Contour interpolation is added to Segment Editor

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Contour interpolation is added to Segment Editor

Andras Lasso-2
Hi all,

I have good news. I gave a try to Dzenan et al's contour interpolation filter and it worked very well! Thank you for implementing this great algorithm.

I've added this contour interpolator to the Segment Editor, available in Smoothing effect / Interpolation mode (in tomorrow's nightly build). See a short demo here:
https://youtu.be/VDlYmmaGxEI

Integration of this filter to the Segment Editor took less than an hour! Of course, we could tune this further (allow interpolating multiple segments at once, make the feature easier to find, etc) - any feedback is welcome.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: October 4, 2016 10:49
To: Dzenan Zukic <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Paul Yushkevich <[hidden email]>; Davide Punzo <[hidden email]>; SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-users] [slicer-devel] New "scissors" effect in Segment Editor for 3D clipping

Dzenan, thanks for mentioning this development!

For completeness and reference, this article contains more details about implementation and its evaluation:
http://insight-journal.org/browse/publication/977

On Tue, Oct 4, 2016 at 10:28 AM, Dzenan Zukic <[hidden email]> wrote:

> Good job Andras!
>
> Murat: slice interpolation is available in ITK as a remote module and
> has been integrated in ITK-SNAP 3.6.0-beta. Integration in this beta
> is a bit clumsy, preventing proper interpolation of all labels.
>
> Regards
>
> Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Tue, Oct 4, 2016 at 12:39 AM, Murat Maga <[hidden email]> wrote:
>>
>> Awesome! Thank you very much!
>>
>>
>>
>> Now please consider adding an interpolated slice by slice
>> segmentation feature.
>>
>>
>>
>>
>>
>> From: slicer-users [mailto:[hidden email]] On
>> Behalf Of Andras Lasso
>> Sent: Monday, October 03, 2016 8:47 PM
>> To: SPL Slicer Users <[hidden email]>; SPL Slicer Devel
>> <[hidden email]>
>> Cc: Davide Punzo <[hidden email]>
>> Subject: [slicer-users] New "scissors" effect in Segment Editor for
>> 3D clipping
>>
>>
>>
>> Hi all,
>>
>>
>>
>> We've just added the long-awaited "scissors" effect in Segment Editor
>> module. The effect allows outlining a region in a viewer and clear or
>> fill it. It can be used for removing unwanted objects, cropping to a
>> region of interest, or splitting a segment into two separate parts.
>> The effect is available in tomorrow's nightly release.
>>
>>
>>
>> Short demo: https://youtu.be/m4zTj8i4tCA
>>
>>
>>
>> Features:
>>
>> .         Outline can be drawn in any 3D or a slice viewer, using
>> free-form curve, circle, or rectangle shape.
>>
>> .         The selected region can be filled, cleared, or assigned to a
>> different segment.
>>
>> .         Standard masking options are supported - for example, filling
>> can be constrained by image intensity range or restricted to a
>> selected segment.
>>
>>
>>
>> Thanks to Davide Punzo for developing the astro cloud segmenter
>> effect, which inspired this new scissors effect (see his demo at
>> https://youtu.be/v6x3uPuLxzM).
>>
>>
>>
>> Andras
>>
>>
>>
>>
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to [hidden email]
>> with unsubscribe as the subject
>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Devel
> opers/FAQ
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Re: Contour interpolation is added to Segment Editor

Murat Maga
Andras,
Do you want to go through the rest of my shopping list for Slicer?

This looks awesome. I will download and try tomorrow. So when are you guys planning to move to 4.6 (or 5.0)?



-----Original Message-----
From: Andras Lasso [mailto:[hidden email]]
Sent: Tuesday, October 04, 2016 1:22 PM
To: Andrey Fedorov <[hidden email]>; Dzenan Zukic <[hidden email]>; Murat Maga <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Paul Yushkevich <[hidden email]>; Davide Punzo <[hidden email]>; SPL Slicer Devel <[hidden email]>
Subject: Contour interpolation is added to Segment Editor

Hi all,

I have good news. I gave a try to Dzenan et al's contour interpolation filter and it worked very well! Thank you for implementing this great algorithm.

