Posted by
Anderson, Charles (DNR) on
Feb 28, 2014; 6:02pm
URL: http://imagej.273.s1.nabble.com/Advice-segmenting-a-short-video-tp5006685p5006723.html
Pedro,
There is something very strange about your images (ignoring that the checkerboard look of the image does not correspond to pixels in the image). One can move the crosshair slowly over the image and see the grey level change irregularly in ways that do not match the visual image. Auto threshold and find edges do not find the patterns that look obvious in the images.
But if I change Image | type | 16-bit, then everything seems to behave sensibly. It appears to work sensibly if changed back to 8-bit as well.
Try converting to 16-bit. Maybe someone else can provide an explanation. [My FIJI is not updating without an error message today, so I hope this is not just a failure of my system.]
Charles
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Pedro J Camello
Sent: Wednesday, February 26, 2014 6:38 AM
To:
[hidden email]
Subject: Advice segmenting a short video
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=sharinghttps://drive.google.com/file/d/0By5p1UZJKft_M0VTV0V1YUd0emM/edit?usp=sharingMy 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
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html