10 Nov. 2020
Provides Jupyter notebooks that are aimed at providing interactive visualization of multiplex images themsevles and analysis results on those images.
This notebook is meant to be run in a Docker container by mounting your data directory - data directory contains your images, masks, and data csv files. Since all the paths are configured in a configs.py file it is possible to run the notebooks outside of a Docker container so long as you configure the paths appropriately.
To run with a Docker container use the following command which allows you to port-forward the Jupyter notebook port locally and to mount your data dir which should be mount to /data in the Docker container.
docker run -it --rm -p####:8888 -v <data_dir>:/data jvizcar/sage_multiplex_interactors:latest
Make sure to fill #### with the local port you want to port-forward to - the token password will be displayed in the terminal, copy paste this to access the notebook. <data_dir> should be the absolute path to your directory containing all the images, image dirs, masks, and csv files.
Look into the configs_example.py file to understand the required files you will need to run the notebooks.