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RobertoDF / De-Filippo-et-al-2022

Code for the reproduction of De Filippo et al., 2022.
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Code for the reproduction of De Filippo et al., 2022.

The complete manuscript (text included) can be reproduced using the Python code present in this repository. Each number present in the text is an f-String that can be traced back to a data structure (see End2EndPaper).

Abstract

Figures

Figure 1 Figure 2
Figure 1 Figure 2
Figure 3 Figure 4 Figure 5
Figure 3 Figure 4 Figure 5

Instructions

  1. Clone this repository and download the pre-computed data from here.
  2. Open a terminal and cd to this repository cd <De-Filippo-et-al-2022>
  3. Create conda environment: conda create --name De-Filippo-et-al-2022 python=3.7 (if conda is not installed see here) and activate environment conda activate De-Filippo-et-al-2022
  4. Install dependencies pip install --no-deps -r requirements_analysis.txt
  5. Change the root_data (location pre-computed data) and root_github_repo (location repository) variables in Utils/Settings.py
  6. Reproduce figures by running the associated code, e.g. Figures/Figure_1/Figure_1.py (output in Output_figures folder). Reproduce text by running Manuscript/De_Filippo_et_al_2022.py (output in Manucript folder, see here)

All data can be recomputed from scratch with the functions provided in the Calculations folder, download the Allen institute Neuropixel dataset and change neuropixel_dataset in Utils/Settings.py. If you want to recompute all the brain renderings using Brainrender, you will need the latest version available on github (not yet on pip).

Main figures data processing flow

Blue cylinder = database, Pink boxes = algorithms, Blue boxes = data structures.