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Re: Help to create macro

Posted by Gabriel Landini on Dec 12, 2019; 9:11am
URL: http://imagej.273.s1.nabble.com/Help-to-create-macro-tp5022778p5022779.html

This kind of problem can be resolved using RCC
https://blog.bham.ac.uk/intellimic/spatial-reasoning-with-imagej-using-the-region-connection-calculus/

Once you segment your objects as binary, you could look for the relation of
regions in one image with the regions in the other image.
See "Computing relations between multiple regions" section in that page. RCC5
should be enough to detect the PP relations between the intranuclear regions
and the nuclei.
Once you have the RCC table generated, then it is a matter of searching the
table across the "nuclear regions axis" and count how many PP relations they
hold with the "intranuclear regions" axis.

There are several papers with examples here:
https://blog.bham.ac.uk/intellimic/references/

Hope it helps.

Gabriel

On Thursday, 12 December 2019 05:31:49 GMT [hidden email] wrote:

> Hello,
> I want to write a macro allowing me to characterize inclusions in the cell
> nucleus (number / nucleus, size and intensity of fluorescence). I think at
> first to segment the nuclei and then look inside this mask for the
> inclusions of interest. My problem is that I do not know how to make a new
> segmentation in the segmentation of the nuclei. Thank you in advance for
> your advice and ideas so that I can write this macro. I attach an image of
> cores (DAPI) and an image with the marker of interest (TxRed). A big thank
> you to all,
> Patricia
>
> _______________________________________
> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr/>
>
> Patricia OBEÏD
> Ingénieur de Recherche /Animateur Informatique Biomics
> Institut de Recherche Interdisciplinaire de Grenoble
> DRF / IRIG / DS /BGE U1038/ Biomics / Bât 4020
> Commissariat à l'énergie atomique et aux énergies alternatives
> Email : [hidden email]<mailto:[hidden email]>
> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>
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