Crop image sequence within a circle

[yuanchen]

Dear friends

When using imageJ to crop a 3D reconstructed images(stacks), basically you
select a ROI and then go crop it and save all the sequences.

Now, my cortical bone sample scanned is just a cylinder with 3 mm in
diameter and 12 in length. To get rid of the cupping effect , I would just
like to crop a sub-cylinder of the original reconstructions. It seems in
imageJ whenever you choose a ROI like a circle and crop it , you acually
get images of circumscribed rectangle of the circle you drew, rather than
the sub-circle of the images and fill the other part of the images with say
black background.

Is there any way to do it ?

Much appreciated !

Yuan Chen

University of Sheffield

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[Gabriel Landini]

On Wednesday 04 Sep 2013 21:23:31 Yuan Chen wrote:
> imageJ whenever you choose a ROI like a circle and crop it , you acually
> get images of circumscribed rectangle of the circle you drew, rather than
> the sub-circle of the images and fill the other part of the images with say
> black background.
>
> Is there any way to do it ?

Edit>Clear_outside command?

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[Christine Labno-2]

On Wednesday, September 04, 2013 4:03 PM Gabriel Landini wrote:

>>On Wednesday 04 Sep 2013 21:23:31 Yuan Chen wrote:
>> imageJ whenever you choose a ROI like a circle and crop it , you acually
>> get images of circumscribed rectangle of the circle you drew, rather than
>> the sub-circle of the images and fill the other part of the images with say
>> black background.
>>
>> Is there any way to do it ?

> Edit>Clear_outside command?

Yes, but first make sure in Edit -> Options -> Colors your background is set to black.  I think this is default, but better safe than sorry.

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[yuanchen]

thanks very much Gabriel!

Best

Yuan


On 4 September 2013 22:03, Gabriel Landini <[hidden email]> wrote:

> On Wednesday 04 Sep 2013 21:23:31 Yuan Chen wrote:
> > imageJ whenever you choose a ROI like a circle and crop it , you acually
> > get images of circumscribed rectangle of the circle you drew, rather than
> > the sub-circle of the images and fill the other part of the images with
> say
> > black background.
> >
> > Is there any way to do it ?
>
> Edit>Clear_outside command?
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[yuanchen]

Yes, this is it.  I solved this , thank you Christine!

Best

Yuan


On 4 September 2013 22:11, Christine Labno <[hidden email]> wrote:

>
>
> On Wednesday, September 04, 2013 4:03 PM Gabriel Landini wrote:
>
> >>On Wednesday 04 Sep 2013 21:23:31 Yuan Chen wrote:
> >> imageJ whenever you choose a ROI like a circle and crop it , you acually
> >> get images of circumscribed rectangle of the circle you drew, rather
> than
> >> the sub-circle of the images and fill the other part of the images with
> say
> >> black background.
> >>
> >> Is there any way to do it ?
>
> > Edit>Clear_outside command?
>
> Yes, but first make sure in Edit -> Options -> Colors your background is
> set to black.  I think this is default, but better safe than sorry.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[Antoinette]

When we are cropping image, we are supposed to select a ROI and then go crop it and save all the sequences. After cropping an area, we can conduct some basic editing applications toward cropped image. For example, we can adjust the size of created cropped image file, add antique effect to cropped image and rotate the orientation of cropped image.