Auto selection of brightest point in a image

[csadangi]

Hello,

Is there any way (a plugin/macro) to auto select the brightest cells in an image. (for eg: the attached image)?

Any help would be highly appreciated.

[Daniel Sage]

Hello,

A short macro can produce a reasonable result. It is based on local maximum on the difference of Gaussian (DoG) filter.

If you want better detect you have probably to write your own model-based segmentation algorithm.

Best,

Daniel


// Parameters
radius=4;
noise = 10;
// DoG Filter
run("8-bit");
run("Duplicate...", "title=1-dog.jpg");
run("32-bit");
run("Duplicate...", "title=1-dog-copy.jpg");
run("Gaussian Blur...", "sigma=" + radius);
selectWindow("1-dog.jpg");
run("Gaussian Blur...", "sigma=" + radius/2);
imageCalculator("Subtract create", "1-dog.jpg","1-dog-copy.jpg");
// Detection
selectWindow("Result of 1-dog.jpg");
run("Find Maxima...", "noise=" + noise + " output=[Single Points] exclude");
// Display
run("Maximum...", "radius=2");
run("Red");
selectWindow("1.jpg");
run("Add Image...", "image=[Result of 1-dog.jpg Maxima] x=0 y=0 opacity=50");

> Hello,
>
> Is there any way (a plugin/macro) to auto select the brightest cells in an
> image. (for eg: the attached image)?
>
> Any help would be highly appreciated.
>
> <http://imagej.1557.x6.nabble.com/file/n5010157/1.jpg>
>
>
>
> -----
> ----
> Chinmaya
> Medical University Innsbruck
> Innsbruck
> Austria
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Auto-selection-of-brightest-point-in-a-image-tp5010157.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Michael Schmid]

Hi Chinmaya,

it's not clear what exactly you need.
Have a look at Threshold and Find Maxima - if they don't do what you need, please state your problem more clearly.

Michael
________________________________________________________________
On Oct 22, 2014, at 22:30, csadangi wrote:

> Hello,
>
> Is there any way (a plugin/macro) to auto select the brightest cells in an
> image. (for eg: the attached image)?
>
> Any help would be highly appreciated.
>
> <http://imagej.1557.x6.nabble.com/file/n5010157/1.jpg>
>
>
>
> -----
> ----
> Chinmaya
> Medical University Innsbruck
> Innsbruck
> Austria

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

[Luciana Sabia]

Hello everybody!

I am experiencing some problems with avi files. I am never able to open all the frames of the video, because the program runs out of memory (although sometimes tha number of frames is really low). The problem arises when I try to open from a specific frame: imagej does not open it from the frame I choose but from an other point of the video I am not able to recognize. How can I analyze the second part of videos that imagej is not able to open at a first instance?
thanks everybody
Luciana
     
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi Luciana,

hmm, it is impossible to determine the reason for your problem with this description.

Can you post a (preferably rather small) example showing the problem temporarily on a Web server (dropbox etc.)?

Information that may also help:
Is there a difference between opening the AVI normally or as virtual stack?
Note that you can open a movie of essentially arbitrary size as virtual stack, ImageJ will then only load the current image into memory. You can also delete frames from a virtual stack with out loading it into memory, but you will need memory for the full stack if you want to process the stack.

What might also help diagnosing the problem:
Open the movie with Edit>Options>Misc debug mode enabled, and post the information in the Log when opening it (a) normally and (b) as virtual stack.

Michael
________________________________________________________________
On Oct 23, 2014, at 11:09, Luciana wrote:

> Hello everybody!
>
> I am experiencing some problems with avi files. I am never able to open all the frames of the video, because the program runs out of memory (although sometimes tha number of frames is really low). The problem arises when I try to open from a specific frame: imagej does not open it from the frame I choose but from an other point of the video I am not able to recognize. How can I analyze the second part of videos that imagej is not able to open at a first instance?
> thanks everybody
> Luciana

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