University of Reims - the Professor there is now retired so he took his
> page off the web, unfortunately all the plugins are gone as well

What a shame, there were quite a few interesting plugins in those pages.
Would it be worth contacting Prof Bonnet and ask him whether he would be happy
to find a new home those plugins somewhere else?
He might have a copy of the pages (or have access to the pages that were taken
down).
The plugins are easy to identify because they all have a "514" (the INSERM
unit) in the name (I have a few of those too, but no description pages).

Cheers

Gabriel

[Gary Sellani]

Is the page on archive.org?

-----Original Message-----
From:         Gabriel Landini <[hidden email]>
Sender:       ImageJ Interest Group <[hidden email]>
Date:         Wed, 11 Aug 2010 17:40:39
To: <[hidden email]>
Reply-To:     ImageJ Interest Group <[hidden email]>
Subject: Re: Removing uneven illuminaiton

On Wednesday 11 August 2010, Amrish Chawla wrote:
> University of Reims - the Professor there is now retired so he took his
> page off the web, unfortunately all the plugins are gone as well

What a shame, there were quite a few interesting plugins in those pages.
Would it be worth contacting Prof Bonnet and ask him whether he would be happy
to find a new home those plugins somewhere else?
He might have a copy of the pages (or have access to the pages that were taken
down).
The plugins are easy to identify because they all have a "514" (the INSERM
unit) in the name (I have a few of those too, but no description pages).

Cheers

Gabriel

[Joel Sheffield]

I have found that the bandpass correction (under FFT) can be very helpful in
removing the sort of background that is in your image.  The idea is to
consider the overall pattern of illumination to be a long wave pattern, and
to filter it out.  Go to FFT>Bandpass correction, and set the short
wavelength to zero, and the long wavelengths to something like 50 or 100,
depending on your resolution, I uncheck anything about adjusting contrast,
etc.

Best of luck,

Joel



On Wed, Aug 11, 2010 at 5:59 PM, Gary Sellani <[hidden email]> wrote:

> Is the page on archive.org?
>
> -----Original Message-----
> From:         Gabriel Landini <[hidden email]>
> Sender:       ImageJ Interest Group <[hidden email]>
> Date:         Wed, 11 Aug 2010 17:40:39
> To: <[hidden email]>
> Reply-To:     ImageJ Interest Group <[hidden email]>
> Subject: Re: Removing uneven illuminaiton
>
>  On Wednesday 11 August 2010, Amrish Chawla wrote:
> > University of Reims - the Professor there is now retired so he took his
> > page off the web, unfortunately all the plugins are gone as well
>
> What a shame, there were quite a few interesting plugins in those pages.
> Would it be worth contacting Prof Bonnet and ask him whether he would be
> happy
> to find a new home those plugins somewhere else?
> He might have a copy of the pages (or have access to the pages that were
> taken
> down).
> The plugins are easy to identify because they all have a "514" (the INSERM
> unit) in the name (I have a few of those too, but no description pages).
>
> Cheers
>
> Gabriel
>

--


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

[Lim Soon Yew]

Hi Johannes,

I also need the posteriori shading corrector jar file as well. Can you please e-mail it to me? Thank you.

Best Regards,
John
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Amrish Chawla [[hidden email]]
Sent: Wednesday, August 11, 2010 10:47 PM
To: [hidden email]
Subject: Re: Removing uneven illuminaiton

hi Johannes,

I need the posteriori shading corrector jar file as well. Can you email it
to me

Thanks,
Amrish
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Johannes-P. Koch
Sent: Wednesday, August 11, 2010 5:43 AM
To: [hidden email]
Subject: Re: Removing uneven illuminaiton

Donny,

either you have a plain image, just with your background, then you can
perform an a priori shading correction, otherwise you can use an a
posteriori corrector...

check this out:
http://imagejdocu.tudor.lu/doku.php?id=howto:working:how_to_correct_backgrou
nd_illumination_in_brightfield_microscopy



BTW: I have the mentioned a posteriori shading corrector from the
University of Reims - the Professor there is now retired so he took his
page off the web, unfortunately all the plugins are gone as well; for me
it works extremely well. if you want to test this particular corrector,
let me know and I will mail you the jar file.

Best,
Johannes


Am 11.08.2010 11:33, schrieb Donny George:
> Hello
>
> I have been trying to look for methods to remove uneven illumination form
> images. I did try  t      he built-in "Subtract Background" command
(Process
> ->
> Subtract Background) and from a thread on i      magej  the plugin
> "Background Correction"
(http://rsb.info.nih.gov/ij/plugins/background.html
> ). But none of them provided useful to me. The images are taken from the
> production line with a camera and the flash system causes the uneven
> illumination. Can someone who has already tried making images homogenous
> help me with my task
>
> thank you
>
>

--
Mag. Johannes-P. KOCH
Department of Biochemistry and Cell Biology
MFPL, University of Vienna
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

phone: [phone]
fax: [phone]

mail to: [hidden email]

[Marko Usaj]

If it possible, i would also like this the posteriori shading correction jar file. Thank you!

