neurotic: NEUROscience Tool for Interactive Characterization¶

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

Distributions:
Source Code:
Tests Status:
Citing:

Version: 1.5.1.dev0+git.32d131e (other versions)

neurotic is an app for Windows, macOS, and Linux 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 (see neo.io for file formats) into ephyviewer without doing any programming. Share a single metadata file with your colleagues and they too will quickly be looking at the same datasets!

Table of Contents¶

Overview¶

To use neurotic, first organize your datasets in a metadata file like this (see Configuring Metadata):

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
          units: uV
          amplitude: [50, 100]
        # etc

another dataset:
    # etc

Open your metadata file in neurotic and choose a dataset. If the data and video files aren’t already on your local computer, the app can download them for you, even from a password-protected server or from Google Drive. Finally, click launch and the app will use a standard viewer layout to display your data to you using ephyviewer.

In the screenshot above, the video frame shows a voracious sea slug (Aplysia californica) swallowing a strip of unbreakable seaweed attached to a force transducer. Implanted electrodes recorded from a muscle and the major nerves controlling feeding. The epoch encoder was used to mark the times when seaweed moved into the mouth. Spikes corresponding to activity of identified neurons were detected by neurotic using customizable parameters.

The viewers are easy and intuitive to navigate (see User Interface):

Pressing the play button will scroll through your 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 in variable increments.
Jump to a time by clicking on an event in the event list or a table entry in the epoch encoder.
To show more or less time at once, right-click and drag right or left to contract or expand time.
Scroll the mouse wheel in the trace viewer or video viewer to 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, stacked, or repositioned on the fly.

Electrophysiologists will find this tool useful even if they don’t need the video synchronization feature!

Portability is easy with neurotic! Use relative paths in your metadata file along with a remotely accessible data store such as GIN or a Shared Drive on Google Drive to make your metadata file fully portable. The same metadata file can be copied to a different computer, and downloaded files will automatically be saved to the right place. Data stores can be password protected and neurotic will prompt you for a user name and password. This makes it easy to share the neurotic experience with your colleagues! 🤪

Installing neurotic¶

neurotic requires Python 3.7 or later.

Standalone Installers (recommended for beginners)¶

Downloadable installers make installing neurotic easy for beginners. They can be downloaded from the GitHub Releases page:

👉 Download installers here (listed under “Assets”) 👈

These installers are intended for users who do not want to independently install Python or conda just to use neurotic. They will install neurotic and everything it needs (including a fully contained Python environment) into a dedicated directory on your computer. On Windows, the installer will also create a Start Menu shortcut for launching the app.

For developers, a recipe for building new installers using conda constructor is maintained here: constructor recipe.

Alternate Method: conda (recommended for Pythonistas)¶

conda users can install neurotic and all of its dependencies with one command:

conda install -c conda-forge neurotic

On Windows, this will also create a Start Menu shortcut for launching the app.

Alternate Method: pip¶

Install neurotic from PyPI using

pip install neurotic

Note that installation via pip skips one dependency: PyAV, which is required for displaying videos, and without which neurotic will ignore videos. PyAV is not easily installed with pip on some systems, especially Windows. The easiest way to separately install PyAV is using conda:

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.

Updating with Standalone Installers¶

If you previously installed neurotic using a standalone installer, you may install a newer version using another installer, either into a different directory or by first uninstalling the old version. Installers can be downloaded from the GitHub Releases page:

👉 Download installers here (listed under “Assets”) 👈

Alternatively, if a new installer is not currently available for your platform, or if you would just like a much faster method, you may use the command line tools provided by the installer (via the “Anaconda Prompt” on Windows, or the Terminal on macOS and Linux):

conda update -c conda-forge neurotic

Updating with conda¶

If you installed neurotic with conda, you can update to the latest release using

conda update -c conda-forge neurotic

Updating with pip¶

If you installed neurotic using pip, you can update to the latest release available on PyPI using

pip install -U neurotic

Development Version¶

If you are interested in trying new, unreleased features of neurotic, you may install the latest development version from GitHub using

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

Note that if you install the development version, you may also need the latest development version of ephyviewer, which you can get using

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:

