Posted by
Jeremy Adler on
URL: http://imagej.273.s1.nabble.com/Index-of-hexagonality-SOLVED-tp5013442p5013445.html
It amounts to counting the number of neighbors each cell has.
for the images you provide it looks fairly simple to identify the cell outlines -
edit and threshold this to produce a binary image showing the outlines
thin to an 8 connected single line - (process binary skeletonize - set binary options to skeletonize with a dark background) should do it
identify the nodes, where three cells meet (process binary option erode count 6 black background), can be easily identified from the number of connections between pixels on the thinned binarized image - at each node there will be a pixel with 3 or 4 neighbors. After the erosion each node will be a single pixel or group of pixels
You now need the number of nodes per cell - threshold the binarized image to show the cells rather than the membrane, use (analyze particles) to produce a ROI for each cell - (exclude cells in the edge) by selecting the option to add each ROI to the ROI maanager
Run through all the ROIs in the ROI manager and use the ROI for each cell (analyze particles) (again) to count the number of nodes - to do this either swell the ROI (edit selection enlarge) by a few pixels so that the nodes fall within the ROI, or swell (process binary dilate) the image of the nodes so that they overlap the ROI of the cells.
________________________________________
From: ImageJ Interest Group [
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[hidden email]]
Sent: 07 July 2015 00:14
To:
[hidden email]
Subject: Index of hexagonality?
Hi all,
I'm looking at some endothelial cells which are meant to be hexagonal and
tightly packed in nature. With stress and/or trauma, these cells exhbit
polymorphism - they turn into polygons of varying types. My aim is to
determine how many cells have lost their hexagon shapes in order to infere
the severity of the insult. I've attached two samples. The first is simply
the cellls. The second has a yellow box to highlight a Hexagon whilst the
red box highlights a cell that has undergone transformation into a a
different polygon (pentagon - in this instance).
<
http://imagej.1557.x6.nabble.com/file/n5013442/Endothelial_Cell.jpg>
<
http://imagej.1557.x6.nabble.com/file/n5013442/Endothelial_Cell_example.jpg>
Any help is appreciated!
NB I have looked at Gary Chinga's shape descriptor plugin and its not what
I'm looking for =)
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