ROI Manager Output

[Serapio M. Baca]

I would like to do the following and I am not sure what is the best  
way to go about it:

1. Run through an image stack with the ROI manager and outline every  
cell of interest.
2. Obtain a matrix of intensity per frame per ROI of all of the cells.
3. Save in a format that is readable by MATLAB or Determine how to  
graphically offset the Intensity-Over-Time plots to get a sense of  
the activity of the different cells over time.

Right now, I do (1) and then I have to reclick onto each ROI, do the  
intensity-over-time plot and then save the values and copy and paste  
to excel. Not that much of a hassle for a few cells, but in my field  
I can have as many as 100, which makes this hacked approach too slow.

Any advice, clever tricks, or pointers to preexisting solutions would  
be greatly appreciated.

Best Regards,

Serapio
__
Serapio M. Baca, PhD
Postdoctoral Fellow
UCLA Neurobiology
Feldman Lab
[hidden email]

[John Bradley]

Serapio,

I think I've been doing something similar:

I use the "Time Series Analyzer" plugin written by Balaji

http://rsb.info.nih.gov/ij/plugins/time-series.html

my method:
1) open stack of interest
2) open ROI manger and add all appropriate ROIs (quickest way is to use 't'
keystroke to add each one); make sure to select "Show All" in ROI manager so
you can see where you have placed ROIs
3) if you do indeed have many ROIs its probably best to save them all - to
do this - hit DESELECT and then SAVE. The default when nothing is selected
in the list is to save all.
4)  then run the time series analyser by pressing GetAverage
5) the output is placed in the Results table - you can then save this as a
delimited text file (Matlab should be able to import this)
6) be aware that the first column in the table is the AVERAGE of all ROIs

good luck, John










On 8/8/07, Serapio M. Baca <[hidden email]> wrote:

>
> I would like to do the following and I am not sure what is the best
> way to go about it:
>
> 1. Run through an image stack with the ROI manager and outline every
> cell of interest.
> 2. Obtain a matrix of intensity per frame per ROI of all of the cells.
> 3. Save in a format that is readable by MATLAB or Determine how to
> graphically offset the Intensity-Over-Time plots to get a sense of
> the activity of the different cells over time.
>
> Right now, I do (1) and then I have to reclick onto each ROI, do the
> intensity-over-time plot and then save the values and copy and paste
> to excel. Not that much of a hassle for a few cells, but in my field
> I can have as many as 100, which makes this hacked approach too slow.
>
> Any advice, clever tricks, or pointers to preexisting solutions would
> be greatly appreciated.
>
> Best Regards,
>
> Serapio
> __
> Serapio M. Baca, PhD
> Postdoctoral Fellow
> UCLA Neurobiology
> Feldman Lab
> [hidden email]
>