neurotic 0.4.2

Curate, visualize, and annotate your behavioral ephys data using Python

neurotic is an app that allows you to easily review and annotate your electrophysiology data and simultaneously captured video. It is an easy way to load your Neo-compatible data into ephyviewer without doing any programming.

You organize your data sets in a YAML file like this:

my favorite dataset:
    description: This time it actually worked!

    data_dir:           C:/local_dir_containing_files
    remote_data_dir:    http://myserver/remote_dir_containing_downloadable_files  # optional
    data_file:          data.axgx
    video_file:         video.mp4
    # etc

    video_offset: -3.4  # seconds between start of video and data acq
    epoch_encoder_possible_labels:
        - label01
        - label02
    plots:
        - channel: I2
          ylim: [-30, 30]
        - channel: RN
          ylim: [-60, 60]
        # etc

    filters:  # used only if fast loading is off (lazy=False)
        - channel: Force
          lowpass: 50
        # etc
    amplitude_discriminators:  # used only if fast loading is off (lazy=False)
        - name: B3 neuron
          channel: BN2
          amplitude: [50, 100]
        # etc

Open your file in the app and choose a data set. If the data and video files aren’t already on your local computer, the app can download them for you. Finally, click launch and the app will use a standard viewer layout to display your data to you using ephyviewer.

(Pictured above is a voracious Aplysia californica making the researcher very happy.)

The viewers are easy and intuitive to navigate:

• Pressing the play button will scroll through the data and video in real time, or at a higher or lower rate if the speed parameter is changed.

• The arrow/WASD keys allow you to step through time.

• Right-clicking and dragging right or left will contract or expand time to show more or less at once.

• Scrolling the mouse wheel in the trace viewer or the video viewer will zoom.

• The “epoch encoder” can be used to block out periods of time during which something interesting is happening for later review or further analysis (saved to a CSV file).

• All panels can be hidden, undocked, or repositioned on the fly.

Electrophysiologists should still find this tool useful even if they don’t need video synchronization.

git clone https://github.com/jpgill86/neurotic.git
conda env create -f neurotic/environment.yml -n neurotic

git clone https://github.com/jpgill86/neurotic.git
pip install -U -r neurotic/requirements.txt

conda install -c conda-forge av

pip install neurotic

pip install git+https://github.com/jpgill86/neurotic.git

python setup.py install

neurotic

neurotic --help