Fwd: noise removal (hot spot removal)

[JimmiB]

Dear all,
I am wondering if anyone is aware of any improvements made to the remove
outliers tool.
We are using an oldish emCCD camera, that is starting to produce frequent
hotspots.   Removal of outliers works well in removing the brightest
pixels, but leaves associated noise that ideally we would like to remove.
 The images show a before and after example.
[image: Inline image 1][image: Inline image 2]
Cheers,
James

*
                       *
*Dr James Burchfield*
The Garvan Institute of Medical Research
384 Victoria Street
Darlinghurst, NSW, 2010
Australia

Email: [hidden email]
Phone:[phone]
Web: *www.garvan.org.au*

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[Michael Schmid]

Hi James,

if there are no saturated pixels other than the hot pixels of the CCD you could try something like this:

run("Duplicate...", "title=mask");
setThreshold(255, 255);
setOption("BlackBackground", false);
run("Convert to Mask");
//extend to neighboring pixels
//(remove the line break introduced by the mailer)
run("Convolve...", "text1=[0 1 0\n0 1 0\n0 1 0\n1 1 0\n0 1 0\n0 0 0\n0 0 0\n]");
run("Create Selection");
selectWindow("image.png");
run("Restore Selection");
run("Median...", "radius=2");

It selects not only the saturated pixels but also their surroundings in the directions given by the 'Convolve' matrix (note that the pattern gets rotated 180° when applied).


Michael
________________________________________________________________
On Aug 13, 2013, at 09:17, James Burchfield wrote:

> Dear all,
> I am wondering if anyone is aware of any improvements made to the remove
> outliers tool.
> We are using an oldish emCCD camera, that is starting to produce frequent
> hotspots.   Removal of outliers works well in removing the brightest
> pixels, but leaves associated noise that ideally we would like to remove.
> The images show a before and after example.
> [image: Inline image 1][image: Inline image 2]
> Cheers,
> James
>
> *
>                       *
> *Dr James Burchfield*
> The Garvan Institute of Medical Research
> 384 Victoria Street
> Darlinghurst, NSW, 2010
> Australia
>
> Email: [hidden email]
> Phone:[phone]
> Web: *www.garvan.org.au*
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[JimmiB]

Thanks Michael,
Much appreciated.
I will give this a go.
Cheers,
James

*
                       *
*Dr James Burchfield*
The Garvan Institute of Medical Research
384 Victoria Street
Darlinghurst, NSW, 2010
Australia

Email: [hidden email]
Phone:[phone]
Web: *www.garvan.org.au*


On Tue, Aug 13, 2013 at 9:48 PM, Michael Schmid <[hidden email]>wrote:

> Hi James,
>
> if there are no saturated pixels other than the hot pixels of the CCD you
> could try something like this:
>
> run("Duplicate...", "title=mask");
> setThreshold(255, 255);
> setOption("BlackBackground", false);
> run("Convert to Mask");
> //extend to neighboring pixels
> //(remove the line break introduced by the mailer)
> run("Convolve...", "text1=[0 1 0\n0 1 0\n0 1 0\n1 1 0\n0 1 0\n0 0 0\n0 0
> 0\n]");
> run("Create Selection");
> selectWindow("image.png");
> run("Restore Selection");
> run("Median...", "radius=2");
>
> It selects not only the saturated pixels but also their surroundings in
> the directions given by the 'Convolve' matrix (note that the pattern gets
> rotated 180° when applied).
>
>
> Michael
> ________________________________________________________________
> On Aug 13, 2013, at 09:17, James Burchfield wrote:
>
> > Dear all,
> > I am wondering if anyone is aware of any improvements made to the remove
> > outliers tool.
> > We are using an oldish emCCD camera, that is starting to produce frequent
> > hotspots.   Removal of outliers works well in removing the brightest
> > pixels, but leaves associated noise that ideally we would like to remove.
> > The images show a before and after example.
> > [image: Inline image 1][image: Inline image 2]
> > Cheers,
> > James
> >
> > *
> >                       *
> > *Dr James Burchfield*
> > The Garvan Institute of Medical Research
> > 384 Victoria Street
> > Darlinghurst, NSW, 2010
> > Australia
> >
> > Email: [hidden email]
> > Phone:[phone]
> > Web: *www.garvan.org.au*
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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