I've added this contour interpolator to the Segment Editor, available in Smoothing effect / Interpolation mode (in tomorrow's nightly build). See a short demo here:
https://youtu.be/VDlYmmaGxEI

Integration of this filter to the Segment Editor took less than an hour! Of course, we could tune this further (allow interpolating multiple segments at once, make the feature easier to find, etc) - any feedback is welcome.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: October 4, 2016 10:49
To: Dzenan Zukic <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Paul Yushkevich <[hidden email]>; Davide Punzo <[hidden email]>; SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-users] [slicer-devel] New "scissors" effect in Segment Editor for 3D clipping

Dzenan, thanks for mentioning this development!

For completeness and reference, this article contains more details about implementation and its evaluation:
http://insight-journal.org/browse/publication/977

On Tue, Oct 4, 2016 at 10:28 AM, Dzenan Zukic <[hidden email]> wrote:

> Good job Andras!
>
> Murat: slice interpolation is available in ITK as a remote module and
> has been integrated in ITK-SNAP 3.6.0-beta. Integration in this beta
> is a bit clumsy, preventing proper interpolation of all labels.
>
> Regards
>
> Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Tue, Oct 4, 2016 at 12:39 AM, Murat Maga <[hidden email]> wrote:
>>
>> Awesome! Thank you very much!
>>
>>
>>
>> Now please consider adding an interpolated slice by slice
>> segmentation feature.
>>
>>
>>
>>
>>
>> From: slicer-users [mailto:[hidden email]] On
>> Behalf Of Andras Lasso
>> Sent: Monday, October 03, 2016 8:47 PM
>> To: SPL Slicer Users <[hidden email]>; SPL Slicer Devel
>> <[hidden email]>
>> Cc: Davide Punzo <[hidden email]>
>> Subject: [slicer-users] New "scissors" effect in Segment Editor for
>> 3D clipping
>>
>>
>>
>> Hi all,
>>
>>
>>
>> We've just added the long-awaited "scissors" effect in Segment Editor
>> module. The effect allows outlining a region in a viewer and clear or
>> fill it. It can be used for removing unwanted objects, cropping to a
>> region of interest, or splitting a segment into two separate parts.
>> The effect is available in tomorrow's nightly release.
>>
>>
>>
>> Short demo: https://youtu.be/m4zTj8i4tCA
>>
>>
>>
>> Features:
>>
>> .         Outline can be drawn in any 3D or a slice viewer, using
>> free-form curve, circle, or rectangle shape.
>>
>> .         The selected region can be filled, cleared, or assigned to a
>> different segment.
>>
>> .         Standard masking options are supported - for example, filling
>> can be constrained by image intensity range or restricted to a
>> selected segment.
>>
>>
>>
>> Thanks to Davide Punzo for developing the astro cloud segmenter
>> effect, which inspired this new scissors effect (see his demo at
>> https://youtu.be/v6x3uPuLxzM).
>>
>>
>>
>> Andras
>>
>>
>>
>>
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to [hidden email]
>> with unsubscribe as the subject
>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Devel
> opers/FAQ
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Re: Contour interpolation is added to Segment Editor

Jean-Christophe Fillion-Robin
Hi Murat,

On Tue, Oct 4, 2016 at 4:27 PM, Murat Maga <[hidden email]> wrote:
I will download and try tomorrow. So when are you guys planning to move to 4.6 (or 5.0)?

As discussed during the developer hangout this morning, we are planning to create the 4.6 release this week or the following (if there are some unexpected breakage)

Announcement will follow.

Jc




--
<a href="tel:%2B1%20919%20869%208849" value="&#43;19198698849" target="_blank">+1 919 869 8849

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Re: Contour interpolation is added to Segment Editor

Csaba Pinter-2
In reply to this post by Andras Lasso-2
This is great!
Thank you Andras!

csaba

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Andras Lasso
Sent: Tuesday, October 4, 2016 16:22
To: Andrey Fedorov; Dzenan Zukic; Murat Maga
Cc: SPL Slicer Users; Davide Punzo; Paul Yushkevich; SPL Slicer Devel
Subject: [slicer-devel] Contour interpolation is added to Segment Editor

Hi all,

I have good news. I gave a try to Dzenan et al's contour interpolation filter and it worked very well! Thank you for implementing this great algorithm.

I've added this contour interpolator to the Segment Editor, available in Smoothing effect / Interpolation mode (in tomorrow's nightly build). See a short demo here:
https://youtu.be/VDlYmmaGxEI

Integration of this filter to the Segment Editor took less than an hour! Of course, we could tune this further (allow interpolating multiple segments at once, make the feature easier to find, etc) - any feedback is welcome.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: October 4, 2016 10:49
To: Dzenan Zukic <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Paul Yushkevich <[hidden email]>; Davide Punzo <[hidden email]>; SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-users] [slicer-devel] New "scissors" effect in Segment Editor for 3D clipping

Dzenan, thanks for mentioning this development!

