minkowski functionals imageJ

[Shirley]

Hi guys,

It's me again :) I have a question regarding to minkowski functionals.

Please see the image below. Firstly, I want to reduce all the black particles to black circles with a same radius and then use imageJ to calculate the connectivity between the particles. Next, I would like to change the size of the circles (increase the radius) to several different values and then calculate the corresponding connectivity between the particles.

However, I am having problem to change all the particles to circles with same radius (and of course calculating connectivity).





Could someone help me with it?

Thank you so much.

[Straub, Volko A. (Dr.)]

How about measuring the centre of mass for each particle and then draw a circle at each of the co-ordinate pairs (this could be done in a new image with the same dimensions)? Use 'Analyse Particles' to add all particles to the ROI manager. You can then use multi-measure to get the co-ordinates of the centre of mass for each particle and use a loop to draw circles at each co-ordinate.
This would at least solve the first part of your question. I can't really help with the analysis of connectivity. Sorry.

Volko

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Shirley
Sent: 14 March 2016 12:07
To: [hidden email]
Subject: minkowski functionals imageJ

Hi guys,

It's me again :) I have a question regarding to minkowski functionals.

Please see the image below. Firstly, I want to reduce all the black particles to black circles with a same radius and then use imageJ to calculate the connectivity between the particles. Next, I would like to change the size of the circles (increase the radius) to several different values and then calculate the corresponding connectivity between the particles.

However, I am having problem to change all the particles to circles with same radius (and of course calculating connectivity).

<http://imagej.1557.x6.nabble.com/file/n5015886/1_copy.png>



Could someone help me with it?

Thank you so much.



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[Michael Schmid]

Hi Shirley,

sounds a bit like you want a Delaunay/Voronoi analysis?
There are plugins for this, and there is also an ImageJ built-in function for an approximate Voronoi diagram. Also the Euclidian distance map might be interesting for you (All in Process>Binary)

For the first step, reducing to single particles, use
-  Process>Find Maxima,
-  Process>Binary>Ultimate Points with subsequent Thresholding from 1 to maximum (255 if you have selected 8-bits output in the binary options),  or
- Analyze particles and analyze the coordinates of the Centroids in the Results Table (this will give you subpixel accuracy)

Michael
________________________________________________________________
On Mar 14, 2016, at 13:07, Shirley wrote:

> Hi guys,
>
> It's me again :) I have a question regarding to minkowski functionals.
>
> Please see the image below. Firstly, I want to reduce all the black
> particles to black circles with a same radius and then use imageJ to
> calculate the connectivity between the particles. Next, I would like to
> change the size of the circles (increase the radius) to several different
> values and then calculate the corresponding connectivity between the
> particles.
>
> However, I am having problem to change all the particles to circles with
> same radius (and of course calculating connectivity).
>
> <http://imagej.1557.x6.nabble.com/file/n5015886/1_copy.png>
>
>
>
> Could someone help me with it?
>
> Thank you so much.

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