Posted by
John Hayes-5 on
Oct 04, 2007; 5:02pm
URL: http://imagej.273.s1.nabble.com/ROI-selection-in-line-scan-pictures-tp3698271p3698274.html
On Oct 4, 2007, at 11:09 AM, Alexandre Santos wrote:
> Hello,
>
> I would like to analyze some confocal line scan pictures I acquired in
> two channels. Each channel (called z slice in imagej) is a picture of
> 512 pixels width and 50,000 pixels height
>
> I would like to be able to select a segment of the line scan, and
> obtain average intensity levels for each line of the scan, in both
> channels.
>
> At the moment I have two difficulties:
>
> 1 - I can't find a way to select a segment as a ROI. If I want to see
> the picture, I need to magnify it a lot, but then I can't draw a
> rectangle encompassing the whole picture.
You may be able to use the Edit|Selection|Specify... command to
define the ROI for the full length of your time-series. I'd highlight
the segment you are interested in and use the specify command to
extend the ROI.
>
> 2 - Once I have the desired rectangle, How do I get average intensity
> values for each line of the rectangle, and not for the whole
> rectangle? (I thought about using the Gel analysis tool, but I don't
> know if that would work)
I've modified the Example Plot plugin to incorporate this feature as
a plugin. You can access it here:
http://128.239.97.54/ImageJ_src/
XT_Plot.java
Save the file into your plugins directory. Then go to Plugins|Compile
and Run and select the file. This will plot the height of your ROI as
time (x-axis) and the average of each line is on the y-axis.
Best regards,
John
--
John A. Hayes, Ph.D.
Department of Applied Science
McGlothlin-Street Hall, Room 318
The College of William & Mary
Williamsburg, VA 23187-8795
Office: 757-221-7808
Fax: 757-221-2050