datajoint-company / DJ-NWB-Gao-2018

DataJoint data pipeline and NWB conversion for Gao et al., 2018 from Li Lab.

Gao et al., 2018

This repository sets up the data pipeline for Gao et al., 2018. A cortico-cerebellar loop for motor planning, replicates a subset of the major results (Figure 2c, 3e-f, and 4i), and exports the data into nwb files.

Link to the publication: https://www.nature.com/articles/s41586-018-0633-x

Link to the original data: http://crcns.org/data-sets/motor-cortex/alm-4/

Link to the exported NWB files: https://drive.google.com/drive/u/1/folders/1I9Sur9TRzts_u35OP_XEFlMYnKBJfCPS

Access to view the notebook: https://nbviewer.jupyter.org/github/vathes/gao2018/blob/master/notebooks/Gao-2018-examples.ipynb?flush_cache=true

This study revealed a cortical-cerebellar loop for motor planning with electrophysiological recording and optogenetics perturbations, within a behavioral paradigm of delayed somatosensory discrimination task. The two brain areas studied were anterior lateral motor cortex (ALM), and cerebellar nuclei (CN). The study first shows that both ALM and CN are responsive during the delay period (Fig 2), and are selective to trials in one location, suggesting their roles in motor planning. Inibibition of either ALM or CN disrupted the selectivity of the other area (Fig 3). Finally, the study compared the effect of activating Dentate and Fastigial cerebellar nuclei on the discriminability of the ALM neurons (Fig 4), and found that Fastigial nucleus is more important for ALM discriminability during the delay period.

Combined schemas:

Instrunctions on setting up the pipeline and notebook locally.

1. This repo is set up with docker, install docker and docker-compose.

2. Set up your local mysql server.

3. git clone https://github.com/vathes/gao2018.git

4. Inside the repository, open a file called .env and paste in the following information and save the file.

   DJ_HOST=host.docker.internal
   DJ_USER=YOUR_USER_NAME
   DJ_PASS=YOUR_PASSWORD
   

5. Create a directory called data, and download the data from the link http://crcns.org/data-sets/motor-cortex/alm-4/, put the two folders datafile and datafile 2 inside the data directory

6. Run the bash script with command bash gao2018.sh The whole script takes a few hours to run. After it's done, you will find nwb files in the directory data/NWB 2.0

7. To run the notebook, open your browser and put in http://localhost:8892/notebooks/Gao-2018-examples.ipynb