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Thinh Nguyen
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Update Background.md
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Background.md

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## Pipeline Development
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Through our interviews and direct collaboration on the precursor projects,
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we identified the common motifs to create the Neuropixels Element with the repository hosted at https://github.com/datajoint/elements-neuropixels.
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we identified the common motifs to create the Array Electrophysiology Element with the repository hosted at https://github.com/datajoint/element-array-ephys.
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Major features of the Neuropixels Element include:
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Major features of the Array Electrophysiology Element include:
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+ Pipeline architecture defining:
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+ Probe, electrode configuration compatible with Neuropixels probes and generalizable to other types of probes (e.g. tetrodes) - supporting both chronic and acute probe insertion mode
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+ Probe-insertion, ephys-recordings, LFP extraction, clusterings, curations, sorted units and the associated data (e.g. spikes, waveforms, etc.)
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+ Ingestion support for spike sorting outputs from Kilosort
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+ Sample data and complete test suite for quality assurance
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Incorporation of SpikeInterface into the Neuropixels Element will be on DataJoint Elements development roadmap.
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Incorporation of SpikeInterface into the Array Electrophysiology Element will be on DataJoint Elements development roadmap.
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Dr. Loren Frank has led a development effort of a DataJoint pipeline with SpikeInterface framework and NeurodataWithoutBorders format integrated (https://github.com/LorenFrankLab/nwb_datajoint).
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## Alpha release: Validation sites
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We engaged several labs to adopt and validate the Neuropixels Element during the alpha testing phase. These include:
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+ Andreas Tolias Lab (BCM) - Anthony Ramos and Saumil Patel
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+ The lab uses Neuropixels 1.0 probes, recording in rodents and monkeys in the near future
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+ The lab has an existing animal, lab management and imaging pipeline, in need of a Neuropixels ephys pipeline
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+ The lab uses OpenEphys acquisition system, we extended the Neuropixels Element to provide support for OpenEphys in order to facilitate adoption/validation with Tolias Lab
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+ The lab uses on-premise institutional resource for data infrastructure and hosting
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+ Repository: https://github.com/cajal/pipeline
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+ BrainCoGs (Princeton Neuroscience Institute) - Manuel Schottdorf, Alvaro Luna
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+ DataJoint NEURO conducted a training workshop on March 1st to 3rd, 2021.
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+ The Neuropixels Element was adopted, connected to an existing BrainCoGs project pipeline. The ingestion routine was successfully validated on the existing Neuropixels dataset (acquired with SpikeGLX) and Kilosort outputs.
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+ Manuel Schottdorf expressed interest in comparison study between different spike sorting algorithms, thus further validating our roadmap to integrate the SpikeInterface framework into the Neuropixels Element
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+ The lab uses local institutional resource for data infrastructure and hosting
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+ Repository: https://github.com/BrainCOGS/U19-pipeline_python
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+ Brody Lab (Princeton) - Adrian Bondy, Alvaro Luna
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+ The Brody Lab performs ephys recordings on chronically inserted Neuropixels and tetrode probes. The lab is in the process of converting their existing MySQL database server into a DataJoint-compatible pipeline, and is in need of an ephys pipeline.
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+ We have extended the Neuropixels Element and provided a design version capable of supporting chronic probe insertion experiments.
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+ Though the ingestion routines are not included for non-Neuropixels probes, the Neuropixels Element’s architecture is compatible to ingest existing tetrode data acquired previously by the Brody Lab
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+ The lab uses local institutional resource for data infrastructure and hosting
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+ Repository: private repository
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We engaged several labs to adopt and validate the Array Electrophysiology Element during the alpha testing phase. These include:
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+ Andreas Tolias Lab (BCM)
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+ BrainCoGs (Princeton Neuroscience Institute)
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+ Brody Lab (Princeton)
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## Beta release
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As the validation progresses, we expect to produce a beta version of the workflow for users to adopt independently by May 1, 2021.

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