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NWB conversion scripts and tutorials.

Project description

jaeger-lab-to-nwb

Convert Jaeger lab data to NWB format.

Currently includes:

  • FRET optical imaging (rsd)
  • Intan electrophysiology (rhd)
  • Labview behavioral data (txt)
  • Optogenetics stimulation data (txt)
  • Treadmill behavior (csv)
  • Bpod behavioral data (mat)

Authors: Luiz Tauffer and Ben Dichter

Install

Create a separate environment:

$ conda create -n env_jaeger python=3.7 pip

Activate environment and install dependencies

$ conda activate env_jaeger
$ pip install jaeger-lab-to-nwb

Use

1. Imported and run from a python script:
Examples for each experiment can be found here

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-jaeger [experiment_name]

Current options for experiment names are: fret, labview, treadmill and bpod. 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.

Project details


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