Awesome Neuropixels

A curated list of awesome Neuropixels resources, in no particular order. Create a pull request or raise a github issue to add any resources to this list.

Contents

• Community
• Neuropixels papers and manuals
• Courses, talks and videos
• Probe setup, care and sharpening
• Chronic implants
• Data acquisition
• Data preprocessing
• Spike-sorting
• Quality control
• Tracking cells across days
• Loading and plotting data
• Trajectory planning and histology
• General frameworks

Community

• Neuropixels slack

Neuropixels papers and manuals

• Neuropixels 1.0, manual
• Neuropixels 2.0, manual
• Neuropixels ultra
• Neuropixels for NHP
• Neuropixels for humans

Courses, talks and videos

• 2023 October - UCL Neuropixels Course 2023, youtube videos
• 2022 October - UCL Neuropixels Course 2022, youtube videos
• 2021 October - UCL Neuropixels Course 2021, youtube videos
• 2020 April - UCL Neuropixels Course 2020, youtube videos
• 2019 April - UCL Neuropixels Course 2019
• 2018 April - UCL Neuropixels Course 2018
• 2017 May - UCL Neuropixels Course 2017

Probe setup, care and sharpening

• Sharpening probes
• Cleaning and caring for probes

Chronic implants

Recoverable implants:

• Melin & Couto implant, Churchland lab (GitHub page)
• Aery Jones implant, Giocomo lab (protocol)
• Apollo (Bimbard & Coen) implant, Carandini/Harris lab (paper, GitHub page)
• Ghestem implant, Ferraris lab (paper, GitHub page)
• van Daal, Aydin & Michon implant, Haesler lab (paper, GitHub page)
• Luo & Bondy implant, Brody lab (paper, GitHub page)
• Juavinett implant, Churchland lab (paper, GitHub page)

Non recoverable implants:

• See Steinmetz et al., 2019

Data acquisition

• SpikeGLX
• Open Ephys GUI
• Synchronizing data streams, optional Arduino code for applying external sync pulses here.
• Generating IMROs and channel maps - scripts
• Generating IMROs and channel maps - via SpikeGLX video 1, video 2
• Some tips to reduce noise

Data preprocessing

• Applying a phase shift to Neuropixels channels (to correct asynchronous sampling across ADCs):
  • details here
  • code
• Common-average-referencing (gets rid of noise):
  • CatGT
  • CAR
• Data compression/decompression:
  • compression/decompression
  • decompression

Spike-sorting

• Kilosort 2/2.5/3
• Python port of Kilosort 2.5 , white paper

Quality control

• Manual curation GUI: Phy, docs
• Bombcell: automated quality control, wiki
• / IBL quality metrics

Tracking cells over days

• UnitMatch, paper here
• Neuron_Tracking, paper here

Loading and plotting data

• NeuroPyxels
• Spikes

Trajectory planning

• Neuropixels Trajectory Explorer
• Pinpoint
• HERBS

Histology

• For classical slice-by-slice histology (2D) AP histology
• For 3D histology (cleared whole brains, brainsaw-ed brains) Brainglobe
• HERBS

General frameworks that incorporate many of these steps

• SpikeInterface
• Allen Institute pipeline, fork specifically tailored to spikeGLX data