henke_et_al
Data used in the manuscript "Distributed coding of duration in rodent prefrontal cortex
during time reproduction" Henke et al. eLife.
Extracellular recordings from neurons in gerbil (Meriones unguiculatus) medial prefrontal cortex.
Data was acquired with chronically implanted tetrodes from three animals.
Overview of the contents
Each folder contains the data of one of the three gerbils used in the study.
Each file in the folders contains data of a single neuron recorded in one recording session.
File names are composed of animalID_sessionNumber_tetrodeNumber_neuronNumber.nix.
A data file comprises
- spike train of the neuron, i.e. array with spike times across the whole session
- measurement phase: time points of stimulus onset and the stimulus duration
(stimulus onsets and stimuli)
- reproduction phase: time points of reproduction onset and the reproduced duration
(reproduction onsets and reproductions)
- reward information for each trial, i.e. rewards, 0 - no reward, 1 - reward
- width of the feedback range in each trial
- running distance covered during the session. Note that the position of the animal
was only tracked during the reproduction phase. In the other trial phases, the animal's
position was not tracked but may have been reset, leading to jump-like artifacts in the
covered distance, which should be ignored during analysis. These jumps are not due to
the behavior of the animals. See also Figure 1–Figure supplement 1.
In some trials technical problems occurred, e.g., the treadmill stuck. These were left
out of in the arrays comprising trial information like time points. The spike times
and distance covered still include these parts, since they are continuous signals
that extend throughout the whole session.
Data is saved in nix format, which uses
HDF5 as a backend, see
Stoewer A, Kellner CJ, Benda J, Wachtler T and Grewe J (2014).
File format and library for neuroscience data and metadata. Front. Neuroinform.
Conference Abstract: Neuroinformatics 2014. https://doi.org/10.3389/conf.fninf.2014.18.00027
Basic usage
Nix uses HDF5 as a backend and you may have a first look at the data
with an HDF viewer.
Basic code to load one of the nix files and plot the data contained is provided
in load_data.py. The script takes the name of the file to load as a command
line parameter. Run the script from IPython with
%run load_data <folder/file_name.nix>.
load_data.py was written and tested for Python 3 (3.8) and
NIXPY 1.5.2.
Author
Kay Thurley, thurley@bio.lmu.de
Kay Thurley