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.
- Community
- Neuropixels papers and manuals
- Courses, talks and videos
- Probe setup, care and sharpening
- Chronic implants
- Data acquisition
- General frameworks
- Data preprocessing
- Spike-sorting
- Quality control
- Classifying cell types
- Tracking cells across days
- Loading and plotting data
- Trajectory planning and histology
Neuropixels slack- Neuropixels 1.0, manual
- Neuropixels 2.0, manual
- Neuropixels ultra
- Neuropixels for NHP
- Neuropixels for humans
- 2024 October - UCL Neuropixels Course 2024,
youtube 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
- Sharpening probes
- Cleaning and caring for probes
- Slack thread about how to store probes, and files for a wall-mounted enclosure
- Some tips to seperate shanks from each other
Recoverable implants:
- Aery Jones implant, Giocomo lab (protocol)
- Apollo (Bimbard & Coen) implant, Carandini/Harris lab (paper, GitHub page)
- Aydin & van Daal, implant, Haesler lab (paper, citation, GitHub page)
- Ghestem implant, Ferraris lab (paper, GitHub page)
- Juavinett implant, Churchland lab (paper, GitHub page)
- Luo & Bondy implant, Brody lab (paper, GitHub page)
- Melin & Couto implant, Churchland lab (GitHub page)
- van Daal, Aydin & Michon implant, Haesler lab (paper, GitHub page)
- Vöröslakos et al. microdrive implant, Buzsáki lab (paper, Github link, modified version for 2.0 probes).
Non recoverable implants:
- SpikeGLX
- Open Ephys GUI
- Synchronizing data streams, optional Arduino code for applying external sync pulses here.
- Generating IMROs and channel maps - via SpikeGLX video 1, video 2
- Some tips to reduce noise
SpikeInterface- Allen Institute pipeline, fork specifically tailored to spikeGLX data
- +
Guido Meijer's PowerPixels pipeline
- SpikeGLX:
- Open Ephys: / matlab, python
- Applying a phase shift to Neuropixels channels (to correct asynchronous sampling across ADCs):
- Common-average-referencing (gets rid of noise):
- Data compression/decompression:
- Kilosort 4, paper
- Kilosort 1/2/2.5/3 (archived), Kilosort 1 paper
- Python port of Kilosort 2.5 , white paper
- Potential errors (spikes missing in chunks) with Kilosort versions before 09 April 2024, github thread.
- Bombcell: automated quality control and metrics, wiki, talk at the annual Neuropixels course about quality control.
Manual curation GUI: Phy, docs. Example workflow here, Video demo here.- / IBL quality metrics
- Striatal and cortical cell types: Bombcell, wiki
- Cerebellar cell types (code not available yet, coming soon!)
- / UnitMatch, paper here
- Neuron_Tracking, paper here
-
3D trajectory planning tools (
⚠️ Note that the 3D tools below use a (scaled) version of the Allen Atlas, and they disagree with other standard atlases like Franklin & Paxinos. More information here⚠️ ) -
atlases:
- For classical slice-by-slice histology (2D) AP histology
- For 3D histology (cleared whole brains, brainsaw-ed brains) Brainglobe
- HERBS