Posted by
schamber789 on
Jan 06, 2011; 5:26pm
URL: http://imagej.273.s1.nabble.com/Counting-empty-circles-tp3686043p3686048.html
Hi Albert, Thanks very much!
I tried that second method, Trainable Segmentation, in Fiji, but I could not get good results as you did. I assumed by second, you mean the second URL? Can you send an image of what objects you delineated to train the program?
Best regards,
Scott Chamberlain
On Jan 6, 2011, at 10:06 AM, Albert Cardona wrote:
> 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_Extraction>
> Trainable Segmentation:
>
http://pacific.mpi-cbg.de/wiki/index.php/Trainable_Segmentation_Plugin>
> I 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
>
> --
>
http://albert.rierol.net