For completeness and reference, this article contains more details about implementation and its evaluation:
http://insight-journal.org/browse/publication/977

On Tue, Oct 4, 2016 at 10:28 AM, Dzenan Zukic <[hidden email]> wrote:

> Good job Andras!
>
> Murat: slice interpolation is available in ITK as a remote module and
> has been integrated in ITK-SNAP 3.6.0-beta. Integration in this beta
> is a bit clumsy, preventing proper interpolation of all labels.
>
> Regards
>
> Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Tue, Oct 4, 2016 at 12:39 AM, Murat Maga <[hidden email]> wrote:
>>
>> Awesome! Thank you very much!
>>
>>
>>
>> Now please consider adding an interpolated slice by slice
>> segmentation feature.
>>
>>
>>
>>
>>
>> From: slicer-users [mailto:[hidden email]] On
>> Behalf Of Andras Lasso
>> Sent: Monday, October 03, 2016 8:47 PM
>> To: SPL Slicer Users <[hidden email]>; SPL Slicer Devel
>> <[hidden email]>
>> Cc: Davide Punzo <[hidden email]>
>> Subject: [slicer-users] New "scissors" effect in Segment Editor for
>> 3D clipping
>>
>>
>>
>> Hi all,
>>
>>
>>
>> We've just added the long-awaited "scissors" effect in Segment Editor
>> module. The effect allows outlining a region in a viewer and clear or
>> fill it. It can be used for removing unwanted objects, cropping to a
>> region of interest, or splitting a segment into two separate parts.
>> The effect is available in tomorrow's nightly release.
>>
>>
>>
>> Short demo: https://youtu.be/m4zTj8i4tCA
>>
>>
>>
>> Features:
>>
>> .         Outline can be drawn in any 3D or a slice viewer, using
>> free-form curve, circle, or rectangle shape.
>>
>> .         The selected region can be filled, cleared, or assigned to a
>> different segment.
>>
>> .         Standard masking options are supported - for example, filling
>> can be constrained by image intensity range or restricted to a
>> selected segment.
>>
>>
>>
>> Thanks to Davide Punzo for developing the astro cloud segmenter
>> effect, which inspired this new scissors effect (see his demo at
>> https://youtu.be/v6x3uPuLxzM).
>>
>>
>>
>> Andras
>>
>>
>>
>>
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to [hidden email]
>> with unsubscribe as the subject
>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Devel
> opers/FAQ
_______________________________________________
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Re: Contour interpolation is added to Segment Editor

Andras Lasso-2
In reply to this post by Murat Maga

Yes, absolutely, thanks to all of you. It's great that at least at the algorithms level all these open source applications can share source code and we don’t have to redevelop things from scratch.

 

Andras

 

From: [hidden email]
Sent: Tuesday, October 4, 2016 17:01
To: [hidden email]
Cc: [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]
Subject: Re: [slicer-users] Contour interpolation is added to Segment Editor

 

Hi Andras,

I am glad that this functionality originally developed by Kitware for ITK-SNAP 3.6 was also a useful addition to Slicer. Dzenan and Jared did a great job implementing this filter. 

Paul

On Tue, Oct 4, 2016 at 4:31 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:
Hi Murat,

On Tue, Oct 4, 2016 at 4:27 PM, Murat Maga <[hidden email]> wrote:
I will download and try tomorrow. So when are you guys planning to move to 4.6 (or 5.0)?

As discussed during the developer hangout this morning, we are planning to create the 4.6 release this week or the following (if there are some unexpected breakage)

Announcement will follow.

Jc




--
<a href="tel:%2B1%20919%20869%208849" value="&#43;19198698849" target="_blank">+1 919 869 8849



--
Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

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Re: Contour interpolation is added to Segment Editor

Steve Pieper-2
Awesome work everyone!

On Tue, Oct 4, 2016 at 5:15 PM, Andras Lasso <[hidden email]> wrote:

Yes, absolutely, thanks to all of you. It's great that at least at the algorithms level all these open source applications can share source code and we don’t have to redevelop things from scratch.

 

Andras

 

From: [hidden email]
Sent: Tuesday, October 4, 2016 17:01
To: [hidden email]
Cc: [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]
Subject: Re: [slicer-users] Contour interpolation is added to Segment Editor

 

Hi Andras,

I am glad that this functionality originally developed by Kitware for ITK-SNAP 3.6 was also a useful addition to Slicer. Dzenan and Jared did a great job implementing this filter. 

