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# Segmentation via Layered Surface Detection
## Table of Content
1. [Description of Repository Content](#1)
2. [Set-up to run tutorials](#2)
3. [Resources and inspiration](#3)
4. [Contributions](#4)
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### 1. Description of Repository Content
## 1. Description of Repository Content
This repository contains tutorials for the using the layered surface detection tool. Included is a few Jupyter notebook tutorials that are designed to give you an idea on how to use the layered surface tool. You should start with the _LayeredSurfaceDetection_tutorial.ipynb_ notebook which discuss the basics of the layered surface tool and applies it to some synthetic data as well as a relatively simple example dataset. More complex examples are provided in the _NerveSegmentation2D_example.ipynb_ and _NerveSegmentation3D_example.ipynb_ notebooks which describe how to apply the layered surface tool to circular regions via radial unwrapping. A Python file containing some helper functions that are used in the tutorials is also included in utilsLS.py_. Some visualization functions are included in the _utilsVisualizationLS.py_.
These tutorials will give you an understanding of how to apply the Layered Surface tool to image data so that you can use the tool on your own datasets. You can open the the tutorials at [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Flab.compute.dtu.dk%2FQIM%2Ftutorials%2Flayered-surfaces/HEAD).
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### 2. Set-up to run tutorials
## 2. Set-up to run tutorials
For running the tool locally on your computer, you need to install the slgbuilder Python package using `pip install slgbuilder`.
If you are using Anaconda, you can automatically install the required packages using the included environment file:
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### 3. Resources and inspiration
## 3. Resources and inspiration
For inspiration, check out the following papers on user cases we have solved with the layered surfaces tool:
- Dahl, Dahl, Larsen. [Surface Detection using Round Cut.](https://ieeexplore.ieee.org/document/7182720) International Conference on 3D Vision, 2014.
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### 4. Contributions
## 4. Contributions
The development of the tutorials is a combined effort from several researchers in the QIM team. The collection of scripts and exercises is in constant development, and actively used to demonstrate the tool and teach at workshops. We would therefore very much appreciate to hear about your experience.
Please contact William Laprade wl@di.ku.dk with issues and feedback.
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