ROI manager measure 'current slice'

[Tony Collins-4]

Hi,

I could be going about this the wrong way, but...

The ROIs in the ROI manager store slice as well as x and y coordinate
information. If I draw the ROIs in slice 2 then the measurements are
made in slice 2 regardless of what the 'current' slice is.

I'd like to draw the ROIs in one slice but measure in the 'current'
slice. Can this be done?

Thanks,
Tony


Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca

[jmutterer]

Tony,
A measure is always done on the current slice. But selecting a ROI from the
ROI manager will display this ROI and change the current slice to the slice
the ROI was created on. Then you can change slices and the following
measures will always be done on the current slice.

In a macro, this means you should save the current slice number before
selecting a ROI from he ROI manager and then go back to the saved slice
number before you measure.

example :

currentSlice =  getSliceNumber();
roiManager ("select", 2);
setSlice (currentSlice);
run ("Measure");

Jerome


On 5/17/07, Tony Collins <[hidden email]> wrote:

>
> Hi,
>
> I could be going about this the wrong way, but...
>
> The ROIs in the ROI manager store slice as well as x and y coordinate
> information. If I draw the ROIs in slice 2 then the measurements are
> made in slice 2 regardless of what the 'current' slice is.
>
> I'd like to draw the ROIs in one slice but measure in the 'current'
> slice. Can this be done?
>
> Thanks,
> Tony
>
>
> Tony J. Collins, Ph.D.
> McMaster Biophotonics Facility
> Dept. Biochemistry and Biomedical Sciences HSC 4H21A
> McMaster University, Hamilton, ON, L8N 3Z5
> [phone] x28812(off.)/x26488(lab)
> [hidden email]     www.macbiophotonics.ca
>

[Wayne Rasband]

The ROI Manager in ImageJ 1.38s adds a More>>Remove Slice Info command
that removes the information in the ROI names that associates them with
particular slices. It also adds a More>>Specify command and it allows
the "Process Stack?" dialog to be avoided when measuring by holding
down the alt key.

-wayne

On May 17, 2007, at 1:55 PM, Tony Collins wrote:

> Hi,
>
> I could be going about this the wrong way, but...
>
> The ROIs in the ROI manager store slice as well as x and y coordinate
> information. If I draw the ROIs in slice 2 then the measurements are
> made in slice 2 regardless of what the 'current' slice is.
>
> I'd like to draw the ROIs in one slice but measure in the 'current'
> slice. Can this be done?
>
> Thanks,
> Tony
>
>
> Tony J. Collins, Ph.D.
> McMaster Biophotonics Facility
> Dept. Biochemistry and Biomedical Sciences HSC 4H21A
> McMaster University, Hamilton, ON, L8N 3Z5
> [phone] x28812(off.)/x26488(lab)
> [hidden email]     www.macbiophotonics.ca
>

[Tony Collins-4]

Ah. I was not selecting *any* ROIs which allows you to measure them
*all* at once. (This is easier than shift-clicking all 50 ROIs in the
list!). Before Wayne's fix, this did not measure the current slice.
Maybe the 'deselect' button could be configured to 'select all' if no
ROIs are currently highlighted selected?

Wayne's fix works very well for me though.

Thanks for clearing this up and the macro tip.

Regards,

Tony
 
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf
Of
> > jerome mutterer
> > Sent: May 17, 2007 2:42 PM
> > To: [hidden email]
> > Subject: Re: ROI manager measure 'current slice'
> >
> > Tony,
> > A measure is always done on the current slice. But selecting a ROI
from
> > the
> > ROI manager will display this ROI and change the current slice to
the
> > slice
> > the ROI was created on. Then you can change slices and the following
> > measures will always be done on the current slice.
> >
> > In a macro, this means you should save the current slice number
before
> > selecting a ROI from he ROI manager and then go back to the saved
slice

> > number before you measure.
> >
> > example :
> >
> > currentSlice =  getSliceNumber();
> > roiManager ("select", 2);
> > setSlice (currentSlice);
> > run ("Measure");
> >
> > Jerome
> >
> >
> > On 5/17/07, Tony Collins <[hidden email]> wrote:
> > >
> > > Hi,
> > >
> > > I could be going about this the wrong way, but...
> > >
> > > The ROIs in the ROI manager store slice as well as x and y

coordinate
> > > information. If I draw the ROIs in slice 2 then the measurements
are
> > > made in slice 2 regardless of what the 'current' slice is.
> > >
> > > I'd like to draw the ROIs in one slice but measure in the
'current'

> > > slice. Can this be done?
> > >
> > > Thanks,
> > > Tony
> > >
> > >
> > > Tony J. Collins, Ph.D.
> > > McMaster Biophotonics Facility
> > > Dept. Biochemistry and Biomedical Sciences HSC 4H21A
> > > McMaster University, Hamilton, ON, L8N 3Z5
> > > [phone] x28812(off.)/x26488(lab)
> > > [hidden email]     www.macbiophotonics.ca
> > >