Endothelial cell count and area measurement? Any ideas?

[Mr_Sonky]

Hi all,

I have an image here of some hexagonal cells. I'm trying to segment out and each individual cell in order to measure its area. The Analyze Particle plugin seems promising but it's not really working for me. Right now I'm manually segmenting and measuring the area. Anyone have any ideas how I can do this quickly?




Jeremiah

[gankaku]

Hi Jeremiah,

attatched you'll find a small macro which might do the job (which depends
on how your other images look like).
To run the macro you need additionally some functions from the BioVoxxel
Toolbox because it uses its lighting correction and another particle
analyzer.
I set the particle analyzer to exclude the cells on two edges only to
account for the fact that you are not depicting the "complete" sample and
thus correcting for potential counting errors (just if you wonder why the
cell on two image borders are missing).

You can either get the additional functions from the BioVoxxel update site
if you are using Fiji or download and install it from here:
http://www.biovoxxel.de/development/

Hope it helps.
Cheers,
Jan


//-----------macro start--------------------------
original = getTitle();
run("8-bit");
run("Pseudo flat field correction", "blurring=50");
close(original + "_background");
selectWindow(original);
run("Median...", "radius=2");
run("Subtract Background...", "rolling=10");
run("Enhance Contrast...", "saturated=0.0 normalize");
run("Auto Threshold", "method=Default white");
run("Analyze Particles...", "size=20-Infinity show=Masks");
run("Invert LUT");
run("Invert");
run("Watershed Irregular Features", "erosion=9");
run("Extended Particle Analyzer", "area=150-Infinity show=Outlines
redirect=None keep=Top-Left display clear summarize");
//-----------macro end--------------------------


2015-04-20 8:55 GMT+02:00 Mr_Sonky <[hidden email]>:

> Hi all,
>
> I have an image here of some hexagonal cells. I'm trying to segment out and
> each individual cell in order to measure its area. The Analyze Particle
> plugin seems promising but it's not really work for me. Right now I'm
> manually segmenting and measuring the area. Anyone have any ideas how I can
> do this quickly?
>
> <http://imagej.1557.x6.nabble.com/file/n5012526/test.png>
>
>
> Jeremiah
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Endothelial-cell-count-and-area-measurement-Any-ideas-tp5012526.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

CEO: Dr. rer. nat. Jan Brocher
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[Mr_Sonky]

Hi all,

I've tried Jan's code and it worked out perfectly for the attached image above. This was what I got:


Thank you so so much Jan! You're a lifesaver  !!