Removing slit-scanning confocal line artifacts

[G. Esteban Fernandez]

Hello all,

 

We sometimes see vertical line artifacts in images acquired with our slit-scanning confocal.  The pattern is highly reproducible and can be divided out with a "blank" image.  However, we sometimes have to filter out the artifacts in Fourier space by masking with a thin horz. rectangle through the middle of the FFT map, save the very center.  Can someone please point out references where line artifacts have been removed with a filter (not by dividing out), whether in Fourier space or not?

 

Those interested can see sample images and FFT mask at http://www.mediafire.com/?sharekey=7b16b66ca9129ce991b20cc0d07ba4d2a83703a20834b252

 

Thanks,

Esteban

--
G. Esteban Fernandez, Ph.D.
Associate Director
Molecular Cytology Core Facility
University of Missouri
120 Bond Life Sciences Center
Columbia, MO  65211

http://www.biotech.missouri.edu/mcc/

573-882-4895
573-884-9395 fax

[Tim Holmes-2]

Esteban:  Check out Fig’s. 53 – 56, and afterwards in:  The Image Processing Handbook by John C. Russ, CRC Press, 1992.  If you want, I can scan the pages and email a pdf to you.

 

Regards

Tim

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of G. Esteban Fernandez
Sent: Tuesday, December 09, 2008 1:26 PM
To: [hidden email]
Subject: Removing slit-scanning confocal line artifacts

 

Hello all,

 

We sometimes see vertical line artifacts in images acquired with our slit-scanning confocal.  The pattern is highly reproducible and can be divided out with a "blank" image.  However, we sometimes have to filter out the artifacts in Fourier space by masking with a thin horz. rectangle through the middle of the FFT map, save the very center.  Can someone please point out references where line artifacts have been removed with a filter (not by dividing out), whether in Fourier space or not?

 

Those interested can see sample images and FFT mask at http://www.mediafire.com/?sharekey=7b16b66ca9129ce991b20cc0d07ba4d2a83703a20834b252

 

Thanks,

Esteban

--
G. Esteban Fernandez, Ph.D.
Associate Director
Molecular Cytology Core Facility
University of Missouri
120 Bond Life Sciences Center
Columbia, MO  65211

http://www.biotech.missouri.edu/mcc/

573-882-4895
573-884-9395 fax

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[Tim Holmes-2]

Forgot to mention: the examples are on pg. 204 of that book.

 

From: Tim Holmes
Sent: Tuesday, December 09, 2008 3:03 PM
To: '[hidden email]'
Subject: FW: Removing slit-scanning confocal line artifacts

 

Esteban:  Check out Fig’s. 53 – 56, and afterwards in:  The Image Processing Handbook by John C. Russ, CRC Press, 1992.  If you want, I can scan the pages and email a pdf to you.

 

Regards

Tim

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of G. Esteban Fernandez
Sent: Tuesday, December 09, 2008 1:26 PM
To: [hidden email]
Subject: Removing slit-scanning confocal line artifacts

 

Hello all,

 

We sometimes see vertical line artifacts in images acquired with our slit-scanning confocal.  The pattern is highly reproducible and can be divided out with a "blank" image.  However, we sometimes have to filter out the artifacts in Fourier space by masking with a thin horz. rectangle through the middle of the FFT map, save the very center.  Can someone please point out references where line artifacts have been removed with a filter (not by dividing out), whether in Fourier space or not?

 

Those interested can see sample images and FFT mask at http://www.mediafire.com/?sharekey=7b16b66ca9129ce991b20cc0d07ba4d2a83703a20834b252

 

Thanks,

Esteban

--
G. Esteban Fernandez, Ph.D.
Associate Director
Molecular Cytology Core Facility
University of Missouri
120 Bond Life Sciences Center
Columbia, MO  65211

http://www.biotech.missouri.edu/mcc/

573-882-4895
573-884-9395 fax

No virus found in this incoming message.
Checked by AVG - http://www.avg.com
Version: 8.0.176 / Virus Database: 270.9.15/1839 - Release Date: 12/9/2008 9:59 AM

[Zoltan]

Hi Esteban,

I can't give you a reference, unfortunately, but I can confirm that we had the same problem years ago with a Zeiss LSM5 live; I wrote an automated pre-processing tool in IDL that removed the critical part from the FFT and did the inverse FFT for all images.  The problem was eventually solved by Zeiss.

  Hope this helps,

Zoltan

On Tue, Dec 9, 2008 at 7:25 PM, G. Esteban Fernandez <[hidden email]> wrote:

Hello all,

 

We sometimes see vertical line artifacts in images acquired with our slit-scanning confocal.  The pattern is highly reproducible and can be divided out with a "blank" image.  However, we sometimes have to filter out the artifacts in Fourier space by masking with a thin horz. rectangle through the middle of the FFT map, save the very center.  Can someone please point out references where line artifacts have been removed with a filter (not by dividing out), whether in Fourier space or not?

