murthy-lab-to-nwb

NWB conversion scripts for Murthy lab 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 install. 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/murthy-lab-to-nwb
cd murthy-lab-to-nwb
conda env create --file make_env.yml
conda activate murthy-lab-to-nwb-env

This create 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 intereference 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/murthy-lab-to-nwb
cd murthy-lab-to-nwb
pip install -e .

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

Pip installation

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

pip install murthy-lab-to-nwb

Repository structure

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

murthy-lab-to-nwb/
├── LICENSE
├── make_env.yml
├── pyproject.toml
├── README.md
├── requirements.txt
├── setup.py
└── src
    ├── __init__.py
    └── murthy_lab_to_nwb
        ├── __init__.py
        ├── cowley2022mapping
        │   ├── cowley2022mapping_courtship_convert_session.py
        │   ├── cowley2022mapping_imaging_convert_session.py
        │   ├── cowley2022mapping_nwbconverter.py
        │   ├── cowley2022mapping_requirements.txt
        │   ├── __init__.py
        │   ├── interfaces
        │   ├── metadata
        │   ├── utils
        │   ├── widget_demostration_courtship.ipynb
        │   └── widget_demostration_imaging.ipynb
        └── li2022ecephys
            ├── __init__.py
            ├── li2022ecephys_convert_session.py
            ├── li2022ecephysinterface.py
            ├── li2022ecephysnwbconverter.py
            └── li2022ecephys.yaml_.py
            └── __init__.py

For example, for the conversion cowley2022mapping you can find a directory located in src/murthy-lab-to-nwb/cowley2022mapping. Inside each conversion directory you can find the following files:

• cowley2022mapping_courtship_convert_session.py: this runs a nwb conversion for a courtship session.
• cowley2022mapping_imaging_convert_session.py: this runs a nwb conversion for an imaging session.
• cowley2022mapping_requirements.txt: dependencies specific to this conversion specifically.
• widget_demostration_courtship.ipynb jupyter notebook with visulization tools for the courtship nwb file
• widget_demostration_imaging.ipynb jupyter notebook with visulization tools for the imaging nwb file

Plus the following directories:

• interfaces directory which holds the interfaces required in this conversion.
• metadata directory which holds the editable yaml metadata files to add extra metadata to the conversions.
• utils miscellaneous utilities for the conversion.

Running a specific conversion

To run a specific conversion for a full session you can see here the following examples

python src/murthy_lab_to_nwb/cowley2022mapping/cowley2022mapping_courtship_convert_session.py
python src/murthy_lab_to_nwb/cowley2022mapping/cowley2022mapping_imaging_convert_session.py
python src/murthy_lab_to_nwb/li2022ecephys/li2022ecephys_convert_session.py

You might need to install first some conversion specific dependencies that are located in each conversion directory:

pip install -r src/murthy_lab_to_nwb/cowley2022mapping/cowley2022mapping_requirements.txt