Python implementation of SAIBR: a tool for performing spectral autofluorescence correction on biological images
Project description
matplotlib-polyroi
Module for selecting polygonal ROIs on images, spline fitting and ROI expansion
Installation
pip install matplotlib-polyroi
Instructions
See the tutorial notebook for instructions on usage. To run the notebook interactively you have two options:
Option 1: Binder
To run in the cloud, click here:
(Please note that it may take several minutes to open the notebook)
Option 2: Docker
Step 1: Make sure Docker is installed and open on your machine
Step 2: Run the Docker container:
docker run --rm -p 8888:8888 tsmbland/matplotlib-polyroi
Once the Docker image has finished downloading, this will print two URLs at the bottom for you to copy and paste into your web browser to open up Jupyter (please try both)
Step 3: Navigate to scripts/Demonstration.ipynb to run the notebook
Step 4: When finished, delete the image:
docker image rm tsmbland/matplotlib-polyroi
Option 3: Conda
You can use the environment.yml file to set up a Conda environment on your machine from which the notebook can be run
conda env create -f environment.yml
conda activate matplotlib-polyroi
jupyter notebook
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
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