fee-lab-to-nwb

NWB conversion scripts for the Fee Lab at MIT data to the Neurodata Without Borders data format.

Clone and install

To run the conversion some basic machinery is needed: python, git and pip. For most users, we recommend you to install conda (installation instructions) as it contains all the required machinery in a single and simple installation. If your system is windows you might also need to install git (installation instructions) to interact with this repository.

From a terminal (note that conda should install one in your system) you can do the following:

git clone https://github.com/catalystneuro/fee-lab-to-nwb
cd fee-lab-to-nwb
conda env create --file make_conda_env.yml
conda activate fee_lab_to_nwb_env

This creates a conda environment which isolates the conversion from your system. We recommend that you run all your conversion related tasks and analysis from that environment to minimize the interference of this code with your own system.

Alternatively, if you want to avoid conda altogether (for example if you use another virtual environment tool) you can install the repository with the following commands using only pip:

git clone https://github.com/catalystneuro/fee-lab-to-nwb
cd fee-lab-to-nwb
pip install -e .

Note: both of the methods above install the repository in editable mode

You can also install the latest release of the package with pip:

pip install fee-lab-to-nwb

Repository structure

Each conversion is organized in a directory of its own in the src directory:

fee-lab-to-nwb/
├── LICENSE
├── make_env.yml
├── pyproject.toml
├── README.md
├── requirements.txt
├── setup.py
└── src
    ├── fee_lab_to_nwb
    │   ├── general_interfaces
    │   └── scherrer_ophys
    │       ├── convert_session.py
    │       ├── metadata.yml
    │       ├── notes.md
    │       ├── requirements.txt
    │       ├── scherrerophysimagingextractor.py
    │       ├── scherrerophysimaginginterface.py
    │       ├── scherrerophysnwbconverter.py
    │       └── __init__.py

    └── __init__.py

For the conversion scherrer_ophys you can find a directory located in src/fee-lab-to-nwb/scherrer_ophys. Inside the conversion directory you can find the following files:

• convert_session.py: this is the central script that you must run in order to perform the full conversion.
• metadata.yml: metadata in yaml format for this specific conversion.
• notes.md: notes and comments about the source data.
• requirements.txt: dependencies specific to this conversion.

The other files that are necessary this specific conversion:

• scherrerophysimagingextractor.py: the extractor for a single ophys file.
• scherrerophysimaginginterface.py: the interface for this ophys dataset.
• scherrerophysnwbconverter.py: the place where the NWBConverter class is defined.

The directory might contain other files that are necessary for the conversion but those are the central ones.

Running a specific conversion

To run a specific conversion, you might need to install first some conversion specific dependencies that are located in each conversion directory:

pip install -r src/fee_lab_to_nwb/scherrer_ophys/requirements.txt

You can run a specific conversion with the following command:

python src/fee_lab_to_nwb/scherrer_ophys/convert_session.py

Note that when installing fee-lab-to-nwb from pip the conversion script will be located wherever pip installs site packages. In this case you will need to manually copy/paste usage scripts to a location where you want to use them.

Questions during a conversion

If you encounter any problems during the conversion, open an issue, and we will help you!