Electrophysiology reference documentation

• If new to the field, start here: Approaches to study neural circuits course (2020) — 11 lectures, 2 dedicated to electrophysiology (lectures 3-4), by Luke Sjulson, Albert Einstein College of Medicine
• Some study design guidelines: Recommendations for the Design and Analysis of In Vivo Electrophysiology Studies, editorial board, J. Neurosci. (2018)
• A good primer: Tools for probing local circuits: high-density silicon probes combined with optogenetics, Buzsaki et al. 2015
• A good protocol with video: Implantation of Chronic Silicon Probes and Recording of Hippocampal Place Cells in an Enriched Treadmill Apparatus, Sariev et al. 2017 (no open source alternative, but too valuable to omit)
• A unified data format: Neurodata Without Borders (NWB), a formatting standard for cell-based neurophysiology data, Teeters et al. 2015
• A classic reference manual (to consult before hitting the search engines): The Axon Guide — Electrophysiology and Biophysics Laboratory Techniques 3rd ed.
• Cool Neuropixels resources: Nick Steinmetz's lab page, includes data, analysis software and training materials.

Electrophysiology troubleshooting

• Always RTFM 🙂
• Electric noise troubleshooting flowchart, Jeffery lab 2018
• More detailed noise debugging tips, Neuralynx 2019

Spike sorting

• Introduction: Past, Present and Future of Spike Sorting Techniques, Rey et al. 2015
• Alternatively, introductory lecture: An Introduction to Spike Sorting, Bhagtat and Moore-Kochlacs, MIT 2017
• Comparing algorithms: SpikeForest, reproducible web-facing ground-truth validation of automated neural spike sorters, Magland et al. 2020
• A popular method developed for Neuropixels data: Kilosort2, Pachitariu 2020
• Ground-truth validated method: A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo, Yger et al. 2018

Behavior reference documentation

• Conceptual start: Neuroscience Needs Behavior: Correcting a Reductionist Bias, Krakauer et al. 2017
• General considerations: A hitchhiker's guide to behavioral analysis in laboratory rodents, Sousa et al. 2006 and Probing perceptual decisions in rodents, Carandini & Churchland 2013
• Head-fixed tasks in virtual reality are growing in popularity — tight control of the stimulus, easier recordings. See a recent introductory review of head-fixed tasks (Bjerre & Palmer 2020). Two approaches stand out for task design (full disclosure: two of the 3Dneuro team worked with co-authors of one as post-docs, and one led the studies in the other):
  1. Standardized tasks that optimize for reproducibility across different labs, The International Brain Laboratory et al. 2020
  2. Tasks that push the limits of what animals can achieve, but are less easily reproducible: e.g. the Virtual-Environment-Foraging Task (1) and (2), Havenith et al. 2018, 2019. Worth the detour to the supplementary note: Seven principles of task design for mice.
• Freely moving tasks typically enable more naturalistic behaviors, from the classic Morris water maze to more recent route planning studies (e.g. Jackson et al. 2020).
• Food/water restriction: the Janelia protocol for water restriction covers weight and health monitoring, task performance vs. weight, and long-term effects (Guo et al. 2014). The choice between food or water restriction affects learning (Goltstein et al. 2018).
• Automated experiments: combined with ephys, e.g. Automated long-term recording and analysis of neural activity in behaving animals, Dhawale et al. 2017. Or behavioral assessment alone, e.g. An automated home-cage-based 5-choice serial reaction time task for rapid assessment of attention and impulsivity in rats, Bruinsma et al. 2019.
• General-purpose animal 3D pose estimation: DeepLabCut (pose, whisker, and eye tracking across species). SimBA, a toolkit for analyzing complex social behavior in rodents (also supports DeepLabCut).

Welfare and handling

Happy animals are good lab animals.

These go beyond the standard 'license to work with animals' training, and help make lab animals less stressed, which improves the odds of pretty much anything you're trying to do with them.

• Rat and mice handling videos, Genzel lab, Radboud University
• Rat tickling course, Gaskill lab, Purdue University

Select open hardware projects & papers

Some projects include software as well.

• General lab equipment, with focus on affordability and education: Open Labware: 3-D Printing Your Own Lab Equipment, Baden et al. 2015. See also the project website for design files.
• A robot for automated craniotomies: Autosurgery — website, see also the paper by Pak et al. 2015
• Implant surgery without stereotaxic device & modular implant designs: RatHat: A Self-Targeting Printable Brain Implant System, Allen et al. 2020
• Implant design for optoelectronic probes: Micro-drive and headgear for chronic implant and recovery of optoelectronic probes, Chung et al. 2017
• Chronic drive implant for tetrode arrays: the Open Ephys ShuttleDrive — webpage and paper by Voigts et al. 2019
• Complete mouse virtual reality rig design: Harvey Lab mouse VR (2020), lab site
• Microscopes: OpenFlexure, UC2

Open hardware/software repositories

Build your own lab.

• Possibly the largest in size and scope: Open Behavior. Their resources page lists many tools and companies for building equipment. See also Open Neuroscience.
• Recording hardware/software: Open Ephys wiki — becoming the standard for both high-channel-count electrophysiology and open hardware projects.
• With a focus on affordability: Lab on the Cheap (not neuroscience specific)

How to open hardware

Spread the love.

• Getting started: Open hardware basics and certification
• Licensing your work: CERN Open Hardware License
• State-of-the-art specification: Open know-how manifesto
• Community: Gathering for Open Science Hardware (GOSH), DocuBricks
• Publish: Journal of Open Hardware, HardwareX

Companies

There's a whole ecosystem for electrophysiology in behaving animals. This section is a work in progress — feedback welcome.

Probes, accessories and electronics

• Probes: Neuronexus, Cambridge NeuroTech, Diagnostic Biochips, Neural Dynamics Technologies, Atlas Neuro, Thomas Recording, MicroProbes
• Probes (nonprofit): Neuropixels
• Recording electronics and accessories (open source): Open Ephys
• Recording electronics and accessories: Neuralynx, TDT, Blackrock, Plexon, White Matter, Ymetry (head fixation)
• Recording electronics and accessories (open and closed source): SpikeGadgets, NeuroTek (including a tetrode drive loading service)

Behavior

• Noldus, Neurotar, imetronic, Labeotech

Consulting

• Assembly service for open hardware: Labmaker, Sanworks, NeuroGig (also equipment re-use), see also #NeuroRigBuilder
• Custom hardware/software: ViSE (also data science, manuscript editing)
• Open hardware: Prometheus Science
• Software: Metacell

Education

• Backyard Brains

Other

• Many great resources: Allen Institute Products & Tools
• Don't make everything yourself: The case for consulting in neuroscience (Voigts, 2019)
• Don't draw everything yourself: SciDraw, a free repository of quality scientific drawings.
• Smart bibliography tool: Connected Papers builds a visual graph of related work around a paper, based on similarity.
• Beyond scope, yet awesome: INSS builds custom multiphoton microscopes, hardware and software, at a fraction of commercial cost.
• Open solution for systems neuroscience research (blog): Labrigger
• For educators on a budget: Reducing the Cost of Electrophysiology in the Teaching Laboratory, Wyttenbach et al. 2018