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
```
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.

Configuring Metadata¶

To load your data with neurotic, you must organize them in one or more YAML files, called metadata files.

YAML files are very sensitive to punctuation and indentation, so mind those details carefully! Importantly, the tab character cannot be used for indentation; use spaces instead. There are many free websites that can validate YAML for you.

You may include comments in your metadata file, which should begin with #.

Top-Level Organization¶

Datasets listed within the same metadata file must be given unique names, which may include spaces. The special name neurotic_config is reserved for neurotic configuration settings and cannot be used for datasets.

In addition to names, a long description can be provided for each dataset.

Details pertaining to each dataset, including the description, are nested beneath the dataset name using indentation. You may need to use double quotes around names, descriptions, or other text if they contain special characters (such as : or #) or are composed only of numbers (such as a date).

experiment 2020-01-01:
    description: Both the name and description will be visible when neurotic loads the metadata
    # other details about this dataset will go here

my favorite dataset:
    description: This time it actually worked!
    # other details about this dataset will go here

Specifying Data Locations¶

Within a dataset’s YAML block, paths to data and video files should be provided.

All files associated with a dataset should be collected into a single directory. A path to the local copy of this directory can be provided using the data_dir key. You may specify data_dir as an absolute path (e.g., C:\Users\me\folder) or as a path relative to the metadata file (e.g., folder). If left unspecified, the directory containing the metadata file is used.

Paths to individual files within the dataset are provided using keys listed below. These paths should be given relative to data_dir. If data_dir is flat (no subdirectories), these should be simply the file names.

Key	Description
`data_file`	A single Neo-compatible data file (see `neo.io` for file formats)
`video_file`	A video file that can be synchronized with `data_file`
`annotations_file`	A CSV file for read-only annotations
`epoch_encoder_file`	A CSV file for annotations writable by the epoch encoder
`tridesclous_file`	A CSV file output by tridesclous’s `DataIO.export_spikes`

Note that the annotations_file must contain exactly 4 columns with these headers: “Start (s)”, “End (s)”, “Type”, and “Label”.

The epoch_encoder_file must contain exactly 3 columns with these headers: “Start (s)”, “End (s)”, and “Type”. (The fourth column is missing because ephyviewer’s epoch encoder is currently unable to attach notes to individual epochs; this may be improved upon in the future.)

The tridesclous_file is described in more detail in tridesclous Spike Sorting Results.

Remote Data Available for Download¶

Data files must be stored on the local computer for neurotic to load them and display their contents. If the files are available for download from a remote server (e.g., a web site, an FTP server, or Google Drive), neurotic can be configured to download them for you to the local directory specified by data_dir if the files aren’t there already.

Specify the URL to the directory containing the data on the remote server using remote_data_dir. neurotic expects the local data_dir and the remote_data_dir to have the same structure and will mirror the remote_data_dir in the local data_dir when you download data (not a complete mirror, just the specified files).

For an example, consider the following:

my favorite dataset:
    data_dir:           C:\Users\me\folder
    remote_data_dir:    http://myserver/remote_folder
    data_file:          data.axgx
    video_file:         video.mp4

With a metadata file like this, the file paths data_file and video_file are appended to remote_data_dir to obtain the complete URLs for downloading these files, and they will be saved to the local data_dir.

If you have many datasets hosted by the same server, you can specify the server URL just once using the special remote_data_root key, which should be nested under the reserved name neurotic_config outside of any dataset’s YAML block. This allows you to provide for each dataset a partial URL to a folder in remote_data_dir which is relative to remote_data_root. For example:

neurotic_config:  # reserved name for global settings
    remote_data_root:   http://myserver

my favorite dataset:
    data_dir:           C:\Users\me\folder1
    remote_data_dir:    remote_folder1
    data_file:          data.axgx
    video_file:         video.mp4

another dataset:
    data_dir:           C:\Users\me\folder2
    remote_data_dir:    remote_folder2
    data_file:          data.axgx
    video_file:         video.mp4

Here, URLs to video files are composed by joining remote_data_root + remote_data_dir + video_file.

Recall that if data_dir is a relative path, it is assumed to be relative to the metadata file. In the example above, if the metadata file is located in C:\Users\me, the paths could be abbreviated:

neurotic_config:
    remote_data_root:   http://myserver

my favorite dataset:
    data_dir:           folder1
    remote_data_dir:    remote_folder1
    data_file:          data.axgx
    video_file:         video.mp4

another dataset:
    data_dir:           folder2
    remote_data_dir:    remote_folder2
    data_file:          data.axgx
    video_file:         video.mp4

Note

Portability is easy with neurotic! Use relative paths in your metadata file along with a remotely accessible data store such as GIN or a Shared Drive on Google Drive (see details below) to make your metadata file fully portable. The example above is a simple model of this style. A metadata file like this can be copied to a different computer, and downloaded files will automatically be saved to the right place. Data stores can be password protected and neurotic will prompt you for a user name and password. This makes it easy to share the neurotic experience with your colleagues! 🤪

URLs to Use with Google Drive¶

After completing some essential manual setup (see Configuring for Google Drive), neurotic can retrieve remote files from Google Drive using URL-like paths of the following form:

gdrive://<drive name>/<folder 1>/<...>/<folder N>/<file name>

The <drive name> may be “My Drive” for files located in a personal Google Drive, or it may be the name of a Shared Drive that the user has permission to access.

Note that these URL-like paths are not equivalent to ordinary URLs associated with Google Drive files, such as shareable links, which are composed of pseudorandom file IDs and do not reveal anything about the name of the file or the folders containing it. Instead, these URL-like paths allow you to structure your metadata with the file tree hierarchy in mind, so that relative paths can be used.

For example, with datasets stored in subdirectories “datasets/A”, “datasets/B”, etc., of a Shared Drive titled “Lab Project Data”, you could use this metadata to mirror the files locally:

neurotic_config:
    remote_data_root:   gdrive://Lab Project Data/datasets

Dataset A:
    data_dir:           A
    remote_data_dir:    A
    data_file:          data.axgx
    video_file:         video.mp4

Dataset B:
    data_dir:           B
    remote_data_dir:    B
    data_file:          data.axgx
    video_file:         video.mp4

URLs to Use with GIN¶

If you have data stored in a public repository on GIN, you can access it from a URL of this form:

https://gin.g-node.org/<username>/<reponame>/raw/master/<path>

For private repositories, you must use a different URL that takes advantage of the WebDAV protocol:

https://gin.g-node.org/<username>/<reponame>/_dav/<path>

The second form works with public repos too, but GIN login credentials are still required. Consequently, the first form is more convenient for public repos.

Global Configuration Settings¶

The top-level name neurotic_config is reserved for configuration settings that apply to all datasets or to the app itself. The following settings may be nested beneath neurotic_config.

Key	Description
`neurotic_version`	A version specification stating the version of neurotic required by the metadata. Presently, if the requirement is not met, only a warning is issued. Quotation marks around the spec are usually required.
`remote_data_root`	A URL prepended to each `remote_data_dir` that is not already a full URL (i.e., does not already begin with a protocol scheme like `https://`)

For example:

neurotic_config:
    neurotic_version:   '>=1.4,<2'
    remote_data_root:   http://myserver

my favorite dataset:
    # dataset details here

Data Reader (Neo) Settings¶

The electrophysiology file specified by data_file is read using Neo, which supports many file types. A complete list of the implemented formats can be found here: neo.io.

By default, neurotic will use the file extension of data_file to guess the file format and choose the appropriate Neo IO class for reading it. If the guess fails, you can force neurotic to use a different class by specifying the class name with the io_class parameter (all available classes are listed here: neo.io).

Some Neo IO classes accept additional arguments beyond just a filename (see the Neo docs for details: neo.io). You can specify these arguments in your metadata using the io_args parameter.

For example, suppose you have data stored in a plain text file that is missing a file extension. The neo.io.AsciiSignalIO class can read plain text files, but you must specify this manually using io_class because the extension is missing. You could do this and pass in supported arguments in the following way:

my favorite dataset:
    data_file: plain_text_file_without_file_extension

    io_class: AsciiSignalIO

    io_args:
        skiprows: 1 # skip header
        delimiter: ' ' # space-delimited
        t_start: 5 # sec
        sampling_rate: 1000 # Hz
        units: mV

Video Synchronization Parameters¶

Constant Offset¶

If data acquisition began with some delay after video capture began, provide a negative value for video_offset equal to the delay in seconds. If video capture began after the start of data acquisition, use a positive value. A value of zero will have no effect.

neurotic warns users about the risk of async if video_file is given but video_offset is not. To eliminate this warning for videos that have no delay, provide zero.

Frame Rate Correction¶

