Resources

For whom?   Anyone concerned with the practical aspects of electrophysiology in the behaving laboratory animal. 

What?    A curated list of resources for how to get started with extracellular (in vivo/behaving) ephys experiments. Mostly in small animals/rodents. Also an easy-access reference list for more experienced users.

How? The aim is for necessary and sufficient. By reading these sources, you should in principle be able to set up in vivo ephys experiments based on open-access information (and gear as far as possible). The list is not comprehensive – it’s based on our own (probably biased) experimental experience, and we are always happy to add open access resources. If you have comments or recommendations, please contact us at: contact -AT- 3dneuro.com

Last revision     July 4, 2020

Use     This work is licensed under a Creative Commons Attribution 4.0 International License. In a nutshell, this means anyone is free to share and adapt it, as long as they give proper credit to the original source (this website).

Table of contents


Electrophysiology reference documentation


Electrophysiology troubleshooting


Spike sorting


Behavior reference documentation

  • Head-fixed tasks in virtual reality are growing in popularity as they enable tight control of the stimulus combined with easier recordings. See recent introductory review of head-fixed tasks (Bjerre & Palmer 2020). In that context, 2 approaches have emerged that are a very good start when you are considering behavioral task design (Full disclosure: Two from the 3Dneuro team worked with co-authors of 1 as post-docs, and one led the studies in 2).
  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. Give special attention to the supplementary note: Seven principles of task design for mice.


Welfare and handling

Happy animals are good lab animals.

These resources go beyond typical ‘license to work with animals’ training, and are great for making lab animals less stressed, which improves the odds of pretty much anything you wish to achieve with them.


Select open hardware projects & papers

Some projects include software as well.


Open hardware/software repositories

Build your own lab.

  • Possibly the largest in size and scope: Open Behavior. Their resources page also lists many tools/companies for building stuff. See also Open Neuroscience
  • Recording hardware/software: Open Ephys wiki. Open Ephys is 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.


Companies

There’s a whole ecosystem for electrophysiology in behaving animals. This section is work in progress and we appreciate your feedback.

Probes, accessories and electronics


Behavior


Consulting


Education


Other

Do you think an important resource is missing? Is something outdated? Do you have a specific problem that’s not included here? Let us know in a comment here, or mail / tweet our way!

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