Re: Index of hexagonality? - SOLVED

Posted by Gabriel Landini on Mar 31, 2016; 7:13am
URL: http://imagej.273.s1.nabble.com/Index-of-hexagonality-SOLVED-tp5013442p5016035.html

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

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