Segmentation - Region growing tool

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Segmentation - Region growing tool

Hollister Herhold

I recently converted to 3D slicer from VG Studio Max. I was showing some colleagues some features of Slicer not in VG Studio (like thresholded sphere brush, for example, which is possibly the best thing since sliced bread) and they were wondering if there is something in 3D slicer that works like the “Region Grower” tool from VG Studio. The basic idea is to click on a center point, then drag out the radius of a spherical area. Within this sphere, voxels with an intensity within a certain threshold window from the center picked point are added to the segmentation. There are a few options for handling the threshold value, labelled “dynamic”, “static”, and “adaptive”. (it’s not always clear what these options really do.)

Having spent some time with both programs, I find the threshold brush tool just as versatile, if not more so. I was just curious as to others’ experiences with other platforms.

Thanks in advance for your thoughts.

-Hollister


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Re: Segmentation - Region growing tool

Steve Pieper-2
Hi Hollister - 

Thanks for the feedback - good news and suggestions are always welcome!

The region grower tool you describe does sound pretty handy.  There is the Wand tool in the Editor module that does something similar (click in a region to paint connected voxels of similar intensity, click more to make the region bigger).  But as I guess you already know, the ability to set a fixed threshold with the paint tools provides a lot more control compared to picking a new intensity reference with every mouse operation.

But also, in case you haven't tried it, the new Segment Editor has many features including the sphere brush (in 4.6.2, but improved in the current Nightly builds).  There's a tutorial here [1].  It has many improvements over the older Editor but I guess it doesn't have a wand tool yet - we should probably port that and see if we can make it behave more like the region grower.

Best,
Steve



On Tue, Mar 28, 2017 at 7:09 PM, Hollister Herhold <[hidden email]> wrote:

I recently converted to 3D slicer from VG Studio Max. I was showing some colleagues some features of Slicer not in VG Studio (like thresholded sphere brush, for example, which is possibly the best thing since sliced bread) and they were wondering if there is something in 3D slicer that works like the “Region Grower” tool from VG Studio. The basic idea is to click on a center point, then drag out the radius of a spherical area. Within this sphere, voxels with an intensity within a certain threshold window from the center picked point are added to the segmentation. There are a few options for handling the threshold value, labelled “dynamic”, “static”, and “adaptive”. (it’s not always clear what these options really do.)

Having spent some time with both programs, I find the threshold brush tool just as versatile, if not more so. I was just curious as to others’ experiences with other platforms.

Thanks in advance for your thoughts.

-Hollister


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[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


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Re: Segmentation - Region growing tool

Andras Lasso-2

Thank you for your feedback. It's very good to hear from happy users (usually people only write if they have problems).

 

I’ve spent some time with evaluating various region growing algorithms, including of course our wand tool, VTK’s region growing filter, simple adaptive threshold methods, but I did not find any of them good enough to add to Segment editor as an effect.

 

Thresholding or painting with a fixed intensity threshold (followed by smoothing and island processing) is good enough if there is strong contrast between different regions. For more difficult cases I use “Grow from seeds” (fast grow-cut) effect: it can handle very complex geometry and low contrast without leaking. If there is no contrast between structures at all, then I draw manually on a number of slices and use “Fill between slices” effect to create a full segmentation.

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 7:31 PM
To: [hidden email]
Cc: [hidden email]
Subject: Re: [slicer-users] Segmentation - Region growing tool

 

Hi Hollister - 

Thanks for the feedback - good news and suggestions are always welcome!

The region grower tool you describe does sound pretty handy.  There is the Wand tool in the Editor module that does something similar (click in a region to paint connected voxels of similar intensity, click more to make the region bigger).  But as I guess you already know, the ability to set a fixed threshold with the paint tools provides a lot more control compared to picking a new intensity reference with every mouse operation.

But also, in case you haven't tried it, the new Segment Editor has many features including the sphere brush (in 4.6.2, but improved in the current Nightly builds).  There's a tutorial here [1].  It has many improvements over the older Editor but I guess it doesn't have a wand tool yet - we should probably port that and see if we can make it behave more like the region grower.