If the average frame rate reported by the video file is a little fast or slow, you may notice your video and data going out of sync late in a long experiment. You can provide the video_rate_correction parameter to fix this. The reported average frame rate of the video file will be multiplied by this factor to obtain a new frame rate used for playback. A value less than 1 will decrease the frame rate and shift video events to later times. A value greater than 1 will increase the frame rate and shift video events to earlier times. A value of 1 has no effect.

You can obtain a good estimate of what value to use by taking the amount of time between two events in the video and dividing by the amount of time between the same two events according to the data record (seen, for example, as synchronization pulses or as movement artifacts).

Discrete Desynchronization Events¶

If you paused data acquisition during your experiment while video capture was continuous, you can use the video_jumps parameter to correct for these discrete desynchronization events, assuming you have some means of reconstructing the timing. For each pause, provide an ordered pair of numbers in seconds: The first is the time according to data acquisition (not according to the video) when the pause occurred, and the second is the duration of the pause during which the video kept rolling.

For example:

my favorite dataset:
    video_file: video.mp4
    # etc

    video_jumps:
        # a list of ordered pairs containing:
        # (1) time in seconds when paused occurred according to DAQ
        # (2) duration of pause in seconds
        - [60, 10]
        - [120, 10]
        - [240, 10]

These values could correct for three 10-second pauses occurring at times 1:00, 2:00, 3:00 according to the DAQ, which would correspond to times 1:00, 2:10, 3:20 according to the video. The extra video frames captured during the pauses will be excised from playback so that the data and video remain synced.

neurotic will automatically suggest values for video_jumps if it reads an AxoGraph file that contains stops and restarts (only if video_jumps is not already specified).

Real-World Date and Time¶

The GUI can optionally display the real-world date and time. This feature is accurate only if the recording is continuous (no interruptions or pauses during recording) and the start time of the recording is known. Some data file formats may store the start time of the recording, in which case neurotic will use that information automatically. However, if the start time is missing or inaccurate, it can be specified in the metadata like this:

my favorite dataset:
    data_file: data.axgx
    rec_datetime: 2020-01-01 13:14:15
    # etc

Plot Parameters¶

Use the plots parameter to specify which signal channels from data_file you want plotted and how to scale them. Optionally, a color may be specified for channels using a single letter color code (e.g., 'b' for blue or 'k' for black) or a hexadecimal color code (e.g., '#1b9e77'; note that with PyQtGraph 0.13.0 and later, hexadecimal color codes must begin with #).

Consider the following example, and notice the use of hyphens and indentation for each channel.

my favorite dataset:
    data_file: data.axgx
    # etc

    plots:
        - channel: Extracellular
          ylabel: Buccal nerve 2 (BN2)
          units: uV
          ylim: [-150, 150]
          color: r

        - channel: Intracellular
          ylabel: B3 neuron
          units: mV
          ylim: [-100, 50]
          color: '#666666'

        - channel: Force
          units: mN
          ylim: [-10, 500]

This would plot the “Extracellular”, “Intracellular”, and “Force” channels from the data_file in the given order. ylabel is used to relabel a channel and is optional. The units and ylim parameters are used together to scale each signal such that the given range fits neatly between the traces above and below it. If units is not given, they are assumed to be microvolts for voltage signals and millinewtons for force signals. If ylim is not given, they default to [-120, 120] for voltages and [-10, 300] for forces.

If plots is not provided, all channels are plotted using the default ranges, except for channels that match these patterns: “Analog Input #*” and “Clock”. Channels with these names can be plotted if given explicitly by plots.

Time Range¶

The amount of time initially visible can be specified in seconds with t_width.

The position of the vertical line, which represents the current time in each plot, can be specified as a fraction of the plot range with past_fraction. A value of 0 places the vertical line at the left edge of each plot; consequently, everything plotted is “in the future”, occurring after the current time. A value of 1 places the vertical line at the right edge of each plot; consequently, everything plotted is “in the past”, coming before the current time. The default value of 0.3 causes the first 30% of the plot range to display “the past” and the last 70% to display “the future”.

Epoch Encoder Parameters¶

The labels available to the epoch encoder can be specified using epoch_encoder_possible_labels. (Additionally, they may be created on the fly using the “New label” button in the epoch encoder.)

For example:

my favorite dataset:
    epoch_encoder_file: epoch-encoder.csv
    # etc

    epoch_encoder_possible_labels:
        - label1
        - label2
        - label3

Filters¶

Highpass, lowpass, and bandpass filtering can be applied to signals using the filters parameter. Note that filters are only applied if fast loading is off (lazy=False).

Consider the following example, and notice the use of hyphens and indentation for each filter.

my favorite dataset:
    data_file: data.axgx
    # etc

    filters:  # used only if fast loading is off (lazy=False)

        - channel: Extracellular
          highpass: 300 # Hz
          lowpass: 500 # Hz

        - channel: Intracellular
          highpass: 300 # Hz

        - channel: Force
          lowpass: 50 # Hz

Filter cutoffs are given in hertz. Combining highpass and lowpass provides bandpass filtering.

Amplitude Discriminators¶

Spikes with peaks (or troughs) that fall within amplitude windows given by amplitude_discriminators can be automatically detected by neurotic on the basis of amplitude. Note that amplitude discriminators are only applied if fast loading is off (lazy=False).

Detected spikes are indicated on the signals with markers, and spike trains are displayed in a raster plot. Optionally, a color may be specified for an amplitude discriminator using a single letter color code (e.g., 'b' for blue or 'k' for black) or a hexadecimal color code (e.g., '#1b9e77'; note that with PyQtGraph 0.13.0 and later, hexadecimal color codes must begin with #).

The algorithm can detect either peaks or troughs in the signal. When both the lower and upper bounds for amplitude windows are positive, the default behavior is to detect peaks. When both are negative, the default is to detect troughs. These defaults can be overridden using type: trough or type: peak, respectively. This is useful when, for example, detecting subthreshold excitatory postsynaptic potentials. If the signs of the bounds differ, explicit specification of the type is required.

In addition to restricting spike detection for a given unit to an amplitude window, detection can also be limited in time to overlap with epochs with a given label.

Consider the following example, and notice the use of hyphens and indentation for each amplitude discriminator.

my favorite dataset:
    data_file: data.axgx
    # etc

    amplitude_discriminators:  # used only if fast loading is off (lazy=False)

        - name: Unit 1
          channel: Extracellular
          units: uV
          amplitude: [50, 150]
          color: r

        - name: Unit 2
          channel: Extracellular
          units: uV
          amplitude: [20, 50]
          epoch: Unit 2 activity
          color: '#e6ab02'

        - name: Unit 3
          channel: Intracellular
          units: mV
          amplitude: [-10, 60]
          type: peak

Here two units are detected on the “Extracellular” channel with different amplitude windows, and a third unit is detected on the “Intracellular” channel. On the “Extracellular” channel, any peaks between 50 and 150 microvolts will be tagged as a spike belonging to “Unit 1”. The discriminator for “Unit 2” detects smaller peaks, between 20 and 50 microvolts, and it provides the optional epoch parameter. This restricts detection of “Unit 2” to spikes within the amplitude window that occur at the same time as epochs labeled “Unit 2 activity”. These epochs can be created by the epoch encoder (reload required to rerun spike detection at launch-time), specified in the read-only annotations_file, or even be contained in the data_file if the format supports epochs. Finally, peaks between -10 and +60 millivolts will be detected on the “Intracellular” channel; because the signs of these bounds differ, the type (peak or trough) must be explicitly given.

tridesclous Spike Sorting Results¶

tridesclous is a sophisticated spike sorting toolkit. The results of a sorting process can be exported to a CSV file using tridesclous’s DataIO.export_spikes function. This file contains two columns: the first is the sample index of a spike, and the second is the ID for a cluster of spikes. If this file is specified with tridesclous_file, then a mapping from the cluster IDs to channels must be provided with tridesclous_channels.

In the following example, notice the lack of hyphens:

my favorite dataset:
    data_file: data.axgx
    tridesclous_file: spikes.csv
    # etc

    tridesclous_channels:
        0: [Channel A, Channel B]
        1: [Channel A]
        2: [Channel B]
        3: [Channel B]
        # etc

Here numeric cluster IDs are paired with a list of channels found in data_file on which the spikes were detected.

To show only a subset of clusters or to merge clusters, add the tridesclous_merge parameter.

In this example, note again the punctuation:

my favorite dataset:
    data_file: data.axgx
    tridesclous_file: spikes.csv
    # etc

    tridesclous_channels:
        0: [Channel A, Channel B]
        1: [Channel A]
        2: [Channel B]
        3: [Channel B]
        # etc

    tridesclous_merge:
        - [0, 1]
        - [3]

Now clusters 0 and 1 are combined into a single unit, and only that unit and cluster 3 are plotted; cluster 2 has been discarded.

Firing Rates¶

If spike trains were generated using Amplitude Discriminators, imported from tridesclous Spike Sorting Results, or included in the data_file, their smoothed firing rates can be computed. Note that firing rates are computed only if fast loading is off (lazy=False).

