matplotlib-polyroi 0.1.5

Python implementation of SAIBR: a tool for performing spectral autofluorescence correction on biological images

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.