https://github.com/catalystneuro/najafi-2018-nwb

Conversion of Churchland's dataset to NWB 2.0 format

https://github.com/catalystneuro/najafi-2018-nwb

Repository

Conversion of Churchland's dataset to NWB 2.0 format

https://github.com/catalystneuro/najafi-2018-nwb/blob/master/

# najafi-2018-nwb

This project presents the data accompanying the paper
> Farzaneh Najafi, Gamaleldin F Elsayed, Robin Cao, Eftychios Pnevmatikakis, Peter E Latham, John Cunningham, Anne K Churchland. "Excitatory and inhibitory subnetworks are equally selective during decision-making and emerge simultaneously during learning" bioRxiv (2018): 354340.

https://doi.org/10.1101/354340

The original data are available from Cold Spring Harbor Laboratory:  http://repository.cshl.edu/36980/

# Converting the original data
The data download instructions are for a Unix-family OS such as Linux or Mac OS with Python 3.7+ on the system path as `python3`. 

## Clone this repository and download the data
In the terminal window, git clone

```console
$ git clone https://github.com/vathes/najafi-2018-nwb.git
$ cd najafi-2018-nwb
``` 

## Download the original data 

The following command will download the original data from CSHL (~70 GB).
```console 
$ mkdir data
$ python3 scripts/download.py
```
This may take several hours.  If the download is interrupted, simply re-run `download.py` and it will pick up where it left.

Verify that all 18 files have downloaded.
```console
$ ls data
FN_dataSharing.tgz-aa	FN_dataSharing.tgz-af	FN_dataSharing.tgz-ak	FN_dataSharing.tgz-ap
FN_dataSharing.tgz-ab	FN_dataSharing.tgz-ag	FN_dataSharing.tgz-al	FN_dataSharing.tgz-aq
FN_dataSharing.tgz-ac	FN_dataSharing.tgz-ah	FN_dataSharing.tgz-am	FN_dataSharing.tgz-ar
FN_dataSharing.tgz-ad	FN_dataSharing.tgz-ai	FN_dataSharing.tgz-an
FN_dataSharing.tgz-ae	FN_dataSharing.tgz-aj	FN_dataSharing.tgz-ao
```

Now unpack the tar files:

```console
$ cat data/FN_dataSharing.tgz-a* | tar -C data -xzf -
```

Verify that the data have unpacked:

```console
$ ls data/FN_dataSharing
bag-info.txt		data			manifest-sha256.txt	tagmanifest-sha256.txt
bagit.txt		manifest-md5.txt	tagmanifest-md5.txt

$ ls data/FN_dataSharing/data
metaData  metaData~  mouse1_fni16  mouse2_fni17  mouse3_fni18  mouse4_fni19
```

The `FN_dataSharing` data directory includes a `manifest.txt` file specifying all available data, and a data folder containing the `.mat` files.


## Conversion to NWB 2.0
The following command will convert the dataset into the NWB 2.0 format (See https://neurodatawithoutborders.github.io/)

```console
$ mkdir data/FN_dataSharing/nwb
$ python3 scripts/convert_to_nwb.py
```

The `convert_to_nwb` uses the configuration file `conversion_config.json` to specify the *manifest* file, the output file, and general data about the experiments.

An example content of the *.json* config file is as follow: 
```json
{
	"manifest": "data/manifest-md5.txt",
	"general": 
		{
			"experimenter" : "Farzaneh Najafi",
			"institution" : "Cold Spring Harbor Laboratory",
			"related_publications" : "https://doi.org/10.1101/354340"
		},
	"output_dir" : "data/FN_dataSharing/nwb"
}
```

The converted NWB files will be saved in the `output_dir` directory. 

# Showcase work with NWB:N files
This repository will contain Jupyter Notebook demonstrating how to navigate and query the dataset. 

See this [Jupyter Notebook](https://github.com/ttngu207/najafi-2018-nwb/blob/master/notebooks/Najafi-2018_example.ipynb) for a tutorial on using [**PyNWB**](https://pynwb.readthedocs.io/en/latest/) API to access NWB 2.0 data, to process and plot some of the figures presented in this study (https://doi.org/10.1101/354340). 

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