Posted by
Daniel James White on
Aug 23, 2011; 7:28am
URL: http://imagej.273.s1.nabble.com/Leveling-Image-tp3683357p3683371.html
Dear Ashan,
Hope you are enjoying Turku, its a nice city!
Gabriel and Michael's comments are spot on.
It is possible to filter out these "dark lines"
using a Fourier domain filter...
BUT, you should first ask WHY do i get that image artifact,
where does it come from, and how can I get rid of it in the first place.
Any image you create by filtering this original image might look a bit like how you imagine
the "real" image should look.... but it will not be really the same.
THe best approach is to get rid of the lines at their source...
How were the images made?
Laser scanning confocal? AFM? Something else?
It might be a simple hardware problem that is fixable.
Image processing folks often fall into the trap of trying to "fix" ugly data.
The right thing to do is get better data in the first place.
One must understand the whole imaging pipeline from sample prep, to imaging, to image analysis,
or else there will be wrong assumptions and errors.
just my 2 cents
cheers
Dan
On Aug 23, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:
>
> Date: Mon, 22 Aug 2011 14:46:10 +0100
> From: Gabriel Landini <
[hidden email]>
> Subject: Re: Leveling Image
>
> On Monday 22 Aug 2011, Ahsan wrote:
>> Thank you much for you reply. The approach you talked about in the end is
>> actually what i am thinking and looking for. I.e. first subtracting a
>> fitted plane to remove the noise and then correcting the image line by
>> line by using the median approach. I have been able to do the plane
>> correction and was wondering if there is any plugin for line wise
>> correction using the median approach.
>
> The Fourier analysis image looks truly impressive, but wouldn't this erase
> areas that also happen to be originally dark and horizontal? I wonder if this
> would be unable to differentiate between the artifact and the data. For
> example is the horizontal dark valley in the original a feature or an
> artifact?
>
> Now that you provided an image, the idea of modelling the background intensity
> goes through the window as there is no obvious background in the image to play
> with.
>
> To answer your other question, to do a line filtering you can reslice your
> image (from Top). This creates a stack which is the image seen from the top
> (so each slice is a line).
> Then you could filter the stack with a median filter as large as the image
> width and reslice back to obtain the horizontally-median-filtered image. The
> only problem is that the maximum filter radius one can use is 100 and your
> image is wider than 200.
>
> Regards
>
> Gabriel
Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany
+49 (0)15114966933 (German Mobile)
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( white (at) mpi-cbg.de )