ROI selection in line scan pictures

[Alexandre Santos-4]

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.

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)

Cheers,

Alexandre Santos
Neuro-MPI, Martinsried, Germany

[Wayne Rasband]

Press "a" (Edit>Selection>Select All) to create a rectangular selection
encompassing the entire image. Press alt-k (Analyze>Plot Profile with
alt key down) to plot the average intensities of the lines. Click on
"List" in the plot window to display the intensity values. The Plot
Profile command plots column averages instead of row averages if you
don't hold the alt key down.

-wayne

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.
>
> 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)
>
> Cheers,
>
> Alexandre Santos
> Neuro-MPI, Martinsried, Germany
>

[John Hayes-5]

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: [phone]

[Harry Parker]

Hello Alexandre,
Check out the menu command, Edit->Selection->Specify. There you can define the region numerically. You can make the rectangle 1 line high to get a single scan line to average. You can use the arrow keys to move one row at a time. The Option key with the arrow keys lets you shrink or grow the size of the ROI.  You can write a simple macro to read your selection limits and loop through the lines, measuring each one.
 
--  
Harry Parker  
Senior Systems Engineer  
Digital Imaging Systems, Inc.

----- Original Message ----
From: Alexandre Santos <[hidden email]>
To: [hidden email]
Sent: Thursday, October 4, 2007 11:09:15 AM
Subject: ROI selection in line scan pictures

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.

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)

Cheers,

Alexandre Santos
Neuro-MPI, Martinsried, Germany





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[Alexandre Santos-4]

I would like to thank Wayne, John and Harry for their answers. I am
now able to properly analyze the data I acquired!

Cheers,
Alexandre Santos

Neuro-MPI, Martinsried, Germany

2007/10/5, Harry Parker <[hidden email]>:

> Hello Alexandre,
> Check out the menu command, Edit->Selection->Specify. There you can define the region numerically. You can make the rectangle 1 line high to get a single scan line to average. You can use the arrow keys to move one row at a time. The Option key with the arrow keys lets you shrink or grow the size of the ROI.  You can write a simple macro to read your selection limits and loop through the lines, measuring each one.
>
> --
> Harry Parker
> Senior Systems Engineer
> Digital Imaging Systems, Inc.
>
> ----- Original Message ----
> From: Alexandre Santos <[hidden email]>
> To: [hidden email]
> Sent: Thursday, October 4, 2007 11:09:15 AM
> Subject: ROI selection in line scan pictures
>
> 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.
>
> 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)
>
> Cheers,
>
> Alexandre Santos
> Neuro-MPI, Martinsried, Germany
>
>
>
>
>
>       ____________________________________________________________________________________
> Luggage? GPS? Comic books?
> Check out fitting gifts for grads at Yahoo! Search
> http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz
>