Getting the values of the pixels inside the sphere of radius (r1) and center (x1, y1, z1)

**I want to get the values ​​of the pixels inside the sphere of radius (r1), center coordinates (x1, y1, z1) in the 3D image (xyz).

I want to know a statistic, for example, the average of the values of color intensity within a sphere in a grayscale image.
Since there is not one sphere, but hundreds or more, so I’m looking for an efficient way to quantify them. I have the values ​​of radius (r1, r2, r3 …) and center coordinates ((x1, y1, z1), (x2, y2, z2), (x3, y3, z3) …) .

Please tell me how to do it easily using the functions of Fiji / Imagej such as plugin.

Also, please tell me how to quantify using Imagej macro without using plugin (example of script) if possible.

You can just tell me which one you know.
If my explanation is inadequate, please ask and I’ll get back to you soon.**

Have a look at the 3D Suite:

There are also stack tools available project values, etc, see:

1 Like

Thanks for your comment.

I see, I can use the 3D ROI manager’s 3D intensity measurements feature.
That’s very helpful.

However, there is one thing that is unclear to me.
How do I specify the regions of interest in 3D?
I want to specify the ROIs of the sphere from the xyz coordinates and radius r.
How do I do this?

I know there are plugins like Specify ROI for 2D images,
but I’m not sure what to do for 3D.
Does 3D ImageJ Suite have the ability to specify the ROIs?

Best regards.

Here are some macros:

Like this:

https://imagejdocu.tudor.lu/_media/plugin/stacks/3d_roi_manager/macromanager3d2_centres.ijm

You might contact @ThomasBoudier for more details.

2 Likes

Thanks for the answer to exactly what I want to know.
I think I can do this.
It was very helpful.
Thank you very much.

Hi @SakuLab,

As mentioned by @Bio7, there are many tools for your 3D Analysis in the 3D ImageJ Suite. I am not sure what you want to do, but if you want to draw some shape you can use the plugin 3D Draw Shape where you can draw 3D ellipsoids with specified radius and centre.

Best,

Thomas

1 Like

Thanks for your comment.

Yes, using the plugin 3D Draw Shape seems to solve the problem.

Thank you very much.