Finding Minima in ROI

[Lee Hampson]

Hi

I hope someone can help me with what I think may be very simple problem.  Basically I would like a macro that would find the, say 10, minimum pixel values in a ROI and calculate the mean pixel value of these minima.  Something similar to the Find Maxima command but with Minima.  I have tried to do this, and had a search online but have not found a way to find the minimum pixels as opposed to the maximum.

Thanks in advance for any help you can give me

Lee

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[Aryeh Weiss]

On 4/11/14, 1:37 PM, Lee Hampson wrote:
> Hi
>
> I hope someone can help me with what I think may be very simple problem.  Basically I would like a macro that would find the, say 10, minimum pixel values in a ROI and calculate the mean pixel value of these minima.  Something similar to the Find Maxima command but with Minima.  I have tried to do this, and had a search online but have not found a way to find the minimum pixels as opposed to the maximum.
>
> Thanks in advance for any help you can give me
>
> Lee
>

Try checking the "Light Background" option in Find Maxima.

--aryeh

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Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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[gankaku]

Hi Lee,

If the Find Maxima plugin gives you in theory what you need you can either
(after ROI positioning)

1.) invert the image before maxima detection. Then your minima should turn
into maxima.
or
2.) run Find Maxima... with the checkbox "Light background" activated.

cheers,
Jan



2014-04-11 12:37 GMT+02:00 Lee Hampson <[hidden email]>:

> Hi
>
> I hope someone can help me with what I think may be very simple problem.
>  Basically I would like a macro that would find the, say 10, minimum pixel
> values in a ROI and calculate the mean pixel value of these minima.
>  Something similar to the Find Maxima command but with Minima.  I have
> tried to do this, and had a search online but have not found a way to find
> the minimum pixels as opposed to the maximum.
>
> Thanks in advance for any help you can give me
>
> Lee
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Jeremy Adler]

Generate(analyse/histogram) the frequency distribution histogram for the ROI - read the values and find the bin(s) with the lowest 10 intensities - hence the mean

Or invert the intensities in the image, find the maxima and correct for the fact they have been inverted.


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Lee Hampson
Sent: den 11 april 2014 12:38
To: [hidden email]
Subject: Finding Minima in ROI

Hi

I hope someone can help me with what I think may be very simple problem.  Basically I would like a macro that would find the, say 10, minimum pixel values in a ROI and calculate the mean pixel value of these minima.  Something similar to the Find Maxima command but with Minima.  I have tried to do this, and had a search online but have not found a way to find the minimum pixels as opposed to the maximum.

Thanks in advance for any help you can give me

Lee

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