Re: Counting empty circles
Posted by
Albert Cardona-2 on
Jan 06, 2011; 4:06pm
URL: http://imagej.273.s1.nabble.com/Counting-empty-circles-tp3686043p3686047.html
2011/1/6 Scott Chamberlain <
[hidden email]>:
> Thanks very much for all of your comments regarding my question. I still have not found a method that works, but am still working on it.
>
> I agree that it is technically easiest to simply count the trichomes manually. However, counting manually takes a lot of time, which is equivalent to a lot of money to pay a student to do the counting. Unfortunately, as a graduate student working on research independent from their advisor, there isn't a lot of money to be had. Thus, finding a technological solution is superior as it saves money and is faster, once the solution is found.
>
> To your subsampling comment Anda, the leaf discs are already subsamples of whole leaves, so I don't want to do further subsampling which would reduce my confidence in our estimate of leaf trichome abundance/density.
>
> Thanks again, Scott
Scott,
Have a look at these two methods:
SIOX:
http://pacific.mpi-cbg.de/wiki/index.php/SIOX:_Simple_Interactive_Object_ExtractionTrainable Segmentation:
http://pacific.mpi-cbg.de/wiki/index.php/Trainable_Segmentation_PluginI gave it a go at the second and I managed to get a reasonable mask.
Then I dilated, closed holes, run watershed, and run analyze particles
to count them. The count was off by 1 too many.
Albert
--
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