neurotic 1.5.0

Installing neurotic

neurotic requires Python 3.6 or later.

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

Windows users who installed using a standalone installer or conda should be able to launch neurotic from the Start Menu.

Mac and Linux users, as well as Windows users, can use the Terminal, command line, or Anaconda Prompt to start the app:

1. Depending on your operating system, installation method, and environment settings, you may be able to just launch the app from the command line by invoking its name:

   neurotic

2. If the command is not recognized, you likely need to first activate the conda environment into which the app was installed:

   conda activate <environment name>

   If you used a standalone installer, the environment name may be “neurotic”, so you would use

   conda activate neurotic

   You can then try again invoking the app name:

   neurotic

Several examples are provided. Select one, download the associated data using the “Download data” menu action, 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 examples or to make changes to it, click “Edit metadata”. See Configuring Metadata for details about the format.

If you like working with Jupyter notebooks, you can launch an example notebook that 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-debug] [--lazy | --no-lazy]
                [--thick-traces | --no-thick-traces]
                [--show-datetime | --no-show-datetime]
                [--ui-scale {tiny,small,medium,large,huge}]
                [--theme {light,dark,original,printer-friendly}]
                [--use-factory-defaults] [--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-debug            disable detailed log messages for debugging (default)
  --lazy                enable fast loading (default)
  --no-lazy             disable fast loading
  --thick-traces        enable support for traces with thick lines, which has
                        a performance cost
  --no-thick-traces     disable support for traces with thick lines (default)
  --show-datetime       display the real-world date and time, which may be
                        inaccurate depending on file type and acquisition
                        software
  --no-show-datetime    do not display the real-world date and time (default)
  --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)
  --use-factory-defaults
                        start with "factory default" settings, ignoring other
                        args and your global config file

alternative modes:
  --launch-example-notebook
                        launch Jupyter with an example notebook instead of
                        starting the standalone app (other args will be
                        ignored)

Defaults for arguments and options can be changed in a global config file,
.neurotic\neurotic-config.txt, located in your home directory.

Citing neurotic

To cite neurotic in your publication, please refer to:

Gill, J. P., Garcia, S., Ting, L. H., Wu, M., & Chiel, H. J. (2020). neurotic: Neuroscience Tool for Interactive Characterization. eNeuro, 7(3). https://doi.org/10.1523/ENEURO.0085-20.2020

Specific versions of the software can be cited from archives at Zenodo.

Documentation

For detailed information on configuring metadata, working examples, the API reference guide, release notes, and more, see the Documentation.