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Re: Reduce contiguous area in Find Maxima plugin

Posted by Giuseppe Lucarelli on Jul 03, 2014; 4:14am
URL: http://imagej.273.s1.nabble.com/Re-Reduce-contiguous-area-in-Find-Maxima-plugin-tp5008519p5008564.html

Thanks a lot for your response Michael!

I looked at the source code of the plugin again and realised that the
cleanupMaxima
function is what dictates the minimum distance between two or more maxima.
Is this correct?

Thanks a lot


On 2 July 2014 02:30, Michael Schmid <[hidden email]> wrote:

> Hi Guiseppe,
>
> please send questions about ImageJ to the mailing list, not to me
> personally; there might be many others having the same wishes or problems!
>
> In principle, one can reduce the 'noise tolerance' with distance. Note,
> however, that this can be done accurately only if the maximum is a single
> point.  The result will become unpredictable if there are several pixels
> having exactly the value of the maximum (an arbitrary one of these will be
> selected; it would be a hell of work to do it in a well-defined way).
> What would be a good function for decreasing the noise tolerance with
> distance? A slow decrease line 1/(1 + r/r0)?  A function that approaches
> zero rather rapidly, like a Gaussian?
>
> I also have Philippe's recent whishlist in mind, see
> https://list.nih.gov/cgi-bin/wa.exe?A2=ind1406&L=IMAGEJ&F=&S=&P=177817
>
> What do you think about the following idea:
>
> Having an external "Find Maxima Plus" plugin, with the following features:
>
> - Philippe's bells&whistles, see the posting above,
> - Threshold being a combination of a fixed value and a fraction
> (percentage of the peak value)
> - Maybe minimum distance between two maxima?
> - Some reduction of the noise tolerance with distance, see above.
>
> I think that this probably should not go into standard ImageJ, it would be
> too complex for most users. It would take a while, but I could try doing it
> this summer.
>
> Regards,
>
> Michael
> ________________________________________________________________
> On Jun 30, 2014, at 04:38, Giuseppe Lucarelli wrote:
>
> > Dear Michael,
> >
> > I am using the Find Maxima plugin in imagej but in ROI with visible (by
> eye) >1 maxima the plugin only finds one unless I lower the noise tolerance
> to a value that picks up other undesired points in the ROI.
> > The problem is that the two peaks I need to select, although far apart,
> are not separated by low value points ("valley") which affects the plugin.
> > I thought I could modify the plugin so that the valley between two
> maxima does not need to be so low.
> >
> > What are your thoughts on this?
> > If you think I should modify the plugin, how do I do that?
> >
> > Thanks a lot for your help.
> >
> > Regards,
> > Giuseppe Lucarelli
>
>


--
Giuseppe Lucarelli
Biochemistry PhD student
Prescott/Devenish Lab, Bld 13 D224a
PH  990 53785

<[hidden email]>

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