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Copy file name to clipboardExpand all lines: Background.md
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## Acquisition tools
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The typical instrumentation used for data acquisition is the Neuropixels probe and headstage interfacing with a PXIe acquisition module (https://www.neuropixels.org/control-system).
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Two main acquisition softwares are used for Neuropixels:
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SpikeGLX - developed by Bill Karsh and Tim Harris at HHMI/Janelia
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OpenEphys - developed by Joshua Siegle at the Allen Institute.
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+ SpikeGLX - developed by Bill Karsh and Tim Harris at HHMI/Janelia
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+ OpenEphys - developed by Joshua Siegle at the Allen Institute.
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These save the data into specific directory structure and file-naming convention as custom binary formats (e.g. “.bin”, “.dat”). Meta data are stored as separate files in xml or text format.
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## Preprocessing tools
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+ SpyKING CIRCUS
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Kilosort provides most automation and has gained significant popularity, being adopted as one of the key spike sorting methods in the majority of the teams/collaborations we have worked with. As part of Year-1 U24 effort, we provide support for data ingestion of spike sorting results from Kilosort.
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Further effort will be devoted for the ingestion support of other spike sorting methods. On this end, a framework for unifying existing spike sorting methods, named SpikeInterface, has been developed by Alessio Buccino, et al. SpikeInterface provides a convenient Python-based wrapper to invoke, extract, compare spike sorting results from different sorting algorithms.
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Further effort will be devoted for the ingestion support of other spike sorting methods.
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On this end, a framework for unifying existing spike sorting methods,
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named [SpikeInterface](https://github.com/SpikeInterface/spikeinterface),
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has been developed by Alessio Buccino, et al.
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SpikeInterface provides a convenient Python-based wrapper to invoke, extract, compare spike sorting results from different sorting algorithms.
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