# Defining Custom Cross-Sectional Planes in 3D Slicer Using Vectors

**URL:** https://discourse.slicer.org/t/defining-custom-cross-sectional-planes-in-3d-slicer-using-vectors/43645
**Category:** Support
**Created:** [July 8, 2025, 12:45pm UTC](https://discourse.slicer.org/t/defining-custom-cross-sectional-planes-in-3d-slicer-using-vectors/43645 "2025-07-08T12:45:37Z")
**Posts on this page:** 2
**Page:** 1

<div class="post-metadata">

### Author: ![Alex-Martin1](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/alex-martin1/32/80591_2.png) [@Alex-Martin1](https://discourse.slicer.org/u/Alex-Martin1)
#### Post date: [July 8, 2025, 12:45pm UTC](https://discourse.slicer.org/t/defining-custom-cross-sectional-planes-in-3d-slicer-using-vectors/43645/1 "2025-07-08T12:45:37Z")

</div>

Hi everyone,

I’m writing here to ask whether something I’ve been doing in **Amira** can be replicated in an open-source software like **3D Slicer**.

Specifically, I need to define a **cross-sectional plane** with a specific orientation and position, in order to extract cross-sectional images from a defined region. In Amira, this can be done by specifying two 3D vectors (to set the plane’s orientation) and a point of origin (to set the location of the plane). This is really useful for standardizing the procedure.

Is there a way to do something similar in **3D Slicer**? Even better, is there a way to **automate** this through the console or scripting interface? In Amira, there’s no way to set the cross-sectional plane using commands - you have to manually copy and paste the coordinates of the vectors and origin, which is quite tedious when working with many samples.

I would really appreciate any help or guidance.

Thanks so much in advance!  
Alex

---

<div class="post-metadata">

### Author: ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)
#### Post date: [July 8, 2025, 5:35pm UTC](https://discourse.slicer.org/t/defining-custom-cross-sectional-planes-in-3d-slicer-using-vectors/43645/2 "2025-07-08T17:35:14Z")

</div>

That all sounds quite doable. Have a look at the example scripts and you’ll find code for making markups, working with planes, transforming images, etc.

> **[Script repository — 3D Slicer documentation](https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html)**