Paul

On Tue, Oct 4, 2016 at 4:31 PM, Jean-Christophe Fillion-Robin <[hidden email]> wrote:
Hi Murat,

On Tue, Oct 4, 2016 at 4:27 PM, Murat Maga <[hidden email]> wrote:
I will download and try tomorrow. So when are you guys planning to move to 4.6 (or 5.0)?

As discussed during the developer hangout this morning, we are planning to create the 4.6 release this week or the following (if there are some unexpected breakage)

Announcement will follow.

Jc




--
<a href="tel:%2B1%20919%20869%208849" value="&#43;19198698849" target="_blank">+1 919 869 8849



--
Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

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Re: Contour interpolation is added to Segment Editor

Dzenan Zukic
In reply to this post by Andras Lasso-2
It is a pleasure to hear the interpolation filter was easy to use!

The filter development was funded by a grant to maintain ITK-SNAP, so the thanks also extend to Paul and NIH.

Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Tue, Oct 4, 2016 at 4:22 PM, Andras Lasso <[hidden email]> wrote:
Hi all,

I have good news. I gave a try to Dzenan et al's contour interpolation filter and it worked very well! Thank you for implementing this great algorithm.

I've added this contour interpolator to the Segment Editor, available in Smoothing effect / Interpolation mode (in tomorrow's nightly build). See a short demo here:
https://youtu.be/VDlYmmaGxEI

Integration of this filter to the Segment Editor took less than an hour! Of course, we could tune this further (allow interpolating multiple segments at once, make the feature easier to find, etc) - any feedback is welcome.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: October 4, 2016 10:49
To: Dzenan Zukic <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Paul Yushkevich <[hidden email]>; Davide Punzo <[hidden email]>; SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-users] [slicer-devel] New "scissors" effect in Segment Editor for 3D clipping

Dzenan, thanks for mentioning this development!

For completeness and reference, this article contains more details about implementation and its evaluation:
http://insight-journal.org/browse/publication/977

On Tue, Oct 4, 2016 at 10:28 AM, Dzenan Zukic <[hidden email]> wrote:
> Good job Andras!
>
> Murat: slice interpolation is available in ITK as a remote module and
> has been integrated in ITK-SNAP 3.6.0-beta. Integration in this beta
> is a bit clumsy, preventing proper interpolation of all labels.
>
> Regards
>
> Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Tue, Oct 4, 2016 at 12:39 AM, Murat Maga <[hidden email]> wrote:
>>
>> Awesome! Thank you very much!
>>
>>
>>
>> Now please consider adding an interpolated slice by slice
>> segmentation feature.
>>
>>
>>
>>
>>
>> From: slicer-users [mailto:[hidden email]] On
>> Behalf Of Andras Lasso
>> Sent: Monday, October 03, 2016 8:47 PM
>> To: SPL Slicer Users <[hidden email]>; SPL Slicer Devel
>> <[hidden email]>
>> Cc: Davide Punzo <[hidden email]>
>> Subject: [slicer-users] New "scissors" effect in Segment Editor for
>> 3D clipping
>>
>>
>>
>> Hi all,
>>
>>
>>
>> We've just added the long-awaited "scissors" effect in Segment Editor
>> module. The effect allows outlining a region in a viewer and clear or
>> fill it. It can be used for removing unwanted objects, cropping to a
>> region of interest, or splitting a segment into two separate parts.
>> The effect is available in tomorrow's nightly release.
>>
>>
>>
>> Short demo: https://youtu.be/m4zTj8i4tCA
>>
>>
>>
>> Features:
>>
>> .         Outline can be drawn in any 3D or a slice viewer, using
>> free-form curve, circle, or rectangle shape.
>>
>> .         The selected region can be filled, cleared, or assigned to a
>> different segment.
>>
>> .         Standard masking options are supported - for example, filling
>> can be constrained by image intensity range or restricted to a
>> selected segment.
>>
>>
>>
>> Thanks to Davide Punzo for developing the astro cloud segmenter
>> effect, which inspired this new scissors effect (see his demo at
>> https://youtu.be/v6x3uPuLxzM).
>>
>>
>>
>> Andras
>>
>>
>>
>>
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to [hidden email]
>> with unsubscribe as the subject
>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
>
> _______________________________________________
> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Devel
> opers/FAQ
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