Image Analysis - How to measure density of roi in an array

We are trying to find the best way to measure change in channels of sponge tissue during a contraction.

The roi's can be found in fig. 2 D R1 - R4. http://jeb.biologists.org/content/210/21/3736.full.pdf+html

There is also a supplemental video showing the contraction. Movie 1 http://jeb.biologists.org/content/suppl/2007/10/12/210.21.3736.DC1/JEB003392-movie1.mov

I know how to select an roi for an array and return std2. Although there appears to be a trend it doesn't match what we see in the video.

Answer 1

[Image Analyst]

Why are you calculating std2? Wouldn't you want mean2? Also, what have you done to adjust the location of your ROI(s) because it looks like to me that they change location slightly as the contractions occur.

Answer 2

[Matthew]

1) I already calculated the mean of my grey scale image array. The resulting graph shows no clear trend/non-significant variation. I’m not clear on how mean2 command differs from mean?

I thought that std2 would be more sensitive to pixel changes over time as my understanding of how the measurement works is as follows: Std2 calculates how much each individual measurement (one frame in image array) deviates from the sample mean of the entire array.

If Std2 isn't appropriate what other types of analysis could measure the event?

2) I am unaware of how to set ROI(s) to track a specific area when it moves over time. On a side note: I think there is a webinar that shows how to do this (track the center line while driving in a car) but it's for analyzing a video file and not an image array.

Therefore I am not analyzing the first part of the video where alot of movement occurs. Instead I will make a script with stationary ROI(s) and only use the latter part of the video segment where the sponge is (relatively) stationary in the frame.

Thanks, -M