Resources
Authors & Affiliations
Jeroen Bos, Guido T Meijer, Francesco P Battaglia
Abstract
There are many great open-source tools available for the processing of neuronal data acquired using Neuropixels probes. Each of these tools, however, focus on a part of the entire pipeline from raw data to spike- and event times. For example, SpikeInterface is an incredibly useful Python module for pre-processing and spike sorting of individual recordings. However, there are more steps in between raw data and spikes, such as synchronization of spike times between probes and histological reconstruction of probe insertions. Large collaborations, like the International Brain Laboratory (IBL), have developed fully integrated end-to-end pipelines, but because these pipelines are embedded in their database architecture. They do not run out-of-the-box on recordings made by researchers from outside the collaboration. Therefore, we developed Power Pixels, which combines parts of the IBL pipeline with SpikeInterface and stand-alone packages into one integrated pipeline. It includes pre-processing, spike sorting, neuron-level quality control metrics (BombCell), synchronization between multiple probes, compression of raw data, and ephys-to-histology alignment. Integrating all these steps into one pipeline greatly simplifies the processing of Neuropixels recording data, especially for novel users who might struggle to find their way around all the available code and tools. In summary, Power Pixels is a pipeline which aims to provide the smooth integrated experience that researchers in large collaborations enjoy to everyone.