OpenScope Credit Assignment Project Code

1. Description

This repository contains the code for analyzing the data from the Credit Assignment project, an Allen Institute for Brain Science OpenScope project.

The dataset is described and characterized in Gillon, Lecoq et al., 2023, Sci Data. Analyses and results are published in Gillon, Pina et al., 2024, J Neurosci.

2. Installation

To run the code, you can install a conda-based environment manager (e.g., Anaconda, Miniconda or Mamba).

Once the conda-based environment manager is installed, use osca.yml to create the osca environment with all the packages needed to run this code. For example, if using Ubuntu or Mac OS, open a terminal, go to the repository directory, and run:

conda env create -f osca.yml

Alternatively, if you prefer to use a different environment manager, install required packages specified in requirements.txt.

This code is written in Python 3, and has been tested with Python 3.8.

3. Use

Once installed, when using the codebase, simply activate the environment:

source activate osca

All of the appropriate libraries should then be loaded, allowing the scripts and notebooks provided in the repo to be run.

4. Scripts and modules

• run_paper_figures.py: run, analyse and plot paper figures (for example usage, see the paper_figures folder)
• analysis: analysis scripts, including the Session and Stim objects
• sess_util: session specific utilities module
• plot_fcts: plotting scripts
• paper_fig_util: scripts to organize and generate the paper figures
• examples: example notebook for using the Session and Stim objects

5. Data

The full dataset for this project is hosted here in the DANDI archive in NWB format. The associated metadata can be found here. The subset of data used in the paper (33 sessions, ~15 GB total) can be downloaded by running, from the main directory of the repository:
python sess_util/sess_download_util.py --output path/to/save/

Code to generate the stimuli used in these experiments can be found here.

6. Figure example notebooks

The following notebooks give examples of how to download the data, and run the paper analyses. Note that the organization of figures and panels has been updated since our preprint Gillon, Pina, Lecoq et al., 2021, bioRxiv was published. See commit tags on the main branch for the bioRxiv versions of this repository.

Run in Binder	Run the Google Colab notebook

The contents of the Binder and Google Colab notebooks differ somewhat, due to the resources available:

• Binder: conda env. is installed automatically (+), but this can be slow, and only limited compute resources are available (-).
• Google Colab: less environment control (-), but more substantial compute resources are available (+).

7. Terminological notes

The following terms used in the codebase are considered equivalent to the corresponding terms used in the papers:

• "expected": equivalent to "consistent" and "pattern-matching" for both stimuli, and "uniform flow" for the visual flow stimulus specifically.
• "unexpected": equivalent to "inconsistent" and "pattern-violating" for both stimuli, and "counter-flow" for the visual flow stimulus specifically.

8. Authors

This code was written by:

• Colleen Gillon (colleen dot gillon at mail dot utoronto dot ca)
• Jay Pina, Joel Zylberberg, and Blake Richards

Please do not hesitate to contact the authors or open an issue/pull request, if you have trouble using the data or the codebase or improvements to propose.

9. Citations

To cite the dataset paper:

@Article{GillonLecoq2023,
  title={Responses of pyramidal cell somata and apical dendrites in mouse visual cortex over multiple days},
  author={Gillon, Colleen J. and Lecoq, J{\'e}r{\^o}me A. and Pina, Jason E. and Ahmed, Ruweida and Billeh, Yazan and Caldejon, Shiella and Groblewski, Peter and Henley, Timothy M. and Kato, India and Lee, Eric and Luviano, Jennifer and Mace, Kyla and Nayan, Chelsea and Nguyen, Thuyanh and North, Kat and Perkins, Jed and Seid, Sam and Valley, Matthew T. and Williford, Ali and Bengio, Yoshua and Lillicrap, Timothy P. and Zylberberg, Joel and Richards, Blake A.},
  journal={Scientific Data},
  year={2023},
  date={May 2023},
  publisher={Cold Spring Harbor Laboratory},
  volume={10},
  number={1},
  pages={287},
  issn={2052-4463},
  doi={10.1038/s41597-023-02214-y},
  url={https://www.nature.com/articles/s41597-023-02214-y},
}

To cite the analysis paper:

@Article{GillonPina2024,
  title={Responses to pattern-violating visual stimuli evolve differently over days in somata and distal apical dendrites},
  author={Gillon, Colleen J. and Pina, Jason E. and Lecoq, J{\'e}r{\^o}me A. and Ahmed, Ruweida and Billeh, Yazan and Caldejon, Shiella and Groblewski, Peter and Henley, Timothy M. and Kato, India and Lee, Eric and Luviano, Jennifer and Mace, Kyla and Nayan, Chelsea and Nguyen, Thuyanh and North, Kat and Perkins, Jed and Seid, Sam and Valley, Matthew T. and Williford, Ali and Bengio, Yoshua and Lillicrap, Timothy P. and Richards, Blake A. and Zylberberg, Joel},
  journal={Journal of Neuroscience},
  year = {2024},
  date = {Jan 2024},
  publisher = {Society for Neuroscience},
  volume = {44},
  number = {5},
  pages = {1-22},
  issn = {0270-6474},
  doi = {10.1523/JNEUROSCI.1009-23.2023},
  url = {https://www.jneurosci.org/content/44/5/e1009232023},
}