Complete one concrete implementation of the Neuropixels analysis pipeline, including Kilosort integration and most pipeline stages (concatenation, time reference, Kilosort 2.5 bridging, PSTH, noise templates)

[vijayiyer05]

This will be a concrete realization of the more abstract pipeline established in Issue #1

For each stage of the pipeline not handled by Kilosort, there will be a few options for implementation:

• Invoke SpikeGLX command-line utilities (i.e. by system commands from MATLAB), where applicable
• Invoke and/or adapt equivalent functionality from the Neuropixel Utils package
• Re-implement Python code in MATLAB

As discussed at the kickoff meeting, the goal is a minimum meaningful use case through the pipeline. As such, the following can be considered optional stages & steps for the minimal concrete implementation:

• PSTH events
• QC metrics
• Manual curation
• intermediate visualization (e.g. with the phy package)