Shadron_Pena_2022
Dataset for "Development shaped by cue reliability in the barn owl's auditory midbrain".
Summary
This dataset contains the data used in the BioRxiv manuscript:
Shadron K and Peña JL (2022) Development shaped by cue reliability in the barn owl’s auditory midbrain. BioRxiv, https://doi.org/10.1101/2022.09.29.510116
Details on the recording paradigm, hypotheses, etc., can be found in the manuscript for brevity. Code should run, just paths have to be updated.
Raw Data
Raw data is divided into folders by recording session (e.g. 2022-0317), while subfolders (e.g. 44.00) denote individual neurons. Subfolders contain the recordings of tuning curves, recorded by custom code built by the Konishi Lab (xdphys) and written as text files. Tuning curves were recorded in order:
xx.yy.0.abi - abi curve, sometimes extra files if testing for monaural (rare)
xx.yy.1.iid - interaural level difference (ILD) curve
xx.yy.2.gen - interarual time difference (ITD) and binaural correlation (BC) curves, not used for current analysis
xx.yy.3.itd - ITD curve
xx.yy.4.bf - frequency curve
xx.yy.5.iid - no sound played, to measure spontaneous firing, not used for current analysis
HRTF_Wagner_Lab contains the HRTF data that was published in von Campenhausen and Wagner (2006). Permission to use and publish given by Dr. Wagner. raw_data contains data from 5 birds. Subfolders are for different conditions:
normal- normal
nocheniger - without auricle feathers (not used here)
nurMikro - without ruff feathers (not used here)
weniger - unsure (not used here)
ohne - without auricle and ruff feathers
Results contain the HRIRs passed through HRIR_Berechnung_translated.m, which are used by Matlab code (below). Code in this folder are from the Wagner lab, and are included (but not described below). Warning that most of the code is written in German.
Python Code
Scripts written in Python and run on Jupyter Notebook used for figures 2-4, 6-7. The code is used to assess tuning curves and analysis thereof, described in the manuscript.
Read_XDPhys_Raw_Data - for a given date/neuron, will output best ITD and half maxes, best frequency and half maxes, best ILD, and fits of Gaussian and Sigmoids onto the ILD curve (helps to determine neural identity). There are sometimes irregularites due to noise, so best not to automate this to run through all the neurons. Excel sheets contain note these cases.
pypxphys - used to extract spike times and counts from each file, used by Read_XDPhys_Raw_Data.
Get_Spike_Counts - the analysis underlying Read_XDPhys_Raw_Data.
Shadron_Pena_2022_Remake_Figures - uses excel sheets (see below) to recreate analysis and figures in manuscript.
Matlab Code
Scripts written in Matlab used for figures 1 and 5. The code uses HRIRs to determine ITD reliability and subsequent analysis.
Shadron_Pena_Fig1.m - Runs code to get figure 1. HRTF analysis assesses the s.d. of interaural phase difference (IPD) across locations and frequencies when masker sounds are present.
Shadron_Pena_Fig5.m - Similar to Shadron_Pena_Fig1, but no masker is present in analysis. Just assesses the spatial tuning of a model frontally-tuned neuron.
circstd.m - get circular s.d.
circmean.m - get circular mean
ERBFilterBank.m - Gammatone filter bank that models the owl's cochlea
f_gsafecmap.m - colors
Excel
Contain meta data for each neuron and outputs from Read_XDPhys_Raw_Data. Blank cells indicate that Read_XDPhys_Raw_Data couldn't provide a clear code, usually due to either low spike counts or high levels of noise (electrical or biological). The column "Use?" for these neurons is set to "no", indicating that they are not used in analysis.
Cazettes_2014_normal.xlsx - data from Cazettes et al., 2014. Raw data from this paper is not included here.
Shadron_Pena_2022_ruff_removed.xlsx - data from ruff-removed owls (#44 and #46).
Shadron_Pena_2022_juvenile.xlsx - data from juvenile owls (#47 and #48). Also includes one recording when one owl was an adult on a separate page, but that data is not used for this analysis.
Concerns or comments can be sent to keanu.shadron@einsteinmed.edu or jose.pena@einsteinmed.edu
