Template structure for pre-processing HSN data.
This is a template repository for pre-processing human single-neuron data, including spike sorting.
This template follows the general purpose ProjectTemplate layout from StructuredScience.
For information on how to use this template in a project, see the HSNPipeline Guide.
This template includes spike sorting, with the default approach using the combinato spike sorter.
Note: if copying this template for use, this section can be removed.
Provide an overview of the project / data here, for example:
This repository manages pre-processing for the XX task / project.
This repository requires Python >= 3.7.
As well as typical scientific Python packages, dependencies include:
The full list of dependencies is listed in requirements.txt.
Note that the above link for combinato is for an updated version adapted for us with the HSNPipeline. The original version is here.
Fill in or edit any additional requirements here.
This repository is set up in the following way:
metadata/contains config files that define metadata fieldsnotebooks/contains notebooks that demonstrate examples of pre-processing and spike sortingprep/contains custom code for pre-processing data and running sorting datascripts/contains stand alone scripts to run processesshell/contains shell scripts that run pre-processing related operations
Add or edit any details about repository layout here.
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 PrepTEMPLATE.