Interactive Jupyter notebooks to accompany
NJ Sofroniew*, YA Vlasov*, SA Hires, J Freeman, & K Svoboda (2015) Neural coding in barrel cortex during whisker-guided locomotion, eLife, 10.7554/eLife.12559
Read the published article on eLife
Download the supporting data from Zenodo
Launch interactive notebooks by clicking the binder badge
The data anlaysis is split into 5 notebooks, three for the calcium imaging analsis, and two for the electrophysiology analysis, representing progressively refined stages of preprocessing and analysis. There is one additional helper module located inside the helper folder. All the raw data is stored and made publicly available on Amazon S3 in the bucket neuro.datasets under the directory svoboda.lab/tactile.coding. See the notebooks for examples of accessing the data.
Loads in the raw pixels from the calcium imaging for each experiment , the manually drawn sources (ROIs/neurons) and the behavioural covariates. The notebook takes you through loading the data, a pixelwise regression analysis, and computing the normalized activity (DF/F) traces for each neuron. Running this notebook in interactive mode is currently not supported
Loads in the activity traces of each neuron and the behavioural covariates and computes tuning curves and summary statistics for each neurons. The results get saved in a table.
Loads in the summary table for imaging data and plots results.
Loads in the spike times of each neuron, after spike sorting, and the behavioural covariates and computes tuning curves and summary statistics for each neurons. The results get saved in a table.
Loads in the summary table for ephys data and plots results.