plugin/macro to automatically find and measure peak width

[John Oreopoulos]

Hello, I'm writing this email on behalf of a colleague who is not part of the ImageJ email listserver. This person is wondering if there is an existing macro or plugin that can automatically find and measure the widths of peaks in an image of point-sources of light. For example, his images might look like this one:

http://fiji.sc/images/2/26/Disc60xwithoutoptovar.gif

The macro/plugin would ideally find each source of light (in this case a pinhole in a Nipkow disk), fit a Gaussian distribution to this point-source along x and y line profiles drawn through the point, then extract the standard deviation / FWHM of both fits, and finally log the results into a text file.

So far I've been able to construct a simple macro that finds the pinholes using the analyze particles function (searching for centroids) and limiting to a threshold, and then using the xy coordinates of the centroids to act as positions for drawing line profiles through. I think the next step would be to use ImageJ's curve-fitting algorithm to get the fitting data.

Again, not want to re-invent the wheel here, so just wanted to check if there's something out there that can already do this. Would the MetroloJ plugin work in this situation, or does that only work with single points of light in an image (like a fluorescent bead in a micrograph)? My colleague would also ideally have the ability to do this calculation rapidly on the fly as the image is acquired (with maybe a few seconds delay maximum). Maybe MicroManager could do this through it's scripting functions?

Any help here is much appreciated!


Sincerely,


John Oreopoulos
Staff Scientist
Spectral Applied Research Inc.
A Division of Andor Technology
Richmond Hill, Ontario
Canada
www.spectral.ca



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[Herbie-3]

John,

finding the maxima is really easy using the menu command "Find
maxima..." which works reliably with the provided image and a proper
tolerance. This operation provides the point selections and you may get
the coordinates simply by e.g. using the menu command "Measure". No big
deal...

Fitting a Gaussian is a different matter. I guess a 2D-Gaussian is
desired and as far as I know there is no standard IJ-command for this,
but maybe you will find a plugin at the IJ-Website. Did you try?

Best

Herbie

:::::::::::::::::::::::::::::::::::::::::
On 01.05.14 14:16, John Oreopoulos wrote:

> Hello, I'm writing this email on behalf of a colleague who is not
> part of the ImageJ email listserver. This person is wondering if
> there is an existing macro or plugin that can automatically find and
> measure the widths of peaks in an image of point-sources of light.
> For example, his images might look like this one:
>
> http://fiji.sc/images/2/26/Disc60xwithoutoptovar.gif
>
> The macro/plugin would ideally find each source of light (in this
> case a pinhole in a Nipkow disk), fit a Gaussian distribution to this
> point-source along x and y line profiles drawn through the point,
> then extract the standard deviation / FWHM of both fits, and finally
> log the results into a text file.
>
> So far I've been able to construct a simple macro that finds the
> pinholes using the analyze particles function (searching for
> centroids) and limiting to a threshold, and then using the xy
> coordinates of the centroids to act as positions for drawing line
> profiles through. I think the next step would be to use ImageJ's
> curve-fitting algorithm to get the fitting data.
>
> Again, not want to re-invent the wheel here, so just wanted to check
> if there's something out there that can already do this. Would the
> MetroloJ plugin work in this situation, or does that only work with
> single points of light in an image (like a fluorescent bead in a
> micrograph)? My colleague would also ideally have the ability to do
> this calculation rapidly on the fly as the image is acquired (with
> maybe a few seconds delay maximum). Maybe MicroManager could do this
> through it's scripting functions?
>
> Any help here is much appreciated!
>
>
> Sincerely,
>
>
> John Oreopoulos Staff Scientist Spectral Applied Research Inc. A
> Division of Andor Technology Richmond Hill, Ontario Canada
> www.spectral.ca
>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Unruh, Jay-2]

My Fiji update site (the stowers site) has a plugin called fit roi gaussian jru v1 which fits a spot in a square roi to a 2D gaussian.  Of course, you will need to convert your maxima to square roi's first.  Note that I'm in the process of updating the plugin to output to a table but that may take a while.  You can download directly from my website here:

http://research.stowers.org/imagejplugins/

Jay

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Herbie
Sent: Thursday, May 01, 2014 9:24 AM
To: [hidden email]
Subject: Re: plugin/macro to automatically find and measure peak width

John,

finding the maxima is really easy using the menu command "Find maxima..." which works reliably with the provided image and a proper tolerance. This operation provides the point selections and you may get the coordinates simply by e.g. using the menu command "Measure". No big deal...