Best,
Steve



On Tue, Mar 28, 2017 at 7:09 PM, Hollister Herhold <[hidden email]> wrote:

I recently converted to 3D slicer from VG Studio Max. I was showing some colleagues some features of Slicer not in VG Studio (like thresholded sphere brush, for example, which is possibly the best thing since sliced bread) and they were wondering if there is something in 3D slicer that works like the “Region Grower” tool from VG Studio. The basic idea is to click on a center point, then drag out the radius of a spherical area. Within this sphere, voxels with an intensity within a certain threshold window from the center picked point are added to the segmentation. There are a few options for handling the threshold value, labelled “dynamic”, “static”, and “adaptive”. (it’s not always clear what these options really do.)

Having spent some time with both programs, I find the threshold brush tool just as versatile, if not more so. I was just curious as to others’ experiences with other platforms.

Thanks in advance for your thoughts.

-Hollister


_______________________________________________
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


_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Segmentation - Region growing tool

Hollister Herhold
In reply to this post by Steve Pieper-2
Andras and Steve-

Thank you for the tips!

I primarily work on micro-CT of fossil insects in amber, and the cuticle and integument of the insect inclusion often have intensity values relatively close to the amber. The Segment Editor module in 4.7 has been my go-to resource, especially the sphere brush with thresolding/editable range. I typically use the latest nightly build (or a few days old), and my workflow is pretty much exactly as you described - 3D brush paint with threshold, followed by smoothing and island removal. I need to spend more time trying out the grow from seeds effect. 

Thanks again!

-Hollister



On Mar 28, 2017, at 8:53 PM, Andras Lasso <[hidden email]> wrote:

Thank you for your feedback. It's very good to hear from happy users (usually people only write if they have problems).
 
I’ve spent some time with evaluating various region growing algorithms, including of course our wand tool, VTK’s region growing filter, simple adaptive threshold methods, but I did not find any of them good enough to add to Segment editor as an effect.
 
Thresholding or painting with a fixed intensity threshold (followed by smoothing and island processing) is good enough if there is strong contrast between different regions. For more difficult cases I use “Grow from seeds” (fast grow-cut) effect: it can handle very complex geometry and low contrast without leaking. If there is no contrast between structures at all, then I draw manually on a number of slices and use “Fill between slices” effect to create a full segmentation.
 
Andras
 
From: [hidden email]
Sent: Tuesday, March 28, 2017 7:31 PM
To: [hidden email]
Cc: [hidden email]
Subject: Re: [slicer-users] Segmentation - Region growing tool
 
Hi Hollister - 

Thanks for the feedback - good news and suggestions are always welcome!

The region grower tool you describe does sound pretty handy.  There is the Wand tool in the Editor module that does something similar (click in a region to paint connected voxels of similar intensity, click more to make the region bigger).  But as I guess you already know, the ability to set a fixed threshold with the paint tools provides a lot more control compared to picking a new intensity reference with every mouse operation.

But also, in case you haven't tried it, the new Segment Editor has many features including the sphere brush (in 4.6.2, but improved in the current Nightly builds).  There's a tutorial here [1].  It has many improvements over the older Editor but I guess it doesn't have a wand tool yet - we should probably port that and see if we can make it behave more like the region grower.

Best,
Steve



On Tue, Mar 28, 2017 at 7:09 PM, Hollister Herhold <[hidden email]> wrote:

I recently converted to 3D slicer from VG Studio Max. I was showing some colleagues some features of Slicer not in VG Studio (like thresholded sphere brush, for example, which is possibly the best thing since sliced bread) and they were wondering if there is something in 3D slicer that works like the “Region Grower” tool from VG Studio. The basic idea is to click on a center point, then drag out the radius of a spherical area. Within this sphere, voxels with an intensity within a certain threshold window from the center picked point are added to the segmentation. There are a few options for handling the threshold value, labelled “dynamic”, “static”, and “adaptive”. (it’s not always clear what these options really do.)

Having spent some time with both programs, I find the threshold brush tool just as versatile, if not more so. I was just curious as to others’ experiences with other platforms.

Thanks in advance for your thoughts.

-Hollister


_______________________________________________
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-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