Measuring distance of a pixels from an object

[Ofra Golani]

Hi,

I have 2D and 3D data in which I have one big object and some other high intensity pixels.
For each such pixel I need to measure its closest distance to the big object.
I than need to calculate the average distance and other parameters based on the distances distribution.
Is there a way to this ImageJ/Fiji ?

If it doesn't work for each pixel, I can do particle analysis, again I'll need to calculate the closest distance from each small particle to the big object.

Thanks,
Ofra Golani


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[Thomas Boudier]

Hi,

In the 3D ImageJ Suite there is function for calculating distances (2D
and 3D) and also have access to closest objects :

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

Do not hesitate if you want more details.

best,

Thomas



Le 11/10/2012 09:44, Ofra Golani a écrit :

> Hi,
>
> I have 2D and 3D data in which I have one big object and some other high intensity pixels.
> For each such pixel I need to measure its closest distance to the big object.
> I than need to calculate the average distance and other parameters based on the distances distribution.
> Is there a way to this ImageJ/Fiji ?
>
> If it doesn't work for each pixel, I can do particle analysis, again I'll need to calculate the closest distance from each small particle to the big object.
>
> Thanks,
> Ofra Golani
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[Michael Schmid]

Hi Ofra,

in 2D you could do something like the following:

- Threshold for big object and run 'Analyze Particles' with a suitable minimum size to get the big object; select output type Mask.
- Get an Euclidian distance (EDM) map of the mask (Process>Binary>Distance Map). If you may have distances>255 pixels, use the Process>Binary>Options before to select 32 bits (float) output for the EDM.
- if you have created a separate 32-bit EDM, close the mask; otherwise rename it to 'EDM' or the like.
- Select your small pixels in the original image and create a selction from it.  E.g. Analyze particles with maximum size; add ROIs to ROI Manager, or create a new mask again and Edit>Selection>Create selection and add it to the Roi Manager)
- In the Euclidian Distance map, select the roi(s) from the roi manager.  For each roi (or the roi with all small pixels), get the intensity. If you have all rois at once, you can also create a histogram (Analyze>Histogram).  The values in the EDM are the distances, so you will have a histogram of distances.

For 3D, it's essentially the same, but with the corresponding 3D functions by Thomas Boudier. If you don't find a 3D EDM in the 3D collection of Thomas Boudier, there should be one on the web site of Bob Dougherty, http://www.optinav.com/imagej.html

Michael
________________________________________________________________
On Oct 11, 2012, at 09:44, Ofra Golani wrote:

> Hi,
>
> I have 2D and 3D data in which I have one big object and some other high intensity pixels.
> For each such pixel I need to measure its closest distance to the big object.
> I than need to calculate the average distance and other parameters based on the distances distribution.
> Is there a way to this ImageJ/Fiji ?
>
> If it doesn't work for each pixel, I can do particle analysis, again I'll need to calculate the closest distance from each small particle to the big object.
>
> Thanks,
> Ofra Golani

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