Measure multi ROI in a stack

[Kathryn Spencer]

Hello all;
        I am very new to ImageJ, and this is a very simple issue. So
simple, that I can't figure it out...
        I have a stack of images, showing cells that increase in
brightness over time. The cells do not move. I want to put one region
over each cell (about 100), then plot each cell's fluorescence intensity
over the stack. I can do this for one cell, but not for multiple cells.
        Is there a pre-made plugin for this? One was not immediately
obvious to me.
        Thank you for your patience.
        Kathy



Kathryn Spencer, Ph.D.
The Scripps Research Institute
ICND 210
10550 N. Torrey Pines Road
La Jolla, CA  92037
[phone]
[hidden email]

[Robert Dougherty]

Kathy,
One approach is to use Analyze/Tools/ROI Manager....  See .More»/Multi Measure at the bottom of the ROI Manager panel.  There is also Multi Measure plugin on my site (optinav.com) that has slightly different capabilities.  If the cells are arranged in a regular pattern (do cells do that?), you might be able to use microarry profile, also on my site.
Bob
Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
[hidden email]
[phone]
http://www.optinav.com

-----Original Message-----
From: "Kathryn Spencer" <[hidden email]>
Date:         Thu, 24 Jan 2008 13:17:04
To:[hidden email]
Subject: Measure multi ROI in a stack

Hello all;
        I am very new to ImageJ, and this is a very simple issue. So
simple, that I can't figure it out...
        I have a stack of images, showing cells that increase in
brightness over time. The cells do not move. I want to put one region
over each cell (about 100), then plot each cell's fluorescence intensity
over the stack. I can do this for one cell, but not for multiple cells.
        Is there a pre-made plugin for this? One was not immediately
obvious to me.
        Thank you for your patience.
        Kathy



Kathryn Spencer, Ph.D.
The Scripps Research Institute
ICND 210
10550 N. Torrey Pines Road
La Jolla, CA  92037
[phone]
[hidden email]

[John Bradley]

Kathy,

I do exactly what I believe you are considering. I measure the average
intensity of many cells (neurons) over time in a stack of images. As Bob
suggested do the following:

- open ROI Manager
- you'll probably use the ellipitcal ROI so click on that on the main menu
of imageJ and select your first cell
- press 't' (or click "Add" on the ROI Manager)
- then, and this is important, click Show All on the ROI Manager
- if you want the same size ROI on all cells its best to move the pointer to
the centre of your first ROI and drag to a new cell - again press 't'.
repeat until all cells selected. do not forget to press 't' after each cell
- in doing this you will see a list of all ROIs appear in the ROI Manager
- to save all of your ROIs click "Save" in the ROI Manager - be sure not to
select any of the ROIs in the list because only those selected will be
saved. If no ROIs are selected in the list then ALL will be saved in a zip
file.
- I use Time series Analyzer to calculate all average intensities in the
image stack
http://rsb.info.nih.gov/ij/plugins/time-series.html

hope this helps.

On Jan 23, 2008 8:00 PM, Robert Dougherty <[hidden email]> wrote:

> Kathy,
> One approach is to use Analyze/Tools/ROI Manager....  See .More»/Multi
> Measure at the bottom of the ROI Manager panel.  There is also Multi Measure
> plugin on my site (optinav.com) that has slightly different capabilities.
>  If the cells are arranged in a regular pattern (do cells do that?), you
> might be able to use microarry profile, also on my site.
> Bob
> Robert P. Dougherty, Ph.D.
> President, OptiNav, Inc.
> [hidden email]
> [phone]
> http://www.optinav.com
>
> -----Original Message-----
> From: "Kathryn Spencer" <[hidden email]>
> Date:         Thu, 24 Jan 2008 13:17:04
> To:[hidden email]
> Subject: Measure multi ROI in a stack
>
> Hello all;
>        I am very new to ImageJ, and this is a very simple issue. So
> simple, that I can't figure it out...
>        I have a stack of images, showing cells that increase in
> brightness over time. The cells do not move. I want to put one region
> over each cell (about 100), then plot each cell's fluorescence intensity
> over the stack. I can do this for one cell, but not for multiple cells.
>        Is there a pre-made plugin for this? One was not immediately
> obvious to me.
>        Thank you for your patience.
>        Kathy
>
>
>
> Kathryn Spencer, Ph.D.
> The Scripps Research Institute
> ICND 210
> 10550 N. Torrey Pines Road
> La Jolla, CA  92037
> [phone]
> [hidden email]
>

[lupitases]

Hi Robert,

I am using the "Multi Measure" plugin from the "Roi Manager" menu, and I would like to know how does it differentiate from the "Time series Analyzer" to calculate average intensities along the image stack.
I have used both, and the numbers I get for the same Rois are quite different. Do you know what are the differences between them and which one would be more suitable to analyse 2-photon GCaMP6 signals?

Thank you in advance.

Guadalupe.