Perks_Sawtell_2022

Perks_Sawtell_2022

This directory contains all materials needed to produce the main Figures and results of the research article titled "Neural Readout of a Latency Code in the Active Electrosensory System" published in Cell Reports (also available on biorxiv at https://doi.org/10.1101/2021.12.14.472594).

There are three main subfolders:

1. scripts All scripts are written in Python3. All python software used for analysis was obtained via the Anaconda Individual distribution. For each of the main Figures in the publication, there is a separate jupyter notebook file (.ipynb) that can be used to recreate all figure panels (raw pdfs were created for each panel within each figure). All filepaths in these notebooks assume that you launched jupyter notebook (or jupyter lab) from within the Perks_Sawtell_2022 directory. If you launch python from a different location, the filepaths will need to be edited. Figure PDFs generated by these notebooks will be saved (if the 'saveas' lines are uncommented) in a folder named 'Perks_Sawtell_2022_FigureComponents' one level up from the location you launched the notebooks (for example, the location that you saved 'Perks_Sawtell_2022' onto your computer.

2. data_processed This folder (and subfolders) contains all processed data files that were created to increase the efficiency of data analysis (for example saving processed data in this way avoided re-processing the raw data everytime an edit needed to be made to a figure, or a different analysis needed to be done with the same raw data, etc). The scripts used to create all processed data files are located in the scripts folder (written and saved as either .py or .ipynb). File formats in this folder include: yaml, pickle, csv, npy, xlsx, txt When running any of the model simulations on a different computer, the file 'grc_model_simulations/grc_model_simulations.pickle' will likely need to be deleted (the script will throw an error). Once deleted, the script will automatically regenerate this file. It should not need to be deleted again if re-running simulations on the same computer.

3. environments Anaconda environments exported as .yaml files from each of the computers used during the processing and analysis of the data for "Neural Readout of a Latency Code in the Active Electrosensory System" published in Cell Reports (also available on biorxiv at https://doi.org/10.1101/2021.12.14.472594). The operating system specs are named in the corresponding file names. Only Mac computers were used in the analysis and processing. Therefore, there are no environment files for a Windows PC in this folder.

data_raw This directory of files is zipped. It contains all of the raw data needed to generate the processed data (using scripts in the scripts directory) used in the analysis and visualization of the results reported in "Neural Readout of a Latency Code in the Active Electrosensory System" published in Cell Reports (also available on biorxiv at https://doi.org/10.1101/2021.12.14.472594). If there are any issues that you find with this data, please email the lead contact as specified in the manuscript.