Re: Arabidopsis auto segmentation

Posted by Ignacio Arganda-Carreras on
URL: http://imagej.273.s1.nabble.com/Arabidopsis-auto-segmentation-tp5001389p5001402.html

Hello Andrew,

You can try using Advanced Weka Segmentation to get better segmentation:
http://fiji.sc/wiki/index.php/Advanced_Weka_Segmentation

Let me know if you need help with it!

ignacio

On Sun, Jan 13, 2013 at 4:12 AM, Andrew Defries <[hidden email]>wrote:

> Dear ImageJ  users,
>
> I have a number of images similar to shown below:
>
> http://biocluster.ucr.edu/~adefries/Test.JPG
>
> I essentially want ROIs similar to the outline of the contrasted seedlings:
>
> http://biocluster.ucr.edu/~adefries/Test2.jpg
>
> I have had good success using auto local threshold and edge detection, but
> encounter problems when seedlings are twisted together. I would like to
> develop a method to outline each plant, if possible (with or without seed),
> and then outline the boundaries of each plant such as cotyledon (green
> part), stem (hypocotyl), and root.
>
> At present I have been collecting only two variables derived from polyline
> rois hand clicked through the hypocotyl and root, so any advice to improve
> my throughput would be greatly appreciated.
>
>
> Thank you,
>
> Andrew
>
>
> --
> ------------------------------------------------
> Andrew Defries
> Lab of Michael Pirrung
> University of California Riverside
> Botany and Plant Sciences
> 2150 Batchelor Hall
> Riverside, CA 92521
>
> (Phone)        951-827-6991
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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