Firing rates are plotted as continuous signals. Colors are inherited from amplitude_discriminators, if they are provided there.

Firing rates are computed using a kernel that is convolved with the spike train. The metadata is specified like this:

my favorite dataset:
    data_file: data.axgx
    # etc

    amplitude_discriminators:  # used only if fast loading is off (lazy=False)

        - name: Unit 1
          channel: Extracellular
          units: uV
          amplitude: [50, 150]

    firing_rates:  # used only if fast loading is off (lazy=False)

        - name: Unit 1
          kernel: GaussianKernel
          sigma: 1.5 # sec

The elephant package’s instantaneous_rate function is used for calculating firing rates. See elephant.kernels for the names of kernel classes that may be used with the kernel parameter. neurotic provides an additional kernel, CausalAlphaKernel, which may also be used. The sigma parameter is passed as an argument to the kernel class and should be given in seconds.

The rate calculation function and kernel classes are sourced from neurotic._elephant_tools, rather than the elephant package itself, to avoid requiring elephant as a package dependency.

Firing Frequency Burst Detectors¶

If spike trains were generated using Amplitude Discriminators, imported from tridesclous Spike Sorting Results, or included in the data_file, a simple burst detection algorithm that relies on instantaneous firing rate thresholds can be run to detect periods of intense activity. Note that burst detectors are only applied if fast loading is off (lazy=False).

Detected bursts are plotted as epochs. Colors are inherited from amplitude_discriminators, if they are provided there.

Burst detectors are specified in metadata like this:

my favorite dataset:
    data_file: data.axgx
    # etc

    amplitude_discriminators:  # used only if fast loading is off (lazy=False)

        - name: Unit 1
          channel: Extracellular
          units: uV
          amplitude: [50, 150]

    burst_detectors:  # used only if fast loading is off (lazy=False)

        - spiketrain: Unit 1
          name: Unit 1 burst  # optional, used for customizing output epoch name
          thresholds: [10, 8] # Hz

The algorithm works by scanning through the spike train with a name matching spiketrain (in this example, the spike train generated by the “Unit 1” amplitude discriminator). When the instantaneous firing frequency (IFF; note this is NOT the same as the smoothed firing rate, but rather the inverse of the inter-spike interval) exceeds the first threshold given (e.g., 10 Hz), a burst of activity is determined to start. After this, at the first moment when the IFF drops below the second threshold (e.g., 8 Hz), the burst is determined to end. After scanning through the entire spike train, many bursts that meet these criteria may be identified.

Note that in general the end threshold should not exceed the start threshold; this would essentially be the same as setting the start and end thresholds both to the greater value.

Rectified Area Under the Curve (RAUC)¶

One way to simplify a high-frequency signal is by plotted a time series of the rectified area under the curve (RAUC). Note that RAUCs are calculated only if fast loading is off (lazy=False).

For each signal, the baseline (mean or median) is optionally subtracted off. The signal is then rectified (absolute value) and divided into non-overlapping bins of fixed duration. Finally, the integral is calculated within each bin. The result is a new time series that represents the overall activity of the original signal. RAUC time series are plotted separately from the original signals in a second tab. Colors are inherited from plots, if they are provided there.

The choice of baseline is controlled by the rauc_baseline metadata parameter, which may have the value None (default), 'mean', or 'median'. The size of the bins determines how smooth the RAUC time series is and is set by rauc_bin_duration, given in seconds. If rauc_bin_duration is not specified (default None), RAUC time series will not be calculated.

Metadata Examples¶

Below, the contents of a fully functioning example metadata file are shown, which contains metadata for several example datasets. This file is included with each installation of neurotic and is loaded automatically when neurotic first starts.

With this metadata file loaded in neurotic, you may use the “Download data” feature to fetch the data files and run the examples, and you may try the “Edit metadata” feature to test modifications (remember to “Reload metadata” after saving changes).

Direct link

# ===  GLOBAL PARAMETERS  ======================================================

neurotic_config:
    neurotic_version: '>=1.4' # required for firing_rates

    # the common URL root used for downloading all files
    # - for web browser access to data files, visit
    #   https://gin.g-node.org/jpgill86/neurotic-data/src/master/examples
    remote_data_root: https://gin.g-node.org/jpgill86/neurotic-data/raw/master/examples

# ===  EXAMPLE 1: APLYSIA FEEDING  =============================================

Aplysia feeding:
    description: '[ 13 MB] Sea slug feeding, identified neurons, swallowing force'
    # see also https://gin.g-node.org/jpgill86/neurotic-data/src/master/examples/aplysia-feeding/README.md

    # FILE PATHS
    # - URLs to files are assembled this way:
    #     remote_data_root + remote_data_dir + *_file
    # - downloaded files are stored in a new local directory with name
    #   data_dir created in a location relative to this metadata file
    data_dir:           aplysia-feeding
    remote_data_dir:    aplysia-feeding
    data_file:          data.axgx # AxoGraph file
    video_file:         video.mp4
    annotations_file:   annotations.csv
    epoch_encoder_file: epoch-encoder.csv

    # VIDEO SYNC PARAMETERS
    video_offset: 2875.3 # seconds

    # EPOCH ENCODER PARAMETERS
    epoch_encoder_possible_labels:
        - I2 protraction activity
        - B8 activity
        - B3/6/9/10 activity
        - B38 activity
        - B4/B5 activity
        - Inward movement

    # SIGNAL PLOTTING PARAMETERS
    plots:
        - channel: I2
          ylabel: I2 muscle EMG
          units: uV
          ylim: [-60, 60]
          color: '#666666'

        - channel: RN
          ylabel: Radular nerve (RN)
          units: uV
          ylim: [-25, 25]
          color: '#666666'

        - channel: BN2
          ylabel: Buccal nerve 2 (BN2)
          units: uV
          ylim: [-45, 45]
          color: '#666666'

        - channel: BN3-DIST
          ylabel: Buccal nerve 3 (BN3)
          units: uV
          ylim: [-60, 60]
          color: '#666666'

        - channel: Force
          units: mN
          ylim: [-50, 450]
          color: '#666666'

    # SIGNAL FILTERS
    # - used here to remove high-frequency noise
    # - only applied if "Fast loading" is turned off (lazy=False)
    filters:
        - channel: I2
          lowpass: 100 # Hz

        - channel: Force
          lowpass: 50 # Hz

    # NEURONAL SPIKE DETECTION
    # - used here to detect activity of identified neurons
    # - only performed if "Fast loading" is turned off (lazy=False)
    amplitude_discriminators:
        - name: B38 neuron
          channel: BN2
          units: uV
          amplitude: [7, 20]
          epoch: B38 activity
          color: '#EFBF46'

        - name: B31/B32/B61/B62 neurons
          channel: I2
          units: uV
          amplitude: [2, 75]
          epoch: I2 protraction activity
          color: '#DC5151'

        - name: B8a/b neurons
          channel: RN
          units: uV
          amplitude: [-30, -8]
          epoch: B8 activity
          color: '#DA8BC3'

        - name: B6/B9 neurons
          channel: BN2
          units: uV
          amplitude: [-25, -9]
          epoch: B3/6/9/10 activity
          color: '#64B5CD'

        - name: B3 neuron
          channel: BN2
          units: uV
          amplitude: [-60, -25]
          epoch: B3/6/9/10 activity
          color: '#4F80BD'

        - name: B4/B5 neurons
          channel: BN3-DIST
          units: uV
          amplitude: [-80, -20]
          epoch: B4/B5 activity
          color: '#00A86B'

    # NEURONAL FIRING RATES
    # - used here to model synaptic output
    # - only calculated if "Fast loading" is turned off (lazy=False)
    firing_rates:
        - name: B38 neuron
          kernel: CausalAlphaKernel
          sigma: 1.0 # seconds

        - name: B6/B9 neurons
          kernel: CausalAlphaKernel
          sigma: 0.5 # seconds

        - name: B3 neuron
          kernel: CausalAlphaKernel
          sigma: 1.0 # seconds

    # NEURONAL BURST DETECTION
    # - used here to classify sequences of spikes into "bursts"
    # - only performed if "Fast loading" is turned off (lazy=False)
    burst_detectors:
        - spiketrain: B38 neuron
          thresholds: [8, 5] # Hz

        - spiketrain: B31/B32/B61/B62 neurons
          thresholds: [10, 5] # Hz

        - spiketrain: B8a/b neurons
          thresholds: [3, 3] # Hz

        - spiketrain: B6/B9 neurons
          thresholds: [10, 5] # Hz

        - spiketrain: B3 neuron
          thresholds: [8, 2] # Hz

        - spiketrain: B4/B5 neurons
          thresholds: [3, 3] # Hz

    # RECTIFIED AND INTEGRATED SIGNALS
    # - only used if "Fast loading" is turned off (lazy=False)
    rauc_bin_duration: 0.1 # seconds


# ===  EXAMPLE 2: HUMAN BALANCE BEAM  ==========================================

Human balance beam:
    description: '[0.5 MB] Narrow beam walking, arm EMG, body kinematics'
    # see also https://gin.g-node.org/jpgill86/neurotic-data/src/master/examples/human-balance-beam/README.md

    # FILE PATHS
    # - URLs to files are assembled this way:
    #     remote_data_root + remote_data_dir + *_file
    # - downloaded files are stored in a new local directory with name
    #   data_dir created in a location relative to this metadata file
    data_dir:           human-balance-beam
    remote_data_dir:    human-balance-beam
    data_file:          data.mat # MATLAB file
    video_file:         video.mp4
    epoch_encoder_file: epoch-encoder.csv

    # VIDEO SYNC PARAMETERS
    video_offset: 0 # seconds

    # INITIAL PLOT WIDTH
    t_width: 10 # seconds

    # EPOCH ENCODER PARAMETERS
    epoch_encoder_possible_labels:
        - Left stance
        - Right stance

    # SIGNAL PLOTTING PARAMETERS
    plots:
        # LEFT ARM
        - channel: Voltage.BCEP_L
