clone repository and install conda environment

git clone https://github.com/adrianomartinelli/code_example.git
cd code_example
conda env create -f example_code_env.yml && conda activate code_example

Either interactively or in the shell with

python minst_example.py

Two plots will be produced:

• examples.png: examples of reconstructed images
• loss.png: Traning/validation and test loss development of the training

python ripleysK.py

A plot will be produced:

• ripleysK.png: RipleysK estimate for random data and test for deviation from CSR.

cellAutoencoder.py: Autoencoder model

trainer.py: General class to train models

minst_example.py: Example on the MINST data set

ripleysK.py: Base implementation of Ripley's K. To be extended with correction methods.

graph_builder module: module to construct graphs from cellmasks. No running example available, only examples on how us the module in example.py file.