slicevis

A Python package for interactive slice and segmentation visualization of 3D datasets in Jupyter notebooks.

Axial slice of murine CT scan with multi-class segmentation in SliceWidget.

Easiest way to install slicevis:

pip install slicevis

How to build slicevis yourself (Windows):

1. Clone this repository git clone https://git.rwth-aachen.de/nicholasbook/sce-project-ss22.git.
2. (Optional) Create a virtual environment py -m venv env and activate it call env/Scripts/activate.bat.
3. Install locally using pip install -e ..

Usage

slicevis is meant to be used in combination with Jupyter notebooks. I recommend that you use VSCode with the Python and Jupyter extension installed. Check out the examples directory in the repository for test data and prepared notebooks.

Minimal usage:

from slicevis import SliceWidget
data = slicevis.load_image("CT280.gff") # 4D image
widget = slicevis.SliceWidget(data.get_timepoint())

License

The slicevis package is licensed under the terms of the MIT license.

The examples directory of the repository contain data that is licensed under CC-BY-SA 4.0. Please refer to examples/LICENSE.txt for more details.

Acknowledgements

The slicevis Python package was developed by me, Nicholas Book, as a final project for the course "Sustainable Computational Engineering", held by Dr. Anil Yildiz and Dr. Hu Zhao of the Chair of Methods for Model-based Development in Computational Engineering (MBD). I would like to extend my gratitude to both for their kind support.