movshon-lab-to-nwb

NWB conversion scripts and tutorials. A collaboration with Movshon Lab.

• Blackrock processing through SpikeInterface
• Blackrock conversion to NWB
• OpenEphys processing through SpikeInterface
• OpenEphys conversion to NWB
• SpikeGLX processing through SpikeInterface
• SpikeGLX conversion to NWB
• Expo conversion to NWB

Install

To clone the repository and set up a conda environment, do:

$ git clone https://github.com/catalystneuro/movshon-lab-to-nwb
$ conda env create -f movshon-lab-to-nwb/make_env.yml
$ source activate env_movshon

Alternatively, to install directly in an existing environment:

$ pip install movshon-lab-to-nwb

Spike sorting

SpikeInterface examples for each experiment can be found in tutorials.

Check SpikeInterface documentation for a list of available spike sorters and how to install them.

NWB conversion

After activating the correct environment, the conversion function can be used in different forms:

1. Imported and run from a python script:
Detailed and simple examples for each experiment can be found in tutorials

2. Graphical User Interface:
To use the GUI, first install nwb-web-gui:

$ pip install nwb-web-gui

The GUI can be run from the terminal:

$ nwbgui-movshon [experiment_name]

Current options for experiment names are: blackrock, openephys, and spikeglx. The NWB Web GUI should open in your browser. If it does not open automatically (and no error messages were printed in your terminal), just open your browser and navigate to localhost:5000.

The GUI eases the task of editing the metadata of the resulting nwb file, it is integrated with the conversion module (conversion on-click) and allows for quick visual exploration the data in the end file with nwb-jupyter-widgets.

4. Tutorial:
At tutorials you can also find Jupyter notebooks with the step-by-step process of conversion.