Place cells

My project on place cells research. I am studying how topological information about environment can be extracted from neurons alone.

The work heavily relies on Cell Groups Reveal Structure of Stimulus Space Curto C, Itskov V (2008) Cell Groups Reveal Structure of Stimulus Space. PLOS Computational Biology 4(10): e1000205.

However, a better method for topological features extraction was applied; I used persistent homologies to calculate Betti numbers (i.e. number of holes). This yielded good results on the real (not synthetic/generated) dataset.

Run

I recommend you to create a new virtual environment for the project

  python -m venv env
  source env/bin/activate

Then,

  pip install -r requirements.txt

  make run

This will run a jupyter notebook(lab) on localhost:8888 (warning: I disabled authentification for the jupyter notebook, so you may want to avoid running it when connected to public networks, or you can just run jupyter notebook normally by typing jupyter lab in terminal)

Presentation (with images)

If you want a very short introduction to topology and this research, you can follow the link to see a presentation I have made to present the results of my work. The presentation has all the information you need to get started.