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Re: Index of hexagonality? - SOLVED

Posted by gankaku on Mar 31, 2016; 1:11pm
URL: http://imagej.273.s1.nabble.com/Index-of-hexagonality-SOLVED-tp5013442p5016036.html

On top of Gabriel's suggestion which you can easily achieve running the
"EDM Binary Operations" from the toolbox wit a iteration number of around
4-5 you may need to run the "Neighbor Analysis" with the setting "particle
neighborhood" instead of "voronoi". Voronoi would mostly ignore the rounded
corners but if you use the particle neighborhood with a pixel size of 2
then it should work.

regards,
Jan

2016-03-31 9:16 GMT+02:00 Gabriel Landini <[hidden email]>:

> On Wednesday 30 Mar 2016 16:17:13 you wrote:
> > Hi Jan,
> >
> > Thanks very much for getting back to me. I noticed that the unites of
> length
> > for my images were in micron, and when I changed it to pixel I was able
> to
> > get the proper results.
> >
> > I'm hoping if you could help me figure out another technical issue with
> the
> > macro. I have some cells that have vertexes with 4 or more edges (see
> > attached images) and irregular shape, which is part of the phenotype I'm
> > trying to analyze. I feel like the macro is having difficulties picking
> > <http://imagej.1557.x6.nabble.com/file/n5016032/raw.jpg>
> > <http://imagej.1557.x6.nabble.com/file/n5016032/mask.jpg>
> > <http://imagej.1557.x6.nabble.com/file/n5016032/color_code_pattern.jpg>
> up
> > those vertexes and gives me somewhat arbitrary results. For my control
> > samples most cells are hexagon so there is no problem.
> >
> > In the images the circle marks the vertex, and the arrow points to a cell
> > that I think has 4 neighbors...Let me know what you think.
>
> In that version of the discrete space tessellation, the cell has indeed
> more
> than 4 neigbours.
> You could run a closing (a minimum filter of radius size (let's say) 5,
> followed by a maximum filter of the same size). That should round the
> corners
> of the tiles and leave the larger boundaries (see attached, unfortunately
> that
> has some extra pixels due to the grey circle and arrow in the original).
> The
> larger the radius of the opening, the more it will round the corners.
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



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