A curated list of awesome Neuropixels resources, in no particular order.
Want to add something to this list? Create a pull request, raise a github issue or send me a message: julie[dot]mfabre[at]gmail[dot]com.
- Community
- Neuropixels papers and manuals
- Images and svgs of the probes
- 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
- Opto-Neuropixels
Images and SVGs of probes can be found in this folder
- 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:
| Feature\Implant | Aery-Jones et al | Aydin, van Daal et al (Neuropixels 2 paper) | Bimbard, Coen et al. - "Apollo" implant | Couto & Melin - "indie" implant | Ghestem et al | Horan et al | Juavinett et al | Luo, Bondy et al | van Daal, Aydin & Michon et al (Nat Protocol) | Vöröslakos, Petersen, Vöröslakos et al |
|---|---|---|---|---|---|---|---|---|---|---|
| Organisms | Mouse | Mouse | Mouse/rat | Mouse | Rat | Mouse/rat | Mouse | Rat / mouse | Mouse/rat | Mouse/rat |
| Brain areas tested | HPC, MEC | > 10 brain regions | > 10 brain regions | > 6 brain regions | HPC, thalamus, amygdala | HPC, MEC, V1, Amygdala | Visual cortex, subiculum, midbrain | > 10 brain regions | > 10 brain regions | HPC, V1 in paper, >10 since then |
| NPX version | 1.0/2.0 | 2.0 | 1.0/2.0 | 2.0 | 1.0 | 1.0/2.0 | 1.0 | 1.0/2.0 | 1.0 | 1.0 |
| # of probes/implant | 1 | 2 | 2 | 1 | 1 | 1 | 1 | 1 | 1 (mouse) or 2 (rat) | 1 |
| max # of probes implantable | 2 | 2 (mice), 4 (rats) | 2 | 6 | 1 | 1 | 1 | 8 (rat, 2.0 probes), 4 (rat, 1.0 probes), 2 (mice) | 1 (mouse) or 2 (rat) | 2 (mice), 3 (rats) |
| Weight per implant | 1.4g for dual 2.0 probes | 0.57g | 2.6g | 1.5g | rat 1.0 implant: 2.6g, mouse: 0.7 - 1.0 g | 2.1g | 0.47g (machined in aluminum), 0.87g (3D print in steel) | |||
| Weight per implant w/ probes + estimated cement | previous: <4g dual 2.0, new: <3g dual 2.0 | 2.5g | 13g w/ HS | 3.5g 2.0 w/ HS | 2.0g | 3.5g - 6.8g w/ HS | ||||
| Implant stability & yield* | Ext. data fig 1e | Fig S2 | Fig 4 | Fig 6 | Fig 3 | Fig 4 | Fig 4 + supplements | Fig 11 | Fig 5 | |
| Additional features | Custom positions, angles and depths for each probe | Tested in social interactions (Eco-HAB) | Custom positions, angles and depths for each probe | Tested for social interactions | Tested in high velocity escape behaviors | Custom positions, angles and depths for each probe | Tested in social interactions (Eco-HAB) | Drivable | ||
| Links | protocol used in paper | paper, citation, GitHub page | paper, GitHub page | GitHub page | paper, GitHub page | paper, protocol, | paper, GitHub page | paper, GitHub page, mouse versions | paper, GitHub page | paper, Github link, modified version for 2.0 probes |
*note that stability and implant yield will depend on the brain regions targeted and curation method.
Non recoverable implants:
- SpikeGLX
- Open Ephys GUI
- Synchronizing data streams, optional Arduino code for applying external sync pulses here.
- Generating IMROs:
- via webinterface
- 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:
- Correcting motion artefacts:
- DREDge: paper
- 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.
- SpikeAgent (Spike sorting AI agent), paper
- / 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
- SpikeAgent (Spike sorting AI agent), paper
- Merging neurons:
-
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
- For 3D histology (cleared whole brains, brainsaw-ed brains) and/or classical slice-by-slice histology (2D) DeepSlice
- HERBS