NeuroLoop utilities v1

Overview

This is a set of libraries and utilities written to support closed-loop neural stimulation experiments. As of October 2020, the emphasis is on detecting transient oscillations in the local field potential ("LFP bursts") and providing stimulation triggers that are phase-aligned to oscillations. In the future the libraries and utilities may be extended to cover additional experiment scenarios.

The NeuroLoop project is copyright (c) 2020-2021 by Vanderbilt University, and is released under the Creative Commons Attribution 4.0 International License.

Documentation

The following directories contain documentation:

• manual -- Output directory for project documentation. Documentation PDFs are here.
• manual-src -- LaTeX build directory for project documentation. Use make -C manual-src to build it.

Applications

Application scripts are intended for direct use. These are found in the code-applications directory. The following scripts are provided:

• nloop_chantool.m -- This is a GUI application that looks at folders containing Intan per-channel data and identifies channels that have spikes and channels that have LFP bursts.

Libraries

Libraries are provided in the libraries directory. With that directory on path, call the addPathsLoopUtil function to add sub-folders.

Library subdirectories are listed below.

"Core" libraries:

• lib-nloop-io -- Library functions for loading and saving data that aren't vendor-specific.
• lib-nloop-plot -- Helper functions for plotting. These are not publication-quality.
• lib-nloop-proc -- Library functions for performing signal processing.
• lib-nloop-util -- Helper functions that don't fall into the other categories.

"Abstraction" libraries:

• lib-nloop-ft -- Library functions for interoperating with Field Trip.
• lib-nloop-intan -- High-level library functions for manipulating data saved in Intan's format.
• lib-vendor-intan -- Low-level library functions for manipulating data saved in Intan's format, derived from code supplied by Intan Technologies (used and re-licensed with permission).
• lib-nloop-openephys -- High-level library functions for manipulating data saved in Open Ephys's format.

"Application" libraries:

• lib-nloop-chantool -- Library functions specific to the nloop_chantool script.
• lib-nloop-check -- Library functions specific to the in-house "sanity checking" script.

Sample Code

Sample code scripts are intended to illustrate how the libraries are used. These are found in the code-examples directory. The following scripts are provided:

code-example-reading folder:

This demonstrates how to read and process ephys data.

• do_test.m -- This is my test script for exercising the "LoopUtil" library. It does the same operations as the channel tool, without a GUI. Referencing is performed a bit differently as of Dec. 2021 (it can do common-average referencing and it does rereferencing before artifact removal rather than after). You'll need to edit the plotdir variable and create a configuration script that points to your data to use it.
• do_config_reider.m, do_config_frey_tungsten.m, and do_config_frey_silicon.m are representative configuration scripts using private datasets. See the preamble of do_test.m for details on what needs to be configured and what optional settings may additionally be configured.

code-example-robinson folder:

This demonstrates how to generate synthetic data using the extended Robinson model functions.

(This is the end of the file.)