Spatialproteomics Workshop

You can follow this workshop either on Google Colab, or run it locally using conda and jupyter lab.

Instructions for Colab

Simply navigate to the folder called notebooks and click on the Open in Colab button on top. For the first notebook, it is encouraged to change the runtime to a GPU-based one, since we will run an exemplary cell segmentation, which benefits from running on a GPU.

Instructions for conda

To follow this workshop on your local machine, you first need to download the material by cloning the git repository (git clone https://github.com/MeyerBender/spatialproteomics_workshop.git). Afterwards, you need to set up a virtual environment like this:

• Create the virtual environment: conda env create -f environments/environment.yml
• Activate the environment: conda activate eccb_env

Once you have activated the virtual environment, you can run jupyter lab. Open the notebooks labeled with task in the notebooks folder, and follow the instructions there. In case you are stuck, you can always refer to the solution, which is provided in the same folder.

Getting help

This tutorial is based on the spatialproteomics documentation. You can always refer to it here or have a look at the GitHub repository.