SortTEMPLATE

Template structure for spike sorting microwire data from human subjects.

TEMPLATE DESCRIPTION

This is a template repository for running spike sorting on a dataset, using the combinato spike sorter.

This template follows the general purpose ProjectTemplate layout from StructuredScience.

For information on how to use this template in a project, see the HSUPipeline Guide.

Note: if copying this template for use, this section can be removed.

Overview

Provide an overview of the data here, for example:

This repository manages spike sorting for the XX task / project.

Requirements

Fill in any extra requirements here.

This repository requires Python >= 3.7.

As well as typical scientific Python packages, dependencies include:

• convnwb
• combinato

The full list of dependencies is listed in requirements.txt.

Repository Layout

This repository is set up in the following way:

• metadata/ contains config files that define metadata fields
• notebooks/ contains notebooks that demonstrate examples of spike sorting related tasks
• scripts/ contains stand alone scripts to run processes
• sort/ inherits from convnwb and contains custom code for pre-processing / sorting data
• shell/ contains shell scripts that run spike sorting related processes

Run Procedures

The main procedures involved are detailed through the notebooks.

To run processes across sessions / subjects, the files in shell and scripts can be used.

For a detailed description of how this approach works, and instructions on making updates, see the SortTEMPLATE.