          ylabel:  L Biceps
          ylim: [-1, 1]
          units: mV
        - channel: Voltage.TCEP_L
          ylabel:  L Triceps
          ylim: [-1, 1]
          units: mV

        # RIGHT ARM
        - channel: Voltage.BCEP_R
          ylabel:  R Biceps
          ylim: [-10, 10]
          units: mV
        - channel: Voltage.TCEP_R
          ylabel:  R Triceps
          ylim: [-10, 10]
          units: mV

        # KINEMATIC MARKERS
        - channel: CLAV Z
          ylabel:  Clavicle Z
          ylim: [1220, 1420]
        - channel: LHEE Z
          ylabel:  L Heel Z
          ylim: [30, 350]
        - channel: RHEE Z
          ylabel:  R Heel Z
          ylim: [30, 350]

    # SIGNAL FILTERS
    # - used here to remove low-frequency motion artifacts
    # - only applied if "Fast loading" is turned off (lazy=False)
    filters:
        - channel: Voltage.BCEP_R
          highpass: 35 # Hz

        - channel: Voltage.TCEP_R
          highpass: 35 # Hz

    # RECTIFIED AND INTEGRATED SIGNALS
    # - used here to represent overall muscle activity
    # - only used if "Fast loading" is turned off (lazy=False)
    rauc_baseline: mean     # subtract the mean before rectification
    rauc_bin_duration: 0.01 # seconds


# ===  EXAMPLE 3: DRONE OPTICAL FLOW  ==========================================

Drone optical flow:
    description: '[7.7 MB] Neural network motion detection from drone flight video'
    # see also https://gin.g-node.org/jpgill86/neurotic-data/src/master/examples/drone-optical-flow/README.md

    # FILE PATHS
    # - URLs to files are assembled this way:
    #     remote_data_root + remote_data_dir + *_file
    # - downloaded files are stored in a new local directory with name
    #   data_dir created in a location relative to this metadata file
    data_dir:           drone-optical-flow
    remote_data_dir:    drone-optical-flow
    data_file:          data.txt # plain text file
    video_file:         video.mp4

    # DATA READER (NEO) PARAMETERS
    # - these arguments are passed to a Neo reader (neo.io.AsciiSignalIO) for
    #   reading the data_file
    io_args:
        skiprows: 1 # skip header
        sampling_rate: 1250 # Hz
        units: mV

    # VIDEO SYNC PARAMETERS
    video_offset: 0 # seconds

    # SIGNAL PLOTTING PARAMETERS
    plots:
        - channel: Column 0
          ylabel: Clockwise Rotate
          units: mV
          ylim: [0, 255]

        - channel: Column 1
          ylabel: Counterclockwise Rotate
          units: mV
          ylim: [0, 255]

        - channel: Column 2
          ylabel: Moving Forward
          units: mV
          ylim: [0, 255]

        - channel: Column 3
          ylabel: Moving Backward
          units: mV
          ylim: [0, 255]

        - channel: Column 4
          ylabel: Down Shift
          units: mV
          ylim: [0, 255]

        - channel: Column 5
          ylabel: Up Shift
          units: mV
          ylim: [0, 255]

        - channel: Column 6
          ylabel: Right Shift
          units: mV
          ylim: [0, 255]

        - channel: Column 7
          ylabel: Left Shift
          units: mV
          ylim: [0, 255]

    # NEURONAL SPIKE DETECTION
    # - used here to detect spikes of simulated neurons
    # - only performed if "Fast loading" is turned off (lazy=False)
    amplitude_discriminators:
        - name: Clockwise Rotate
          channel: Column 0
          units: mV
          amplitude: [150, 255]

        - name: Counterclockwise Rotate
          channel: Column 1
          units: mV
          amplitude: [150, 255]

        - name: Moving Forward
          channel: Column 2
          units: mV
          amplitude: [150, 255]

        - name: Moving Backward
          channel: Column 3
          units: mV
          amplitude: [150, 255]

        - name: Down Shift
          channel: Column 4
          units: mV
          amplitude: [150, 255]

        - name: Up Shift
          channel: Column 5
          units: mV
          amplitude: [150, 255]

        - name: Right Shift
          channel: Column 6
          units: mV
          amplitude: [150, 255]

        - name: Left Shift
          channel: Column 7
          units: mV
          amplitude: [150, 255]

Configuring for Google Drive¶

neurotic can download files from Google Drive (see URLs to Use with Google Drive for details on how to specify remote URLs). However, before this capability can be used, you must complete these manual configuration procedures.

Generating a Client Secret File¶

Because of limitations stated in Google’s Terms of Service on what client-identifying credentials may be included with open source desktop applications, it is not possible for neurotic to supply users with an essential file needed for Google Drive access [1]. This file is called the client secret file, and you will need to generate one yourself. The instructions in this section will walk you through this one-time process. This is a normal part of setting up PyDrive2, the library neurotic uses for this feature [2].

The file produced by following these steps, client_secret.json, does not provide access to your Google account, so your account is not compromised if the file falls into the “wrong hands”. However, it does identify you to Google as the creator of that file whenever neurotic uses it to download files; for this reason, you are discouraged from distributing this file to others, as abuse of it could cause Google to invalidate it and sanction your account.

Follow these steps to create your client secret file:

Visit the Google Cloud Platform project dashboard:

https://console.cloud.google.com/projectselector2
Click the “Create Project” button, and name the new project “neurotic”, or something similar (the exact name does not matter). Note that you can delete unwanted projects later from the Cloud Resource Manager.
Once created, you will be taken to a “Getting Started” page for the new project. The project name should appear at the top of the page, indicating the correct project is selected.
Using the search bar at the top of the page, search for and then navigate to “Google Drive API”. On that page, click the “Enable” button.
Using the search bar at the top of the page, search for and then navigate to “OAuth consent screen”. Complete the form to configure the consent screen that will be displayed when authorizing neurotic to access your Google Drive. The following settings are recommended. Understand that from Google’s perspective you are the developer of the application which will access Google Drive.
- User type: External
- App name: “neurotic”
- User support email: <your email>
- Developer contact information: <your email>
- Other optional fields may be left blank
- Scopes: Search for and add “drive.readonly”
- Test users: Add email addresses for all Google Drive accounts you would like to use with neurotic, including the Google account you are using to make this project if so desired
Using the search bar at the top of the page, search for and then navigate to “Credentials”. Click the “Create Credentials” button and choose “OAuth client ID” from the menu. Set Application Type to “Desktop app”. Use the name “Desktop client 1”.
After the OAuth client credentials are created, you will see an entry on the Credentials page named “Desktop client 1”. Click the download button on the far right of the entry to download a JSON file. It will have a name like client_secret_XXX.apps.googleusercontent.com.json, where XXX is a long random string.
Rename the downloaded file to client_secret.json.
Launch neurotic. Under the Help menu, click “Open Google Drive credentials directory”. Move the client_secret.json file into this folder.

Authorizing neurotic to Access Google Drive¶

After you have created a client secret file and saved it to the right location, you can attempt to download files from Google Drive using a properly configured metadata file (see URLs to Use with Google Drive for details). When you do this for the first time, or when you use the “Request Google Drive authorization now” action under the Help menu, you will need to complete the following steps to authorize neurotic to access your Google Drive:

Your web browser will open and ask you to sign into a Google account before continuing to neurotic. You will need to select one of your Google accounts that was added as a “test user” when creating the client secret file. Other accounts will be denied access.
Next you will see a notification that the app has not been verified by Google. Your own email address will be listed as the software developer because this notice is associated with the client secret file you created. The message will also state that the app is being tested (rather than is a finalized product) because the project you created for the client secret file is private.

Due to the terms-of-service limitations mentioned earlier, it is not possible for neurotic to distribute a client secret file that would avoid presenting you with this notice. This policy exists because open source desktop applications can be modified by anyone with access to the system at any time, making it impossible for Google to certify that the mutable app has any particular identity and is safe. If you trust the application and are willing to proceed, click “Continue”.
To download files from your Google Drive, neurotic needs the privileges to access and read those files. Click “Allow” to indicate that you want to allow this.
Click “Allow” another time to confirm.
When you see this message in your browser, you can close it: “The authentication flow has completed.”

The authorization process should now be complete, and you can begin using neurotic to access and download Google Drive files.

Making Google Drive Authorization Persistent¶

By default, authorization persists only until neurotic is closed. Each time neurotic is restarted and you want to download from Google Drive again, you will need to repeat the authorization procedure described above. You can avoid this by configuring neurotic to retain the products of authorization (access and refresh tokens) indefinitely. See Changing Default Behavior for details on the global configuration file; by setting the save_tokens parameter under the gdrive heading to true, you can minimize the frequency of authorization requests.

Warning

Enabling save_tokens is not recommended on systems used by others you do not trust. These others will be able to download files from your Google Drive using neurotic with the same level of ease you experience, and with access to the token file they could use it outside of neurotic to gain read-only access to your Google Drive and your Shared Drives.

