Hi all,
I need to build a 2D map of the contraction (=reduction of transversal
diameter) of a segment of intestine recorded as wmv:
- Contraction must be visualized as color code
- the horizontal lines of the map must represent the length of the intestine
(each pixel a pixel of the horizontal axis of intestine representing in
color the value of the diameter at that place of the image)
- the vertical direction of the image is formed simply adding consecutive
lines corresponding to consecutive frames (reports how the diamter changes
in every pixel=location along time)
By now I can transform from wmv to AVI. I import AVI as a virtual stack, I
threshold it so that the I get a binary stack. I can get a plot profile of
each frame using a rectangle surrounding the gut. However I need to do it
for hundreds of images.
My questions are:
- would be possible to automatize plot profile for each slice in the stack?
Note that I need to add values of each plot in columns in the results window.
- would be possible to create with imagej the 2D map from that numbers?
I have tried to reslice the stack, but it is not useful: it gives a
black/white image (using a line along the intestine) or a black/white stack
(if I use a rectangle selection or a wide line), in both cases with no
apparent information regarding the diameter of the gut.
I have used a plugin from Bart Blanckaert
(
http://www.heymans.ugent.be/En/DownloadsEn.htm) from Gent University,
Netherlands), but it involves gnuplot and I would prefer a simpler method.
Any idea would be helpful
Thanks in advance
Pedro
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