shenoy-lab-to-nwb

This repository hosts conversion pipelines and analysis/visualization pipelines for datasets associated with 3 experiments at Shenoy Lab, Stanford University.

1. Conversion of center-out-reaching task. Datasets associated with the paper: Even-Chen N*, Sheffer B*, Vyas S, Ryu SI, Shenoy KV (2019) Structure and variability of delay activity in premotor cortex. PLoS Computational Biology. 15(2): e1006808
2. Conversion of electrophysiology/behavioral datasets of Neuropixels implanted in Monkeys.
3. Conversion of maze-task. Datasets of the paper: Churchland MM*, Cunningham JP*, Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV (2012) Neural population dynamics during reaching. Nature. 487:51-56

Instructions to directly stream nwb file from DANDI:

1. This conda environment contains only those files necessary to visualize an NWB file hosted on DANDI hub. Files for the aims 3 (maze task) are here and for aim 1 (center out task in in monkeys) is here

git clone https://github.com/catalystneuro/shenoy-lab-to-nwb.git
cd shenoy_lab_to_nwb
conda env create -f environment.yml
conda activate shenoy_lab_nwb

2. Open the jupyter notebook:

# add the conda environment to show up in a jupyter notebook
python -m ipykernel install --user --name=shenoy_lab_nwb
cd nwb_usage/
jupyter notebok analysis_script.ipynb

Intructions to convert datasets to NWB:

Each of the three aims have a folder that houses the conversion modules and conversion_scipt.py. The folder structure each conversion script expects is like on this google drive