neurotic 1.4.0

Installing neurotic

neurotic requires Python 3.6 or later.

Note that the latest release of one of neurotic’s dependencies, pyqtgraph 0.10.0, is incompatible with Python 3.8 or later on Windows unless that dependency is installed via conda-forge (recommended method) (details).

conda install -c conda-forge neurotic

pip install neurotic

conda install -c conda-forge av

Updating neurotic

The recommended method of updating neurotic depends on the original method of installation.

If you are unsure what method you used, updating using conda or pip is likely to work. Standalone installers may be safe too, though this could lead to having multiple version installed simultaneously.

conda update -c conda-forge neurotic

conda update -c conda-forge neurotic

pip install -U neurotic

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

pip install -U git+https://github.com/NeuralEnsemble/ephyviewer.git

Getting Started

If you installed neurotic into a conda environment, first activate it:

conda activate <environment name>

Launch the app from the command line:

neurotic

A simple example is provided. Select the “example dataset”, download the associated data (~7 MB), and then click “Launch”. See User Interface for help with navigation.

Disabling “Fast loading” before launch will enable additional features including amplitude-threshold spike detection and signal filtering.

To inspect the metadata file associated with the example or to make changes to it, click “Edit metadata”. See Configuring Metadata for details about the format.

If you prefer Jupyter notebooks, you can launch an example notebook instead, which includes a tutorial for using neurotic’s API:

neurotic --launch-example-notebook

The command line interface accepts other arguments too:

usage: neurotic [-h] [-V] [--debug] [--no-lazy] [--thick-traces]
                [--show-datetime] [--ui-scale {tiny,small,medium,large,huge}]
                [--theme {light,dark,original,printer-friendly}]
                [--launch-example-notebook]
                [file] [dataset]

neurotic lets you curate, visualize, annotate, and share your behavioral ephys
data.

positional arguments:
  file                  the path to a metadata YAML file (default: an example
                        file)
  dataset               the name of a dataset in the metadata file to select
                        initially (default: the first entry in the metadata
                        file)

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         show program's version number and exit
  --debug               enable detailed log messages for debugging
  --no-lazy             do not use fast loading (default: use fast loading)
  --thick-traces        enable support for traces with thick lines, which has
                        a performance cost (default: disable thick line
                        support)
  --show-datetime       display the real-world date and time, which may be
                        inaccurate depending on file type and acquisition
                        software (default: do not display)
  --ui-scale {tiny,small,medium,large,huge}
                        the scale of user interface elements, such as text
                        (default: medium)
  --theme {light,dark,original,printer-friendly}
                        a color theme for the GUI (default: light)
  --launch-example-notebook
                        launch Jupyter with an example notebook instead of
                        starting the standalone app (other args will be
                        ignored)