Advice segmenting a short video

Posted by Pedro J CamelloDr Pedro J Camello on Feb 26, 2014; 12:38pm
URL: http://imagej.273.s1.nabble.com/Advice-segmenting-a-short-video-tp5006685.html

Hi all,

I need to segment/threshold  a grey video containing a small segment of intestine which develops continuous contractions. The are to be segmented (the intestine) is dark, in a clear background.

Here I have two examples:
https://drive.google.com/file/d/0By5p1UZJKft_c0tCUnNMRkYtMk0/edit?usp=sharing
https://drive.google.com/file/d/0By5p1UZJKft_M0VTV0V1YUd0emM/edit?usp=sharing

My problem is that, when the intestine dilates, its pixel values approaches the value of the backgorund pixels. Therefore this forces me to make a manual thresholding inspecting all the stack to be sure that the threshold limit marks the intestine in all the frames. Though I can do this successfully, it is time consuming (I have to do in hundreds of videos) and what´s worse it introduces subjetive decissions I want to avoid.


Has anybody experience using an automated threshold method for videos or for series of images? The trainable Weka segmentation is too slow, and since the illumination conditions changed from video to video, I should change the training every few videos.

I was thinking of some automated method of segmentation not based on threshold, such as snakes, but I have no experience with it.



Thanks in advance

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