ROI Manager and Time Series

[Declan James]

Could I get some help on the following problem;

I am using the Time-series plugin to obtain intensity readings
from 'selected' ROI as they change over an entire stack. I have a larger
number of ROIs (over 1000) and the time-series plugin requires that I
select all of them within ROI manager (ROI manager does not have a select
All function anymore).  

Is there a way to select all ROIs in ROI manager as the Time Series V4_2H
plug-in requires selected ROIs before measurements can be made?  

or

Can ROI manager measure intensity changes for an ROI over an entire stack?
(ie this is the same as getting a Z-profile for each ROI- in my case over
1000 ROIs)

Maybe all of this can be done by an easier more streamlined method I
welcome any help or suggestions on this.


Thank you

Declan

[Jacqueline Ross]

Hi Declan,

I think you will find that if you don't select any ROIs in ROI Manager,
all of them are automatically selected, i.e. the default is that all are
automatically measured.

If you want to see all the ROIs, then you can click on "Show All".

You can also highlight individual ROIs as before if you just want to
measure particular ones.

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.health.auckland.ac.nz/biru/ 
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Declan James
Sent: 11 March 2007 15:45
To: [hidden email]
Subject: ROI Manager and Time Series

Could I get some help on the following problem;

I am using the Time-series plugin to obtain intensity readings
from 'selected' ROI as they change over an entire stack. I have a larger

number of ROIs (over 1000) and the time-series plugin requires that I
select all of them within ROI manager (ROI manager does not have a
select
All function anymore).  

Is there a way to select all ROIs in ROI manager as the Time Series
V4_2H
plug-in requires selected ROIs before measurements can be made?  

or

Can ROI manager measure intensity changes for an ROI over an entire
stack?
(ie this is the same as getting a Z-profile for each ROI- in my case
over
1000 ROIs)

Maybe all of this can be done by an easier more streamlined method I
welcome any help or suggestions on this.


Thank you

Declan

[Wayne Rasband]

The "Measure" button in the ROI Manager measures all the ROIs on all
the images in a stack as long as none of the ROIs are selected, and
none are associated with a particular slice (all have names like
"xxxx-yyyy") or all are associated with the first slice (all have names
like "0001-xxxx-yyyy"). If this is not the case,  use the More>>"Multi
Measure" function, added in ImageJ 1.38m. "Multi Measure", based on a
similar function in Bob Dougherty's Multi_Measure plugin, measures all
the ROIs on all the images, creating a results table with either one
row per image or one row per measurement.

-wayne

> Could I get some help on the following problem;
>
> I am using the Time-series plugin to obtain intensity readings
> from 'selected' ROI as they change over an entire stack. I have a
> larger
> number of ROIs (over 1000) and the time-series plugin requires that I
> select all of them within ROI manager (ROI manager does not have a
> select
> All function anymore).
>
> Is there a way to select all ROIs in ROI manager as the Time Series
> V4_2H
> plug-in requires selected ROIs before measurements can be made?
>
> or
>
> Can ROI manager measure intensity changes for an ROI over an entire
> stack?
> (ie this is the same as getting a Z-profile for each ROI- in my case
> over
> 1000 ROIs)
>
> Maybe all of this can be done by an easier more streamlined method I
> welcome any help or suggestions on this.
>
>
> Thank you
>
> Declan
>