Fitting a Gaussian is a different matter. I guess a 2D-Gaussian is desired and as far as I know there is no standard IJ-command for this, but maybe you will find a plugin at the IJ-Website. Did you try?

Best

Herbie

:::::::::::::::::::::::::::::::::::::::::
On 01.05.14 14:16, John Oreopoulos wrote:

> Hello, I'm writing this email on behalf of a colleague who is not part
> of the ImageJ email listserver. This person is wondering if there is
> an existing macro or plugin that can automatically find and measure
> the widths of peaks in an image of point-sources of light.
> For example, his images might look like this one:
>
> http://fiji.sc/images/2/26/Disc60xwithoutoptovar.gif
>
> The macro/plugin would ideally find each source of light (in this case
> a pinhole in a Nipkow disk), fit a Gaussian distribution to this
> point-source along x and y line profiles drawn through the point, then
> extract the standard deviation / FWHM of both fits, and finally log
> the results into a text file.
>
> So far I've been able to construct a simple macro that finds the
> pinholes using the analyze particles function (searching for
> centroids) and limiting to a threshold, and then using the xy
> coordinates of the centroids to act as positions for drawing line
> profiles through. I think the next step would be to use ImageJ's
> curve-fitting algorithm to get the fitting data.
>
> Again, not want to re-invent the wheel here, so just wanted to check
> if there's something out there that can already do this. Would the
> MetroloJ plugin work in this situation, or does that only work with
> single points of light in an image (like a fluorescent bead in a
> micrograph)? My colleague would also ideally have the ability to do
> this calculation rapidly on the fly as the image is acquired (with
> maybe a few seconds delay maximum). Maybe MicroManager could do this
> through it's scripting functions?
>
> Any help here is much appreciated!
>
>
> Sincerely,
>
>
> John Oreopoulos Staff Scientist Spectral Applied Research Inc. A
> Division of Andor Technology Richmond Hill, Ontario Canada
> www.spectral.ca
>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[George Patterson]

Hi John,
I've not used it, but here's a link to a plugin which might help.
Best,
George

http://rsb.info.nih.gov/ij/plugins/fwhm/index.html


On Thu, May 1, 2014 at 8:16 AM, John Oreopoulos <[hidden email]
> wrote:

> Hello, I'm writing this email on behalf of a colleague who is not part of
> the ImageJ email listserver. This person is wondering if there is an
> existing macro or plugin that can automatically find and measure the widths
> of peaks in an image of point-sources of light. For example, his images
> might look like this one:
>
> http://fiji.sc/images/2/26/Disc60xwithoutoptovar.gif
>
> The macro/plugin would ideally find each source of light (in this case a
> pinhole in a Nipkow disk), fit a Gaussian distribution to this point-source
> along x and y line profiles drawn through the point, then extract the
> standard deviation / FWHM of both fits, and finally log the results into a
> text file.
>
> So far I've been able to construct a simple macro that finds the pinholes
> using the analyze particles function (searching for centroids) and limiting
> to a threshold, and then using the xy coordinates of the centroids to act
> as positions for drawing line profiles through. I think the next step would
> be to use ImageJ's curve-fitting algorithm to get the fitting data.
>
> Again, not want to re-invent the wheel here, so just wanted to check if
> there's something out there that can already do this. Would the MetroloJ
> plugin work in this situation, or does that only work with single points of
> light in an image (like a fluorescent bead in a micrograph)? My colleague
> would also ideally have the ability to do this calculation rapidly on the
> fly as the image is acquired (with maybe a few seconds delay maximum).
> Maybe MicroManager could do this through it's scripting functions?
>
> Any help here is much appreciated!
>
>
> Sincerely,
>
>
> John Oreopoulos
> Staff Scientist
> Spectral Applied Research Inc.
> A Division of Andor Technology
> Richmond Hill, Ontario
> Canada
> www.spectral.ca
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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