Defining cell types by their electrophysiology
What can the intrinsic physiology of genetically-identified cells tell us about their function?
The Allen Institute for Brain Science Cell Types Database contains information about the gene expression and electrophysiological properties of single cells in both mice and human brains. In this lab, we'll focus on the electrophysiology recordings. You'll dive into some of the different structures of dendrites, and how these might relate to the shape of their action potentials, and ultimately their role in neural computation.
This lesson plan is described in this Journal of Undergraduate Neuroscience article.
Learning objectives:
Relate the diverse intrinsic electrophysiological features of neurons to their structure and function
Compare electrophysiological characteristics of neurons in humans and mice
Practice using Jupyter Notebooks to run and edit Python code
Develop a sense of belonging and self-efficacy in coding and neuroscience research
Steps to Completing this Lesson
Understand how the data was collected.
Access the Allen Cell Types Dataset on their website. In this part, you can use the web interface to look at raw electrophysiology recordings and biocytin fills from mouse and human cells.
Learn about the basics of coding & using Jupyter notebooks and work through a sample Jupyter notebook. If you'd like to learn a bit of Python, this is a great chance to do so!
Analyze data through the Allen Software Development Kit (SDK)
For Instructors
There are multiple ways to implement these activities in your classroom. These activities were first implemented in an upper-division Neurobiology Laboratory course taught at a large, R1 university, but can be adapted for different course needs. Yi-Yun Ho & Bruce Johnson recently expanded on this lesson for a different course setting and needs (Ho et al., 2021, JUNE).
There is a full Google docs version of this lesson here, please feel free to download and modify for your purposes.
Here's a full recorded webinar with background information from Allen Institute scientist Tom Chartrand as well as an interactive walkthrough of the CellTypes Notebook. You'll also find related videos and teaching materials below.
Post a question on the Allen Brain Map Community Forum or get in touch if you have any questions: ajuavinett[at]ucsd.edu.
Related Videos & Teaching Materials
Webinar explaining the background & working through the CellTypesNotebook
Overview of the Cell Types Database
Virtual tour of patch clamping at the Allen Institute for Brain Science.
Sample publications with this dataset
Kalmbach et al. (2018) “h-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex” [Neuron][bioRxiv]
Gouwens et al. (2019) “Classification of electrophysiological and morphological types in mouse visual cortex” [Nature][bioRxiv]
Additional (from Ho et al. 2021): Billeh et al., 2020; Huang et al., 2021; Mosher et al., 2020; Nandi et al., 2020; Schneider-Mizell et al., 2020