Regards,
Marko

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Lim Soon Yew
Sent: Thursday, August 12, 2010 4:01 AM
To: [hidden email]
Subject: Re: Removing uneven illuminaiton

Hi Johannes,

I also need the posteriori shading corrector jar file as well. Can you please e-mail it to me? Thank you.

Best Regards,
John
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Amrish Chawla [[hidden email]]
Sent: Wednesday, August 11, 2010 10:47 PM
To: [hidden email]
Subject: Re: Removing uneven illuminaiton

hi Johannes,

I need the posteriori shading corrector jar file as well. Can you email it
to me

Thanks,
Amrish
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Johannes-P. Koch
Sent: Wednesday, August 11, 2010 5:43 AM
To: [hidden email]
Subject: Re: Removing uneven illuminaiton

Donny,

either you have a plain image, just with your background, then you can
perform an a priori shading correction, otherwise you can use an a
posteriori corrector...

check this out:
http://imagejdocu.tudor.lu/doku.php?id=howto:working:how_to_correct_backgrou
nd_illumination_in_brightfield_microscopy



BTW: I have the mentioned a posteriori shading corrector from the
University of Reims - the Professor there is now retired so he took his
page off the web, unfortunately all the plugins are gone as well; for me
it works extremely well. if you want to test this particular corrector,
let me know and I will mail you the jar file.

Best,
Johannes


Am 11.08.2010 11:33, schrieb Donny George:
> Hello
>
> I have been trying to look for methods to remove uneven illumination form
> images. I did try  t      he built-in "Subtract Background" command
(Process
> ->
> Subtract Background) and from a thread on i      magej  the plugin
> "Background Correction"
(http://rsb.info.nih.gov/ij/plugins/background.html
> ). But none of them provided useful to me. The images are taken from the
> production line with a camera and the flash system causes the uneven
> illumination. Can someone who has already tried making images homogenous
> help me with my task
>
> thank you
>
>

--
Mag. Johannes-P. KOCH
Department of Biochemistry and Cell Biology
MFPL, University of Vienna
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

phone: [phone]
fax: [phone]

mail to: [hidden email]

[Johannes-P. Koch]

Gabriel,

yes, indeed, it's quite bad...

I contacted him one year ago, because I had some troubles with another
plugin, and he told me that he was already retired; he would have a look
into it anyway....

Quite some people contacted me concerning the shading corrector, so:

I don't know about copyright issues, but as those plugins were freely
available, we could load them on one of the imagej plugin homepages
(indicating Prof. Bonnet as the author of course!)- there is
unfortunately not much documentation - but I could contribute basic
information on the shading corrector, the segmentation plugin, the
seeded watershed (this is a very useful plugin!!) and his gradient (Shen
Castan gradient) plugin...I think there were some more, but maybe you
and some other people could also contribute??? Ideas?

Johannes

Am 11.08.2010 18:40, schrieb Gabriel Landini:

> On Wednesday 11 August 2010, Amrish Chawla wrote:
>    
>> University of Reims - the Professor there is now retired so he took his
>> page off the web, unfortunately all the plugins are gone as well
>>      
> What a shame, there were quite a few interesting plugins in those pages.
> Would it be worth contacting Prof Bonnet and ask him whether he would be happy
> to find a new home those plugins somewhere else?
> He might have a copy of the pages (or have access to the pages that were taken
> down).
> The plugins are easy to identify because they all have a "514" (the INSERM
> unit) in the name (I have a few of those too, but no description pages).
>
> Cheers
>
> Gabriel
>
>    

--
Mag. Johannes-P. KOCH
Department of Biochemistry and Cell Biology
MFPL, University of Vienna
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

phone: [phone]
fax: [phone]

mail to: [hidden email]

[Gabriel Landini]

On Thursday 12 August 2010, you wrote:
> I don't know about copyright issues, but as those plugins were freely
> available, we could load them on one of the imagej plugin homepages
> (indicating Prof. Bonnet as the author of course!)- there is
> unfortunately not much documentation - but I could contribute basic
> information on the shading corrector, the segmentation plugin, the
> seeded watershed (this is a very useful plugin!!) and his gradient (Shen
> Castan gradient) plugin...I think there were some more, but maybe you
> and some other people could also contribute??? Ideas?

I tired to contact Prof Bonnet and the email bounces, but contacted another of
the authors and we are in the process of finding those plugins a new home
(actually Johannes Schindelin found a way to salvage some of the material).
We will have some news on this soon.

Cheers

Gabriel

[fiona]

Hi Johannes,

I also need the posteriori shading corrector jar file . Can you please e-mail it to me? Thank you.

Best Regards,
Fiona