 

Those interested can see sample images and FFT mask at http://www.mediafire.com/?sharekey=7b16b66ca9129ce991b20cc0d07ba4d2a83703a20834b252

 

Thanks,

Esteban

--
G. Esteban Fernandez, Ph.D.
Associate Director
Molecular Cytology Core Facility
University of Missouri
120 Bond Life Sciences Center
Columbia, MO  65211

http://www.biotech.missouri.edu/mcc/

573-882-4895
573-884-9395 fax

--

Zoltan Cseresnyes
Facility manager, Imaging Suite

[JOEL B. SHEFFIELD]

Hi,

ImageJ has an FFT/Bandpass filter built in that can selectively
remove either vertical or horizontal lines without a need to
construct an FFT mask.

Let me know if you need more information.

Joel

>
> Hi Esteban, I can't give you a reference, unfortunately, but I can
> confirm that we had the same problem years ago with a Zeiss LSM5
> live; I wrote an automated pre-processing tool in IDL that removed
> the critical part from the FFT and did the inverse FFT for all
> images. The problem was eventually solved by Zeiss.
> Hope this helps,
> Zoltan
>
>
> On Tue, Dec 9, 2008 at 7:25 PM, G. Esteban Fernandez
> <[hidden email]> wrote:
>     Hello all,
>
> We sometimes see vertical line artifacts in images acquired with our
> slit-scanning confocal. The pattern is highly reproducibleand can
> be divided out with a "blank" image.However, we sometimes have
> tofilter out the artifacts in Fourier spaceby masking with a thin
> horz. rectangle through the middle of the FFT map, save the very
> center. Can someone please point out references where line artifacts
> have been removedwith a filter (not by dividing out), whether in
> Fourier space or not?
>
> Those interested can see sample images and FFT mask at
> http://www.mediafire.com/?sharekey=7b16b66ca9129ce991b20cc0d07ba4d2a83
> 703a20834b252
>
>
> Thanks,
> Esteban
>
> --
> G. Esteban Fernandez, Ph.D.
> Associate Director
> Molecular Cytology Core Facility
> University of Missouri
> 120 Bond Life Sciences Center
> Columbia, MO 65211
>
> http://www.biotech.missouri.edu/mcc/
>
> 573-882-4895
> 573-884-9395 fax
>
>
>
> --
>
> Zoltan Cseresnyes
> Facility manager, Imaging Suite

--
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

[Roman Veith]

Hi!

We had the same problem with a Zeiss LSM Live microscope. The problem
was first thought to be related to dust at the CCD line (and therefore
producing a vertical line, because one or more pixels are "covered").
The ZEISS service tried to solve the problem, it resulted at least in
some hardware exchange at the LIVE unit, so maybe the dust was not the
only porblem. Now it's better, but in certain cases one can still see
some lines. If the lines recently occured maybe it's really dust.

Regards,
Roman


G. Esteban Fernandez schrieb:

> Hello all,
>  
> We sometimes see vertical line artifacts in images acquired with our
> slit-scanning confocal.  The pattern is highly reproducible and can be
> divided out with a "blank" image.  However, we sometimes have
> to filter out the artifacts in Fourier space by masking with a thin
> horz. rectangle through the middle of the FFT map, save the very
> center.  Can someone please point out references where line artifacts
> have been removed with a filter (not by dividing out), whether in
> Fourier space or not?
>  
> Those interested can see sample images and FFT mask at
> http://www.mediafire.com/?sharekey=7b16b66ca9129ce991b20cc0d07ba4d2a83703a20834b252 
> <https://webmail.um.umsystem.edu/exchweb/bin/redir.asp?URL=http://www.mediafire.com/?sharekey=7b16b66ca9129ce991b20cc0d07ba4d2a83703a20834b252>
>  
> Thanks,
> Esteban
>
> --
> G. Esteban Fernandez, Ph.D.
> Associate Director
> Molecular Cytology Core Facility
> University of Missouri
> 120 Bond Life Sciences Center
> Columbia, MO  65211
>
> http://www.biotech.missouri.edu/mcc/
>
> 573-882-4895
> 573-884-9395 fax

--
--
Roman Veith
Diplom-Biologe

Institut für physikalische und
theoretische Chemie
AG Biophysikalische Chemie
Universität Bonn
Wegelerstraße 12
53115 Bonn

Tel-Nr.: 0228-733089
Fax-Nr.: 0228-739424

http://www.thch.uni-bonn.de/pc/kubitscheck/

[Arwed Weigel]

A similar problem exists in structured illumination microscopy that uses
a linear grid. the following references might help:

http://dx.doi.org/10.1046/j.1365-2818.2001.00894.x 
<http://dx.doi.org/10.1046/j.1365-2818.2001.00894.x>
http://dx.doi.org/10.1111/j.0022-2720.2004.01411.x 
<http://dx.doi.org/10.1111/j.0022-2720.2004.01411.x>

--
arwed weigel
abteilung fuer neurophysiology und zellulaere biophysik
universitaet goettingen
humboldtallee 23
37073 goettingen

phon [phone]
fax  [phone]

[Stephen Cody-2]

G'day,
 
Interestingly the old Bio-Rad DVC-250 slit scanner was also prone to this problem; it was caused by dust accumutating in the slit. Perhaps the 5Live may be prone to dust settling on the "AchroGate" beam splitter, confocal slit or as already suggested at the detector.
 
Cheers
Stephen Cody