Purging Google Drive Authorization¶

If you need to use a different Google account than the one you previously authorized neurotic to use, or if you had set save_tokens=true and now want to remove the persistent access and refresh tokens from your system, you can use the “Purge Google Drive authorization token” action from the Help menu. After using this, you will need to complete the authorization procedure again, and you will have the opportunity to select a different Google account.

[1]	See this StackOverflow question for an informal discussion.

[2]	See also PyDrive2 Getting Started.

Changing Default Behavior¶

Default parameters used by the app and by the command line interface, such as which metadata file to open initially or whether Google Drive access tokens should be stored indefinitely, can be configured using global configuration settings located in .neurotic/neurotic-config.txt in your home directory:

Windows: C:\Users\<username>\.neurotic\neurotic-config.txt

macOS: /Users/<username>/.neurotic/neurotic-config.txt

Linux: /home/<username>/.neurotic/neurotic-config.txt

The file can be opened easily using the “View global config file” menu action. You may edit it to customize your settings. The next time you launch the app or use the command line interface, your changes should be in effect.

If this file does not exist when neurotic is launched, the following template is created for you:

# --- neurotic global config --------------------------------------------------
# Use this file to configure the way neurotic behaves. This file uses the TOML
# format.


[defaults]
# When the app is launched, the following customizable defaults are used unless
# overridden by command line arguments. Example uses include:
#   - Uncomment the "file" parameter and insert the path to your favorite
#     metadata file so that it always opens automatically
#   - Uncomment the "lazy" parameter and set it to false to always disable fast
#     loading, ensuring that expensive procedures like spike detection and
#     filtering are performed by default
# To open the example metadata file by default, either leave the "file"
# parameter unset, set it to false, or set it to "example". To initially select
# the first dataset in the file, either leave the "dataset" parameter unset,
# set it to false, or set it to "first".

# file = false
# dataset = false
# debug = false
# lazy = true
# thick_traces = false
# show_datetime = false
# ui_scale = "medium"
# theme = "light"


[gdrive]
# The "save_tokens" parameter controls how often you need to authorize neurotic
# to access your Google Drive account for downloads:
#   - Set "save_tokens" to true to remember Google Drive access tokens after
#     authorization, so that permissions only need to be granted once. This is
#     not recommended if others you do not trust have access to this computer,
#     as it could let them download files from your Google Drive account.
#   - Set "save_tokens" to false or leave it unset to forget access
#     authorization after neurotic closes. Each time you restart neurotic, you
#     will be required to re-grant permissions when you download a Google Drive
#     file.

# save_tokens = false


[app]
# When the app is launched, neurotic automatically checks for updates unless
# the "auto_check_for_updates" parameter is set to false.

# auto_check_for_updates = true

API Reference Guide¶

In addition to using neurotic as a standalone app, you can also leverage its API in your own code.

Note

TL;DR: The easiest way to use neurotic in an interactive session or script is by invoking neurotic.quick_launch(). For example:

>>> metadata = {'data_file': 'data.axgx'}
>>> neurotic.quick_launch(metadata=metadata)

or

>>> neurotic.quick_launch(blk=my_neo_block)

The core of the API consists of two classes and one function:

neurotic.datasets.metadata.MetadataSelector: Read metadata files, download datasets
neurotic.datasets.data.load_dataset(): Read datasets, apply filters and spike detection
neurotic.gui.config.EphyviewerConfigurator: Launch ephyviewer

All public package contents are automatically imported directly into the neurotic namespace. This means that a class like neurotic.datasets.metadata.MetadataSelector can be accessed more compactly as neurotic.MetadataSelector.

`neurotic.datasets.data`¶

The neurotic.datasets.data module implements a function for loading a dataset from selected metadata.

neurotic.datasets.data.load_dataset(metadata, blk=None, lazy=False, signal_group_mode='split-all', filter_events_from_epochs=False)[source]¶

Load a dataset.

metadata may be a MetadataSelector or a simple dictionary containing the appropriate data.

The data_file in metadata is read into a Neo Block using an automatically detected neo.io class if lazy=False or a neo.rawio class if lazy=True. If data_file is unspecified, an empty Neo Block is created instead. If a Neo Block is passed as blk, data_file is ignored.

Epochs and events loaded from annotations_file and epoch_encoder_file and spike trains loaded from tridesclous_file are added to the Neo Block.

If lazy=False, parameters given in metadata are used to apply filters to the signals, to detect spikes using amplitude discriminators, to calculate smoothed firing rates from spike trains, to detect bursts of spikes, and to calculate the rectified area under the curve (RAUC) for each signal.

`neurotic.datasets.download`¶

The neurotic.datasets.download module implements a general purpose download function that handles connecting to remote servers, performing authentication, and downloading files with progress reporting. The function handles various errors and will automatically reprompt the user for login credentials if a bad user name or password is given.

The module installs an urllib.request.HTTPBasicAuthHandler and a neurotic.datasets.ftpauth.FTPBasicAuthHandler at import time.

neurotic.datasets.download.download(url, local_file, overwrite_existing=False, show_progress=True, bytes_per_chunk=8192)[source]¶: Download a file.

`neurotic.datasets.ftpauth`¶

The neurotic.datasets.ftpauth module implements a urllib.request-compatible FTP handler that prompts for and remembers passwords.

class neurotic.datasets.ftpauth.FTPBasicAuthHandler(password_mgr=None)[source]¶

This subclass of urllib.request.FTPHandler implements basic authentication management for FTP connections. Like urllib.request.HTTPBasicAuthHandler, this handler for FTP connections has a password manager that it checks for login credentials before connecting to a server.

This subclass also ensures that file size is included in the response header, which can fail for some FTP servers if the original FTPHandler is used.

This handler can be installed globally in a Python session so that calls to urllib.request.urlopen('ftp://...') will use it automatically:

>>> handler = FTPBasicAuthHandler()
>>> handler.add_password(None, uri, user, passwd)  # realm must be None
>>> opener = urllib.request.build_opener(handler)
>>> urllib.request.install_opener(opener)

neurotic.datasets.ftpauth.setup_ftpauth()[source]¶

Install neurotic.datasets.ftpauth.FTPBasicAuthHandler as the global default FTP handler.

Note that urllib.request.install_opener() used here will remove all other non-default handlers installed in a different opener, such as an urllib.request.HTTPBasicAuthHandler.

`neurotic.datasets.gdrive`¶

The neurotic.datasets.gdrive module implements a class for downloading files from Google Drive using paths, rather than file IDs or shareable links.

class neurotic.datasets.gdrive.GoogleDriveDownloader(client_secret_file, tokens_file=None, save_tokens=False)[source]¶

A class for downloading files from Google Drive using paths.

Files can be specified for download using URL-like paths of the form

gdrive://<drive name>/<folder 1>/<…>/<folder N>/<file name>

The “<drive name>” may be “My Drive” for files located in a personal Google Drive, or it may be the name of a Shared Drive that the user has permission to access.

Note that these URL-like paths are not equivalent to ordinary URLs associated with Google Drive files, such as shareable links, which are composed of pseudorandom file IDs and do not reveal anything about the name of the file or the folders containing it.

This class can only download files that are uniquely identifiable by their paths. Google Drive does not require file or folder names to be unique, so two or more files or folders with identical names may coexist in a folder. Such files and folders cannot be distinguished by their paths, so they cannot be downloaded using this class. A download will fail while traversing the file tree if at any step there is more than one folder or file that matches the path.

This class manages access authorization, optionally saving authorization tokens to a file so that the authorization flow does not need to be repeated in the future.

The client_secret_file should be the path to a client secret file in JSON format, obtained from the Google API Console. The Drive API must be enabled for the corresponding client.

If save_tokens=False, the authorization flow (a request via web browser for permission to access Google Drive) will always run the first time a new instance of this class is used, and authorization will not persist after the instance is destroyed. If save_tokens=True and a file path is provided with tokens_file, access/refresh tokens resulting from a successful authorization are stored in the file, and tokens are loaded from the file in the future, so that the authorization flow does not need to be repeated.

GetSharedDrivesList()[source]¶: Return information about available Shared Drives.

GetUserEmail()[source]¶: Get the email address for the authorized Google Drive account.

authorize()[source]¶

Obtain tokens for reading the contents of a Google Drive account.

If save_tokens=True, tokens will be loaded from the tokens_file if possible. If tokens cannot be restored this way, or if the loaded tokens have expired, an authorization flow will be initiated, prompting the user through a web browser to grant read-only privileges to the client associated with the client_secret_file. When the authorization flow completes, if save_tokens=True, the newly created tokens will be stored in the tokens_file for future use.

Authorization is performed automatically when needed, but this method can be called directly to retrieve (and possibly store) tokens without initiating a download.

deauthorize()[source]¶: Forget tokens and delete the tokens_file. The authorization flow will be required for the next download.

