How to make a 3D spatial density map out of ...

[Raji]

Hi There,  I have produced 10 images (allattached), each of which is a real-time snapshot of a system of varying numberof particles (~100k particles). In fact, each particle represents aninteraction in a 3D space with a particular strength. Thus, each particle has(X,Y,Z) coordinate plus a weight factor between 0 and 1, showing the strengthof interaction in that coordinate. In the attached images, particles are representedas reddish small dots; the redder the dot, the stronger the interaction is.
The question is: how one can produce a 3D (spatial) density map of theseparticles in ImageJ? Is there a way to, say, take the average of these imagesbased on the red-color intensity?
Any ideas/comments are welcome!
PS, Since I have the numerical data for particles (X,Y,Z;w)  I can analyze those data in other software aswell. So, you are welcome to suggest any other analytical approach/software 

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[Anderson, Charles (DNR)]

G'day, Raji.

Two packages available in R (the statistical program from CRAN) can do nonparametric density estimation in 3d: the sm and ks packages will do kernel smoothing (up to 3d and 6d, respectively).

It is not clear how the image data (image#; x,y; R,G,B) relate to your numerical data (time; X,Y,Z; w), so I'm doubtful that ImageJ is the right tool for this analysis.  Mechanically, you could split the color channels, select the red one, invert (the background has R=255), and run a Gaussian filter. The blurred image would represent the local average red in the vicinity of pixel (x,y).  And you could use the image calculator to sum these up (32 bit), then divide by 10 to get a grand average.  But again, I don't understand what the three projected axes in the corner of each image represent in terms of your numerical data, so I'm doubtful of the value of this approach.

Perhaps some additional explanation of the data would enable someone to give another answer.

Charles Anderson

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Raji
Sent: Thursday, July 16, 2015 9:29 PM
To: [hidden email]
Subject: How to make a 3D spatial density map out of ...

Hi There,  I have produced 10 images (allattached), each of which is a real-time snapshot of a system of varying numberof particles (~100k particles). In fact, each particle represents aninteraction in a 3D space with a particular strength. Thus, each particle has(X,Y,Z) coordinate plus a weight factor between 0 and 1, showing the strengthof interaction in that coordinate. In the attached images, particles are representedas reddish small dots; the redder the dot, the stronger the interaction is.
The question is: how one can produce a 3D (spatial) density map of theseparticles in ImageJ? Is there a way to, say, take the average of these imagesbased on the red-color intensity?
Any ideas/comments are welcome!
PS, Since I have the numerical data for particles (X,Y,Z;w)  I can analyze those data in other software aswell. So, you are welcome to suggest any other analytical approach/software 

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

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