A collection of personal plotting code for all kinds of projects
Still very unclean, just a very long Jupyter Notebook that uses the functions contained in plotting.py to export images for an experiment we ran (demo image below).
Import plotting.py to make use of the functions, they should be pretty straightforward.
Will rebuild this repo with proper functions you can actually use
Tested on Python >= 3.7 To run:
- clone this repo
- install requirements:
pip install -r requirements.txt
Can plot overlays for segmentations such as this one:
Other features:
- automatic slice selection (e.g. the center of mass of the tumor)
- fully customizable color specification for each label
- padding of images to final shape
- saving images with or without overlay
- and much more..
Written during my time at IBBM Group Munich, Germany and CIBL at Dana-Farber Cancer Institute in Boston, MA. The responsibility for the contents of this repository however remain solely with me as this is only a utilities repository.