# What are the underlying methods used in Segment Editor?

**URL:** <https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871>\
**Category:** Development\
**Tags:** segmentation\
**Created:** [July 22, 2021, 5:53am UTC](https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871 "2021-07-22T05:53:16Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![Saima](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@Saima](https://discourse.slicer.org/u/Saima)\
**Post date:** [July 22, 2021, 5:53am UTC](https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871/1 "2021-07-22T05:53:16Z")

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Hi Andras,  
I need to know what method is used to convert a volume to labelmap using createlabelvolumefromvolume. What is the method behind it. Does it use thresholding? can I get more details on this how this function convet a volume to label map.

Also where can I find details of methods for the split island module and then the segmentation statistics module. I need to know about the underlying methods behind all these modules.

Thank you so much

Regards,  
Saima Safdar

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 22, 2021, 11:50am UTC](https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871/2 "2021-07-22T11:50:49Z")

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You can find full source code of Segmentations and Segment Editor modules [here](https://github.com/Slicer/Slicer/tree/master/Modules/Loadable/Segmentations). Segmentation data management and conversions are implemented in the [segmentation core library](https://github.com/Slicer/Slicer/tree/master/Libs/vtkSegmentationCore) (a somewhat older version also made available as a standalone library, PolySeg).

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**Author:** ![Saima](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@Saima](https://discourse.slicer.org/u/Saima)\
**Post date:** [August 2, 2021, 6:34am UTC](https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871/3 "2021-08-02T06:34:12Z")

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Hi andras,  
How can i cite the split island filter. or what is the method behind the splitting? can I get any reference for it. Similarly if I am using createlabelvolumefromvolume or segment statistics what methods I should mention and what are the references. sorry I couldnt find references or methods behind these tasks.

Example, there is thresholding method, growcut method and watershed.

Regards,  
Saima Safdar

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [August 2, 2021, 5:10pm UTC](https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871/4 "2021-08-02T17:10:43Z")

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Most of these methods will not have a citable paper. You can cite the SegmentEditor as a tool and refer to its github page and then you can cite the Slicer as a general biomedical analysis platform. These two are the common ones people use:

Fedorov, A., Beichel, R., Kalpathy-Cramer, J., Finet, J., Fillion-Robin, J.-C., Pujol, S., Bauer, C., Jennings, D., Fennessy, F., Sonka, M., Buatti, J., Aylward, S., Miller, J. V., Pieper, S., & Kikinis, R. (2012). 3D Slicer as an image computing platform for the Quantitative Imaging Network. _Magnetic Resonance Imaging_ , _30_ (9), 1323–1341. [Redirecting](https://doi.org/10.1016/j.mri.2012.05.001)

Kikinis, R., Pieper, S. D., & Vosburgh, K. G. (2014). 3D Slicer: A Platform for Subject-Specific Image Analysis, Visualization, and Clinical Support. In _Intraoperative Imaging and Image-Guided Therapy_ (pp. 277–289). Springer, New York, NY. [3D Slicer: A Platform for Subject-Specific Image Analysis, Visualization, and Clinical Support | SpringerLink](https://doi.org/10.1007/978-1-4614-7657-3_19)

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [August 2, 2021, 5:29pm UTC](https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871/5 "2021-08-02T17:29:24Z")

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Yes, citing 3D Slicer platform paper (as described [here](https://slicer.readthedocs.io/en/latest/user_guide/about.html#how-to-cite)) and indicating the Slicer version number and module/tool names should be sufficient to specify what algorithms you used exactly.

If you want to reward developers of selected features that you have found particularly useful then you can look up more specific papers. For example, the overall framework of Segment Editor is described in [this paper](https://doi.org/10.1016/j.cmpb.2019.02.011). Reference paper for algorithms used in non-trivial Segment Editor effects (such as Grow from seeds and Fill between slices) are described in the [Segment Editor documentation](https://slicer.readthedocs.io/en/latest/user_guide/modules/segmenteditor.html).

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [August 2, 2021, 5:45pm UTC](https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871/6 "2021-08-02T17:45:28Z")

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> [@lassoan](#):
>
> For example, the overall framework of Segment Editor is described in [this paper](https://doi.org/10.1016/j.cmpb.2019.02.011).

I wasn’t aware of that paper. I think you should also have a How to Cite section under the Segment Editor since it is a very heavily used module. Documentation page doesn’t seem to point out to that paper.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [August 3, 2021, 12:41pm UTC](https://discourse.slicer.org/t/what-are-the-underlying-methods-used-in-segment-editor/18871/7 "2021-08-03T12:41:41Z")

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FYI, I’ve added a “How to cite” section to Segment Editor documentation - [Slicer/segmenteditor.md at master · Slicer/Slicer · GitHub](https://github.com/Slicer/Slicer/blob/master/Docs/user_guide/modules/segmenteditor.md#how-to-cite)