download(gdrive_url, local_file, overwrite_existing=False, show_progress=True, bytes_per_chunk=5242880)[source]¶: Download a file from Google Drive using a URL-like path beginning with “gdrive://”.

is_authorized()[source]¶: Get the current authorization state.

`neurotic.datasets.metadata`¶

The neurotic.datasets.metadata module implements a class for reading metadata files.

class neurotic.datasets.metadata.MetadataSelector(file=None, local_data_root=None, remote_data_root=None, initial_selection=None)[source]¶

A class for managing metadata.

A metadata file can be specified at initialization, in which case it is read immediately. The file contents are stored as a dictionary in all_metadata.

>>> metadata = MetadataSelector(file='metadata.yml')
>>> print(metadata.all_metadata)

File contents can be reloaded after they have been changed, or after changing file, using the load() method.

>>> metadata = MetadataSelector()
>>> metadata.file = 'metadata.yml'
>>> metadata.load()

A particular metadata set contained within the file can be selected at initialization with initial_selection or later using the select() method. After making a selection, the selected metadata set is accessible at metadata.selected_metadata, e.g.

>>> metadata = MetadataSelector(file='metadata.yml')
>>> metadata.select('Data Set 5')
>>> print(metadata.selected_metadata['data_file'])

A compact indexing method is implemented that allows the selected metadata set to be accessed directly, e.g.

>>> print(metadata['data_file'])

This allows the MetadataSelector to be passed to functions expecting a simple dictionary corresponding to a single metadata set, and the selected metadata set will be used automatically.

Files associated with the selected metadata set can be downloaded individually or all together, e.g.

>>> metadata.download('video_file')

or

>>> metadata.download_all_data_files()

The absolute path to a local file or the full URL to a remote file associated with the selected metadata set can be resolved with the abs_path() and abs_url() methods, e.g.

>>> print(metadata.abs_path('data_file'))
>>> print(metadata.abs_url('data_file'))

abs_path(file)[source]¶: Convert the relative path of file to an absolute path using data_dir.

abs_url(file)[source]¶: Convert the relative path of file to a full URL using remote_data_dir.

all_metadata = None¶: A dictionary containing the entire file contents, set by load().

download(file, **kwargs)[source]¶

Download a file associated with the selected metadata set.

See neurotic.datasets.download.download() for possible keyword arguments.

download_all_data_files(**kwargs)[source]¶

Download all files associated with the selected metadata set.

See neurotic.datasets.download.download() for possible keyword arguments.

keys¶: The available metadata keys.

load()[source]¶: Read the metadata file.

select(selection)[source]¶: Select a metadata set.

selected_metadata¶: The access point for the selected metadata set.

`neurotic.gui.config`¶

The neurotic.gui.config module implements a class for configuring and launching ephyviewer for a loaded dataset.

class neurotic.gui.config.EphyviewerConfigurator(metadata, blk, lazy=False)[source]¶

A class for launching ephyviewer for a dataset with configurable viewers.

At initialization, invalid viewers are automatically disabled (e.g., the video viewer is disabled if video_file is not given in metadata). Viewers can be hidden or shown before launch using the built-in methods. Valid viewer names are:

traces

traces_rauc

freqs

spike_trains

traces_rates

epochs

epoch_encoder

video

event_list

data_frame

launch_ephyviewer() is provided for starting a new Qt app and launching the ephyviewer main window all at once. create_ephyviewer_window() generates just the ephyviewer window and should be used if there is already a Qt app running.

create_ephyviewer_window(theme='light', ui_scale='medium', support_increased_line_width=False, show_datetime=False, datetime_format='%Y-%m-%d %H:%M:%S')[source]¶: Load data into each ephyviewer viewer and return the main window.

disable(name)[source]¶: Disable the viewer name.

enable(name)[source]¶: Enable the viewer name.

hide(name)[source]¶: Hide the viewer name.

hide_all()[source]¶: Hide all viewers.

is_enabled(name)[source]¶: Return whether the viewer name is enabled.

is_shown(name)[source]¶: Return whether the viewer name is shown.

launch_ephyviewer(theme='light', ui_scale='medium', support_increased_line_width=False, show_datetime=False, datetime_format='%Y-%m-%d %H:%M:%S')[source]¶: Start a Qt app and create an ephyviewer window.

show(name)[source]¶: Show the viewer name.

show_all()[source]¶: Show all viewers.

`neurotic.gui.epochencoder`¶

The neurotic.gui.epochencoder module implements a subclass of ephyviewer.datasource.epochs.WritableEpochSource.

class neurotic.gui.epochencoder.NeuroticWritableEpochSource(filename, possible_labels, color_labels=None, channel_name='', backup=True)[source]¶: A subclass of ephyviewer.datasource.epochs.WritableEpochSource for custom CSV column formatting and automatic file backup.

`neurotic.gui.notebook`¶

The neurotic.gui.notebook module implements Jupyter notebook widget counterparts for the MetadataSelector and the EphyviewerConfigurator.

class neurotic.gui.notebook.MetadataSelectorWidget(file=None, local_data_root=None, remote_data_root=None, initial_selection=None)[source]¶

Interactive list box for Jupyter notebooks that allows the user to select which metadata set they would like to work with.

>>> metadata = MetadataSelectorWidget(file='metadata.yml')
>>> display(metadata)

After clicking on an item in the list, the selected metadata set is accessible at metadata.selected_metadata, e.g.

>>> metadata.selected_metadata['data_file']

A compact indexing method is implemented that allows the selected metadata set to be accessed directly, e.g.

>>> metadata['data_file']

This allows the MetadataSelectorWidget to be passed to functions expecting a simple dictionary corresponding to a single metadata set, and the selected metadata set will be used automatically.

class neurotic.gui.notebook.EphyviewerConfiguratorWidget(metadata, blk, lazy=False)[source]¶

Interactive button grid for Jupyter notebooks that allows the user to select which ephyviewer viewers they would like to display and then launch ephyviewer.

disable(name)[source]¶: Disable the viewer name.

enable(name)[source]¶: Enable the viewer name.

hide(name)[source]¶: Hide the viewer name.

show(name)[source]¶: Show the viewer name.

`neurotic.gui.standalone`¶

The neurotic.gui.standalone module implements the main window of the app.

class neurotic.gui.standalone.MainWindow(file=None, initial_selection=None, lazy=True, theme='light', ui_scale='medium', support_increased_line_width=False, show_datetime=False)[source]¶: The main window of the app.

`neurotic.scripts`¶

The neurotic.scripts module handles starting the app from the command line. It also provides a convenience function for quickly launching the app using minimal metadata or an existing Neo Block, and another for starting a Jupyter server with an example notebook.

neurotic.scripts.quick_launch(metadata={}, blk=None, lazy=True)[source]¶

Load data, configure the GUI, and launch the app with one convenient function.

This function allows neurotic to be used easily in interactive sessions and scripts. For example, dictionaries can be passed as metadata:

>>> metadata = {'data_file': 'data.axgx'}
>>> neurotic.quick_launch(metadata=metadata)

An existing Neo Block can be passed directly:

>>> neurotic.quick_launch(blk=my_neo_block)

This function is equivalent to the following:

>>> blk = load_dataset(metadata, blk, lazy=lazy)
>>> ephyviewer_config = EphyviewerConfigurator(metadata, blk, lazy=lazy)
>>> ephyviewer_config.show_all()
>>> ephyviewer_config.launch_ephyviewer()

neurotic.scripts.launch_example_notebook()[source]¶: Start a Jupyter server and open the example notebook.

`neurotic._elephant_tools`¶

The neurotic._elephant_tools module contains functions and classes copied from the elephant package, which are included for convenience and to eliminate dependency on that package. Original code that builds on this work (e.g., a new kernel) is also contained in this module.

Warning

This module and the functions and classes it contains are not intended to be part of neurotic’s public API, so the module name begins with an underscore. This module may be moved, renamed, or removed at a future date and replaced with explicit dependence on the elephant package.

class neurotic._elephant_tools.CausalAlphaKernel(sigma, invert=False)[source]¶

This modified version of elephant.kernels.AlphaKernel shifts time such that convolution of the kernel with spike trains (as in elephant.statistics.instantaneous_rate()) results in alpha functions that begin rising at the spike time, not before. The entire area of the kernel comes after the spike, rather than half before and half after, as with AlphaKernel. Consequently, CausalAlphaKernel can be used in causal filters.

The equation used for CausalAlphaKernel is

\[\begin{split}K(t) = \left\{\begin{array}{ll} (1 / \tau^2) \ t\ \exp{(-t / \tau)}, & t > 0 \\ 0, & t \leq 0 \end{array} \right.\end{split}\]

with \(\tau = \sigma / \sqrt{2}\), where \(\sigma\) is the parameter passed to the class initializer.

In neuroscience a popular application of kernels is in performing smoothing operations via convolution. In this case, the kernel has the properties of a probability density, i.e., it is positive and normalized to one. Popular choices are the rectangular or Gaussian kernels.

Exponential and alpha kernels may also be used to represent the postynaptic current / potentials in a linear (current-based) model.

sigma : Quantity scalar: Standard deviation of the kernel.
invert: bool, optional: If true, asymmetric kernels (e.g., exponential or alpha kernels) are inverted along the time axis. Default: False

Release Notes¶

neurotic 1.5.0¶

2021-01-17

This release’s biggest feature is Google Drive integration: Use neurotic to fetch data files from either My Drive or Shared Drives (formerly known as Team Drives). Read more here: URLs to Use with Google Drive and Configuring for Google Drive.

Additionally, you can now customize some default settings for neurotic, such as which metadata file is opened by default. Read more here: Changing Default Behavior.

New features¶

Add capability to download files from Google Drive (#294, #297, #309)
Allow users to change defaults in a global configuration file (#285, #304)

Improvements¶

Automatically check for updates when the app is launched (#307, #310)
Remove incomplete files when a download is interrupted (#280)
