Creating a new ROI out of a ROI boundary

[Rafael Ballester]

Hi all,

Given a ROI, I would like to obtain via ImageJ API another ROI consisting of
its boundary pixels.
I guess this may be done by dilating the original ROI's mask and then
substracting the original ROI's mask from it. But even if I do that, I can't
figure out a way to create then a new ROI from the resulting mask. Any idea
on this (or some different path to get a boundary ROI)?

Thanks,

Rafa

[Albert Cardona-2]

2011/11/7 Rafael Ballester <[hidden email]>:
> Hi all,
>
> Given a ROI, I would like to obtain via ImageJ API another ROI consisting of
> its boundary pixels.
> I guess this may be done by dilating the original ROI's mask and then
> substracting the original ROI's mask from it. But even if I do that, I can't
> figure out a way to create then a new ROI from the resulting mask. Any idea
> on this (or some different path to get a boundary ROI)?

Rafa,

you are mixing "mask" and "ROI". The latter, in ImageJ parlance, is a
vector graphics representation of the former.

Could you reformulate your question? I am not sure you are but trying
to paint a ROI onto a black image to obtain the contour as painted
pixels.

Albert

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

[ctrueden]

Hi Rafael,

Does Edit > Selection > Make Band do what you need?

Regards,
Curtis


On Mon, Nov 7, 2011 at 12:28 PM, Rafael Ballester <[hidden email]> wrote:

> Hi all,
>
> Given a ROI, I would like to obtain via ImageJ API another ROI consisting
> of
> its boundary pixels.
> I guess this may be done by dilating the original ROI's mask and then
> substracting the original ROI's mask from it. But even if I do that, I
> can't
> figure out a way to create then a new ROI from the resulting mask. Any idea
> on this (or some different path to get a boundary ROI)?
>
> Thanks,
>
> Rafa
>
>
> --
> View this message in context:
> http://imagej.588099.n2.nabble.com/Creating-a-new-ROI-out-of-a-ROI-boundary-tp6971550p6971550.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[Rafael Ballester]

> Could you reformulate your question?

Firstly I get my roi from the RoiManager:

...
Roi roi = table.get(label);

Now I get its outline:

BinaryProcessor bp = new BinaryProcessor((ByteProcessor)roi.getMask());
bp.invert();
bp.outline();

Now, my question is: how to create a new Roi, so that its mask is bp?


@Curtis: thanks, but I would like to do it with Java code, via ImageJ's API.

2011/11/7 Albert Cardona <[hidden email]>

> 2011/11/7 Rafael Ballester <[hidden email]>:
> > Hi all,
> >
> > Given a ROI, I would like to obtain via ImageJ API another ROI
> consisting of
> > its boundary pixels.
> > I guess this may be done by dilating the original ROI's mask and then
> > substracting the original ROI's mask from it. But even if I do that, I
> can't
> > figure out a way to create then a new ROI from the resulting mask. Any
> idea
> > on this (or some different path to get a boundary ROI)?
>
> Rafa,
>
> you are mixing "mask" and "ROI". The latter, in ImageJ parlance, is a
> vector graphics representation of the former.
>
> Could you reformulate your question? I am not sure you are but trying
> to paint a ROI onto a black image to obtain the contour as painted
> pixels.
>
> Albert
>
> --
> http://albert.rierol.net
> http://www.ini.uzh.ch/~acardona/
>

[Albert Cardona-2]

2011/11/7 Rafa Ballester <[hidden email]>:

>> Could you reformulate your question?
>
> Firstly I get my roi from the RoiManager:
>
> ...
> Roi roi = table.get(label);
>
> Now I get its outline:
>
> BinaryProcessor bp = new BinaryProcessor((ByteProcessor)roi.getMask());
> bp.invert();
> bp.outline();
>
> Now, my question is: how to create a new Roi, so that its mask is bp?

Use the ThresholdToSelection class:

bp.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection ts = new ThresholdToSelection();
Roi roi = ts.convert(bp);


Albert


--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

[Rafael Ballester]

Thanks, this method worked like a charm.

2011/11/8 Albert Cardona <[hidden email]>

> 2011/11/7 Rafa Ballester <[hidden email]>:
> >> Could you reformulate your question?
> >
> > Firstly I get my roi from the RoiManager:
> >
> > ...
> > Roi roi = table.get(label);
> >
> > Now I get its outline:
> >
> > BinaryProcessor bp = new BinaryProcessor((ByteProcessor)roi.getMask());
> > bp.invert();
> > bp.outline();
> >
> > Now, my question is: how to create a new Roi, so that its mask is bp?
>
>
> Use the ThresholdToSelection class:
>
> bp.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
> ThresholdToSelection ts = new ThresholdToSelection();
> Roi roi = ts.convert(bp);
>
>
> Albert
>
>
> --
> http://albert.rierol.net
> http://www.ini.uzh.ch/~acardona/
>