# Spatial information in 2D segmentations

**URL:** <https://discourse.slicer.org/t/spatial-information-in-2d-segmentations/46642>\
**Category:** Support\
**Created:** [April 2, 2026, 6:40pm UTC](https://discourse.slicer.org/t/spatial-information-in-2d-segmentations/46642 "2026-04-02T18:40:43Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Antmaker](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/antmaker/32/81424_2.png) [@Antmaker](https://discourse.slicer.org/u/Antmaker)\
**Post date:** [April 2, 2026, 6:40pm UTC](https://discourse.slicer.org/t/spatial-information-in-2d-segmentations/46642/1 "2026-04-02T18:40:44Z")

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According to [this post](https://discourse.slicer.org/t/2d-segmentation-possible/33743/2), 2D segmentation is possible in 3D Slicer. I am trying to figure out whether it is possible to incorporate spatial information such that I may calculate “area” instead of “volume (Volume Statistics extension)”.

Is it possible to incorporate spatial information into an image that is being segmented in 3D Slicer? If so, how would I approach integrating it and then calculate the segmented area? If not, how may I segment and calculate the pixel counts?

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**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [April 2, 2026, 11:33pm UTC](https://discourse.slicer.org/t/spatial-information-in-2d-segmentations/46642/2 "2026-04-02T23:33:22Z")

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If you enter a 2D image in Slicer it will automatically converted to 3D. Then you can change the spacing (z-axis) of the scalarVolumeNode in Slicer to be 1mm. If you calculate the volume for a segmentation of this image it will be also the area just change the unit to mm2

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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:** [April 3, 2026, 12:32pm UTC](https://discourse.slicer.org/t/spatial-information-in-2d-segmentations/46642/3 "2026-04-03T12:32:41Z")

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Segment Statistics module computes area and volume of each segment. Area is computed in 3D, which means both sides of a flat single-slice segments are included. You can divide the reported surface value by 2 to get the cross-sectional area, i.e., the area that you see on a single image.

There are also several modules for computing area. I generated this summary using ChatGPT, but I confirm that it is accurate (I reviewed it and fixed minor inaccuracies):

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### 📌 1. **Segment Cross‑Section Area** (in **Sandbox** extension)

- This module computes cross‑sectional area of a segmentation **along an image axis** (e.g., axial, sagittal, coronal or any IJK axis you choose).
- You can install it by opening the **Extensions Manager** in Slicer and installing the **Sandbox** extension.

👉 Best when you want area per slice along standard image axes.

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### 📌 2. **SegmentGeometry** (in **SlicerBiomech** extension)

- This extension can compute **cross‑sectional area** (plus other shape metrics) **along an arbitrary direction or line** , not just the image axes.
- It’s useful if you want cross‑sections in non‑orthogonal directions or aligned with a specific anatomical axis.
- It outputs area and additional geometric properties like perimeter, Feret diameter, moments of inertia, etc.

👉 Best when you need cross‑section metrics oriented in a custom way.

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### 📌 3. **VMTK modules** (in **SlicerVMTK** extension)

- The **Vascular Modeling Toolkit (VMTK)** extension includes modules like _Cross‑section analysis_ or _Stenosis measurement_.
- These can compute cross‑sections **along a centerline or curved path** , often used for vessels or tubular structures.

👉 Best for vascular work or when the structure follows a path rather than straight sections.

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### 📌 3. **Markups module**

- If you need the area of a structure in a **single 2D slice** , you can draw a closed curve markup and enable **area measurement** in the Markups module’s **Measurements** section.

👉 Best for measuring area of a simple shape in a single 2D slice.

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<div class="post-metadata">

**Author:** ![Antmaker](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/antmaker/32/81424_2.png) [@Antmaker](https://discourse.slicer.org/u/Antmaker)\
**Post date:** [April 3, 2026, 9:09pm UTC](https://discourse.slicer.org/t/spatial-information-in-2d-segmentations/46642/4 "2026-04-03T21:09:58Z")

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@mau_igna_06, that is a great idea! Thank you, this is a very intuitive and explainable approach.

@lassoan, regarding dividing the area calculated by the Segment Statistics module, wouldn’t the surface area be a slight overestimation because it would include half of the perimeter of the segmented area?

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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:** [April 3, 2026, 9:44pm UTC](https://discourse.slicer.org/t/spatial-information-in-2d-segmentations/46642/5 "2026-04-03T21:44:41Z")

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> [@Antmaker](#):
>
> wouldn’t the surface area be a slight overestimation because it would include half of the perimeter of the segmented area?

Probably the extra surface on the side is negligible (\<1%), but you can measure the surface using all the other methods that I described to confirm.

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**Author:** ![Antmaker](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/antmaker/32/81424_2.png) [@Antmaker](https://discourse.slicer.org/u/Antmaker)\
**Post date:** [April 3, 2026, 9:55pm UTC](https://discourse.slicer.org/t/spatial-information-in-2d-segmentations/46642/6 "2026-04-03T21:55:40Z")

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Yeah, I agree that the difference would be minimal. I was trying to confirm my understanding of the method. Thanks!