deepcelltypes interactive demo

Cell-type prediction for multiplexed spatial proteomic data.

To run the demo, you will need: #. Python #. A running docker daemon #. The prototype model and example data

Setup

Docker

Ensure that your docker daemon is running and doesn't require elevated permissions:

docker run hello-world

Python

Create a Python virtual environment and install the necessary dependencies:

python -m venv demo-env
source demo-env/bin/activate  # or whichever script is appropriate for your shell
pip install -r requirements.txt

Model and example data

The model is not (yet) publicly available as it is currently under development. For access to the demo data and model prototype, direct inquiries to [email protected].

The model and data should be unpacked in the top-level directory of this repository:

tar -xzf demo_data_model.tar.gz

Running the demo

The demo is available in the form of a markdown-based jupyter notebook. Launch a new session with:

jupyter notebook

Then right-click presentation.md and select Jupytext Notebook from the Open with menu.