Separate ROI in each stack slice

[Madhoosudan]

Hellow,
I want to define separate ROI for each individual slice in the imported
image stack of around 31 images. I could do it once but again I am not sure
I am not able to select the separate ROI for each image. Whenever I draw
ROI for one image it by default gets applied to all the images and clicking
on any image outside the ROI will remove ROI from all images. Could anyone
help me in this regards.

Thanks.


​
​Regards,


​Madhoosudan Patil,
Post Doctoral Fellow,
​Skaggs School of Pharmacy,​

​Anschutz Medical Campus,​
​University of Colorado, Denver, USA.
​Ph.: 001 [phone]
E-Mail: [hidden email]

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[ctrueden]

Hi Madhoosudan,

To work with multiple ROIs, including slice-specific ROIs, use the ROI
Manager. Press the T key to add your current selection. Then draw
additional selections, pressing T each time.

See:
* https://imagej.net/docs/guide/146-30.html#sub:ROI-Manager...
* http://imagej.github.io/presentations/fiji-segmentation/#/
* http://imagej.net/Segmentation

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Aug 17, 2016 at 11:53 AM, madhoosudan patil <
[hidden email]> wrote:

> Hellow,
> I want to define separate ROI for each individual slice in the imported
> image stack of around 31 images. I could do it once but again I am not sure
> I am not able to select the separate ROI for each image. Whenever I draw
> ROI for one image it by default gets applied to all the images and clicking
> on any image outside the ROI will remove ROI from all images. Could anyone
> help me in this regards.
>
> Thanks.
>
>
> ​
> ​Regards,
>
>
> ​Madhoosudan Patil,
> Post Doctoral Fellow,
> ​Skaggs School of Pharmacy,​
>
> ​Anschutz Medical Campus,​
> ​University of Colorado, Denver, USA.
> ​Ph.: 001 [phone]
> E-Mail: [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Madhoosudan]

Hi Thank you Curtis for the reply. Now with the use of ROI manager I can
select different ROI in different slices of the stack. However, Once I
could do it without even going to ROI and pressing t every time. Is there
any global setting for this.

​
​Regards,


​Madhoosudan Patil,
Post Doctoral Fellow,
​Skaggs School of Pharmacy,​

​Anschutz Medical Campus,​
​University of Colorado, Denver, USA.
​Ph.: 001 [phone]
E-Mail: [hidden email]

On 17 August 2016 at 11:48, Curtis Rueden <[hidden email]> wrote:

> Hi Madhoosudan,
>
> To work with multiple ROIs, including slice-specific ROIs, use the ROI
> Manager. Press the T key to add your current selection. Then draw
> additional selections, pressing T each time.
>
> See:
> * https://imagej.net/docs/guide/146-30.html#sub:ROI-Manager...
> * http://imagej.github.io/presentations/fiji-segmentation/#/
> * http://imagej.net/Segmentation
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Aug 17, 2016 at 11:53 AM, madhoosudan patil <
> [hidden email]> wrote:
>
> > Hellow,
> > I want to define separate ROI for each individual slice in the imported
> > image stack of around 31 images. I could do it once but again I am not
> sure
> > I am not able to select the separate ROI for each image. Whenever I draw
> > ROI for one image it by default gets applied to all the images and
> clicking
> > on any image outside the ROI will remove ROI from all images. Could
> anyone
> > help me in this regards.
> >
> > Thanks.
> >
> >
> > ​
> > ​Regards,
> >
> >
> > ​Madhoosudan Patil,
> > Post Doctoral Fellow,
> > ​Skaggs School of Pharmacy,​
> >
> > ​Anschutz Medical Campus,​
> > ​University of Colorado, Denver, USA.
> > ​Ph.: 001 [phone]
> > E-Mail: [hidden email]
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Madhoosudan,

> However, Once I could do it without even going to ROI and pressing t
> every time. Is there any global setting for this.

Not to my knowledge. I do not believe ImageJ ever worked this way in the
past.

The only exception I can think of is the multipoint tool: if you
right-click the point tool and change it to multipoint, you can create any
number of points within a single selection, each of which resides on a
dedicated slice.

https://imagej.net/docs/guide/146-19.html#sec:Multi-point-Tool

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Fri, Aug 19, 2016 at 10:18 AM, madhoosudan patil <
[hidden email]> wrote:

> Hi Thank you Curtis for the reply. Now with the use of ROI manager I can
> select different ROI in different slices of the stack. However, Once I
> could do it without even going to ROI and pressing t every time. Is there
> any global setting for this.
>
> ​
> ​Regards,
>
>
> ​Madhoosudan Patil,
> Post Doctoral Fellow,
> ​Skaggs School of Pharmacy,​
>
> ​Anschutz Medical Campus,​
> ​University of Colorado, Denver, USA.
> ​Ph.: 001 [phone]
> E-Mail: [hidden email]
>
> On 17 August 2016 at 11:48, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Madhoosudan,
> >
> > To work with multiple ROIs, including slice-specific ROIs, use the ROI
> > Manager. Press the T key to add your current selection. Then draw
> > additional selections, pressing T each time.
> >
> > See:
> > * https://imagej.net/docs/guide/146-30.html#sub:ROI-Manager...
> > * http://imagej.github.io/presentations/fiji-segmentation/#/
> > * http://imagej.net/Segmentation
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - http://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Wed, Aug 17, 2016 at 11:53 AM, madhoosudan patil <
> > [hidden email]> wrote:
> >
> > > Hellow,
> > > I want to define separate ROI for each individual slice in the imported
> > > image stack of around 31 images. I could do it once but again I am not
> > sure
> > > I am not able to select the separate ROI for each image. Whenever I
> draw
> > > ROI for one image it by default gets applied to all the images and
> > clicking
> > > on any image outside the ROI will remove ROI from all images. Could
> > anyone
> > > help me in this regards.
> > >
> > > Thanks.
> > >
> > >
> > > ​
> > > ​Regards,
> > >
> > >
> > > ​Madhoosudan Patil,
> > > Post Doctoral Fellow,
> > > ​Skaggs School of Pharmacy,​
> > >
> > > ​Anschutz Medical Campus,​
> > > ​University of Colorado, Denver, USA.
> > > ​Ph.: 001 [phone]
> > > E-Mail: [hidden email]
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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