Add amplitude discriminator parameter for extrema type (detect peaks or troughs) (#284)
Annotate detected spike trains with amplitude discriminator units and epoch (#281, #282, #284)

Documentation¶

Many aesthetic and content improvements to the documentation (#256, #268, #269, #272, #273, #274, #275, #295, #298, #302, #303, #305, #306, #308)

Testing¶

Transition to GitHub Actions for automated testing (#286, #287, #299, #301)
Add tests for and declare support for Python 3.9 (#283)
Exclude py files not part of the main package from coverage reports (#300)

neurotic 1.4.1¶

2020-03-15

Improvements¶

Add neurotic_version parameter to metadata (#247)
Revised and added new example datasets (#250, #251)

Bug fixes¶

Fix broken import of Neo’s generate_one_simple_block in example notebook (#253)
Fix default font size determination in scripts and Jupyter notebooks (#249)

Other changes¶

Make “large” UI scale larger and “huge” UI scale huger (#244)
Scale loading message with other fonts (#245)
Address numpy FutureWarning when epoch list is empty (#248)

Documentation¶

Add project acronym to package description, app, and docs (#252)
Building of standalone installers is now automated (#254)

neurotic 1.4.0¶

2020-03-04

New features¶

Add computation of smoothed firing rates for spike trains (#189)
Add quick_launch function for easier scripting and interactive sessions (#191, #196)
Add blk param to load_dataset for using existing Neo Block (#196)
Add rec_datetime metadata parameter for setting real-world start time (#190)
Add past_fraction metadata parameter for controlling the placement of the vertical line marking the current time (#220)
Add color options for signal plots to metadata (#177)
Add options for scaling the user interface (#222, #241, #242)
Add launch via double click in standalone app (#218)

Help & feedback¶

Display loading indicator when launching in the standalone app (#223)
Prompt the user to reload metadata after using the menu to edit metadata (#226)
Show “Downloads complete” in app status bar and in log (#219)
Add menu action status tips to standalone app (#221, #240)
Add “Check for updates” to help menu (#201)
Add Help menu actions for opening common URLs (#198, #230)
Add Python version and neurotic install path to About window (#181)
Display common error messages to status bar in standalone app (#225)
Display a splash screen when first starting the standalone app (#224)

Jupyter tutorial¶

Start the tutorial using neurotic --launch-example-notebook or view it here.

Add API tutorial to example Jupyter notebook (#234, #236)
Add shell commands to example Jupyter notebook for installing neurotic (#185)

Other changes¶

Move RAUC calculations to load_dataset and store them as annotations (#188)
Disable RAUC calculations by default (#193)
Allow data_file to be unspecified in metadata and signals to be optional (#195)
Ignore video_file if PyAV is not installed (#231)
Rename elephant functions (#183)

Bug fixes¶

Fix crash when plots list is empty (#217)
Fix plotted signal sampling rate and start time if units are not Hz and sec, respectively (#194)
Fix incompatibility with old versions of tqdm and unknown download size (#184)

Documentation¶

Improve installation and updating documentation (#180, #229)

Logging¶

Add package logger and permanent log file (#174)
Log fatal errors in standalone app instead of crashing (#176)
Add CLI and GUI options for enabling debug log messages (#178)
Raise the default threshold for PyAV messages from warning to critical (#179)

neurotic 1.3.0¶

2020-01-07

Improvements¶

Add burst detection via firing rate thresholding (#156)
Add button for auto-scaling signals to main window (#150)
Add metadata color parameters for amplitude_discriminators (#166)
Add metadata parameters rauc_baseline and rauc_bin_duration (#151)
Make data_dir default to metadata file directory (#163)

Bug fixes¶

Unmask FileNotFoundError when local data file is missing (#154)

Documentation¶

Add Zenodo archive badge (#162)

neurotic 1.2.1¶

2019-12-09

Bug fixes¶

Fix loading using Neo IOs lacking signals_group_mode (TypeError: read_block() got an unexpected keyword argument 'signal_group_mode') (#143)

neurotic 1.2.0¶

2019-12-06

neurotic should now have broader compatibility with file types supported by Neo’s neo.io classes thanks to two new metadata parameters: io_class and io_args. See Data Reader (Neo) Settings for details.

neurotic is now available on conda-forge! See Alternate Method: conda (recommended for Pythonistas) for details on how to install.

Improvements¶

Add metadata parameters io_class and io_args (#137)

Documentation¶

Add conda-forge installation instructions (#128)

neurotic 1.1.1¶

2019-10-17

Changes¶

Remove elephant as a dependency (#120)

neurotic 1.1.0¶

2019-10-09

Improvements¶

Add API parameters and CLI argument for displaying the real-world date and time (potentially inaccurate) (#110, #118)
Add printer-friendly theme (white background) (#114)

Documentation¶

Add documentation of GIN URLs for public and private repos (#113)

neurotic 1.0.0¶

2019-07-27

🎊 First stable release! 🎉

Improvements¶

Major API changes (#104, #100, #106)
- In preparation for this stable release, many formerly public classes and functions were made private. This was done to minimize the number of public classes/functions, which beginning with this release will be treated as stable APIs that are ideally modified only in backwards compatible ways. Users should trust that public classes and functions will not be changed without good reason and a major version bump.
Many improvements to the documentation, including the addition of an API Reference Guide
Add example Jupyter notebook and command line argument for launching it (#108)
Add file overwrite option to download functions (#106)
Reserve the metadata keyword neurotic_config for global parameters (#93)
- The remote_data_root key must now be nested under neurotic_config.

Bug fixes¶

Fix crash when epoch encoder file contains labels not listed in metadata (#97)
Allow amplitude discriminators to be specified with arbitrary units (#99)

neurotic 0.7.0¶

2019-07-21

Improvements¶

New documentation hosted at Read the Docs: https://neurotic.readthedocs.io
Add menu action for opening metadata in editor (#83)
Add menu action for opening the selected data directory (#84)
Add list of installed versions of dependencies and doc links to About window (#44, #65)

Bug fixes¶

Fix files remaining locked after closing a fast-loaded window (#69)
Fix launching from command line with bad metadata argument (#82)

neurotic 0.6.0¶

2019-07-10

Improvements¶

Add a basic “About neurotic” window with version and website information (#38)
Update logo (#39)
Add keywords and project URLs to package metadata (#40)

neurotic 0.5.1¶

2019-07-09

Compatibility updates¶

Compatibility update for RawIOs with non-zero offset (#37)

neurotic 0.5.0¶

2019-07-06

Improvements¶

Support fast (lazy) loading in Neo < 0.8.0 (#35)
Add “git.” and conditionally “.dirty” to dev local version identifier (#34)

neurotic 0.4.2¶

2019-07-06

Bug fixes¶

Fix for EstimateVideoJumpTimes regression introduced in 0.4.0 (#33)

neurotic 0.4.1¶

2019-07-02

Compatibility updates¶

Change sources of development versions of dependencies (#32)
Compatibility update for scaling of raw signals (#31)

neurotic 0.4.0¶

2019-07-01

Improvements¶

Show epochs imported from CSV files with zero duration in epoch viewer (#27)
Show epochs/events imported from data file in events list/epoch viewer (#28)
Alphabetize epoch and event channels by name (#29)

neurotic 0.3.0¶

2019-06-29

Improvements¶

Remove dependency on ipywidgets by making notebook widgets optional (#25)
- Notebook widget classes renamed: MetadataSelector → MetadataSelectorWidget, EphyviewerConfigurator → EphyviewerConfiguratorWidget
Add app description and screenshot to README (#22)
Promote to beta status (#23)

neurotic 0.2.0¶

2019-06-28

Improvements¶

Add basic command line arguments (#14)
Add continuous integration with Travis CI for automated testing (#13)
Add some tests (#15, #16)
Migrate example data to GIN (#18)

Bug fixes¶

Fix crash when downloading from a server that does not report file size (#17)
Raise an exception if a Neo RawIO cannot be found for the data file (#12)

neurotic 0.1.1¶

2019-06-22

Bug fixes¶

Fix various downloader errors (#7)

neurotic 0.1.0¶

2019-06-22

First release

neurotic: NEUROscience Tool for Interactive Characterization¶

Table of Contents¶

Overview¶

Installing neurotic¶

Standalone Installers (recommended for beginners)¶

Alternate Method: conda (recommended for Pythonistas)¶

Alternate Method: pip¶

Updating neurotic¶

Updating with Standalone Installers¶

Updating with conda¶

Updating with pip¶

Development Version¶

Getting Started¶

Citing neurotic¶

Configuring Metadata¶

Top-Level Organization¶

Specifying Data Locations¶

Remote Data Available for Download¶

URLs to Use with Google Drive¶

URLs to Use with GIN¶

Global Configuration Settings¶

Data Reader (Neo) Settings¶

Video Synchronization Parameters¶

Constant Offset¶

Frame Rate Correction¶

Discrete Desynchronization Events¶

Real-World Date and Time¶

Plot Parameters¶

Time Range¶

Epoch Encoder Parameters¶

Filters¶

Amplitude Discriminators¶

tridesclous Spike Sorting Results¶

Firing Rates¶

Firing Frequency Burst Detectors¶

Rectified Area Under the Curve (RAUC)¶

Metadata Examples¶

Configuring for Google Drive¶

Generating a Client Secret File¶

Authorizing neurotic to Access Google Drive¶

Making Google Drive Authorization Persistent¶

Purging Google Drive Authorization¶

Changing Default Behavior¶

API Reference Guide¶

neurotic.datasets.data¶

neurotic.datasets.download¶

neurotic.datasets.ftpauth¶

neurotic.datasets.gdrive¶

neurotic.datasets.metadata¶

neurotic.gui.config¶

neurotic.gui.epochencoder¶

neurotic.gui.notebook¶

neurotic.gui.standalone¶

neurotic.scripts¶

neurotic._elephant_tools¶

Release Notes¶

neurotic 1.5.0¶

New features¶

Improvements¶

Documentation¶

Testing¶

neurotic 1.4.1¶

Improvements¶

Bug fixes¶

Other changes¶

Documentation¶

neurotic 1.4.0¶

New features¶

Help & feedback¶

Jupyter tutorial¶

Other changes¶

Bug fixes¶

Documentation¶

Logging¶

neurotic 1.3.0¶

Improvements¶

Bug fixes¶

Documentation¶

neurotic 1.2.1¶

Bug fixes¶

`neurotic.datasets.data`¶

`neurotic.datasets.download`¶

`neurotic.datasets.ftpauth`¶

`neurotic.datasets.gdrive`¶

`neurotic.datasets.metadata`¶

`neurotic.gui.config`¶

`neurotic.gui.epochencoder`¶

`neurotic.gui.notebook`¶

`neurotic.gui.standalone`¶

`neurotic.scripts`¶

`neurotic._elephant_tools`¶