This repository contains code to reproduce all figures of the behavior paper by the International Brain Laboratory. If reusing any part of this code please cite the bioRxiv paper in which these figures appear.
These instructions require anaconda (https://www.anaconda.com/distribution/#download-section) for Python 3 and git (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
In an Anaconda prompt window:
- Clone or download the paper-bahavior repository
- Install the other dependencies by running
pip install -r requirements.txt
To call the functions in this repo, either run python from within the paper-bahavior folder or
add the folder to your python path:
import sys
sys.path.extend([r'path/to/paper-behavior'])All the scripts start with the name of the figure they produce. The figure panels will appear in the exported_figs subfolder. When running the scripts for the first time the required data will be downloaded to ./data
NB: Since December 2023 our DataJoint servers were retired and some scripts no longer execute, however the main figure scripts should still work.
If you have any problems running this code, please open an issue in the iblenv repository where we support users in using the IBL software tools.
You can read more about the IBL dataset types and additional computations on the behavioral data, such as training status and psychometric functions.
The data used in this paper have a number of issues. The authors are confident that these issues do not affect the results of the paper but nevertheless users should be aware of these shortcomings.
- NaN values may be found throughout the data. These resulted from failures to either produce an event (for example the go cue tone wasn't played) or to record an event (e.g. the stimulus was produced but the photodiode failed to detect it).
- Some events violated the task structure outlined in the paper. For example during some sessions the go cue tone happened much later than the stimulus onset. Although this conceivably affected the reaction time on some trials, it did not occur frequently enough to significantly affect the median reaction times.