The Virtual Science Lab - Defining Cell Types by their Electrophysiology Q&A

Thanks for attending the webinar or viewing the video of “The Virtual Lab: Defining Cell Types by their Electrophysiology” with @ajuavinett and @tmchartrand! This webinar demonstrated a lesson plan for college neuroscience classes that uses Allen Cell Types Database data. Please feel free to chime in here with additional questions or follow-ups, and to continue the conversation more generally here in this thread. You can find the recording of this webinar and information about upcoming webinars at alleninstitute.org/virtual-lab-webinars .

1 Like

Question: Is there is glossary/legend that go along with the cell feature search page? Thanks! For example, explains what the abbreviations are?
Kaitlyn: We do! At the top of the Cell Feature Search page, click help. It’ll pop up a window with a list of the abbreviations and brief definitions. You can also go there directly with this link.
Ashley: Here’s an additional glossary for some of the pre-computed features that we’ll see in the notebook today.
Tom: And the most detailed definitions are in our white papers available here, or of course in the feature extraction code and its documentation.

Question: Are all recordings done in current clamp? Or do you have mIPSC and mEPSC data?
Tom: The IVSCC is primarily in current clamp, with synaptic blockers (there may be a few voltage clamp sweeps, but primarily for QC, not feature extraction). However, we have a whole synaptic physiology project focused on this here. These cells do have a shorter set of intrinsic electrophysiology characterization, in addition to recorded PSP/PSCs from spikes triggered in other cells that are being patched simultaneously!

Question: Can you tell us a bit about the decision making process for picking 1 s long current steps as the default? I’m curious as I could easily make that the default duration in my future recordings.
Tom: I can’t give you a complete answer as this was before I arrived here, but it’s an attempt to balance overall recording duration with enough time to see delayed spikes (suprathreshold) and for all channels to equilibrate (subthreshold). If you want a super detailed answer from some electrophysiologists our Community Forum (that’s here!) would be a good place to bring it up!

Question: Are there morphoelectrical/transcriptomic data on astrocytes and microglial
Kaitlyn: We do have transcriptomic data on astrocytes/microglia! It’s mixed in with the neuronal transcriptomic data. You can find the transcriptomic data here. We don’t have morphology or ephys on the non-neuronal cells.

Question: Coursera also offers nice coding courses. Also comp neuro for grad students or postdocs where they incorporate some Matlab and Python training.
Kaitlyn: Good recommendations! We love when students can see the applications of code when they learn by doing analyses, but online resources are really valuable for learning the language.
Ashley: Yes! I also have my students use dataquest.io for introductory lessons. For more advanced lessons, I’d recommend Neuromatch Academy.

Question: New to google Colab: if students leave this page from their browser, does it clear all their work? Thanks!
Ashley: Yes, but they can create their own copy of the notebook and update/save that permanently. Instructions: 1) File > Save. 2) Go to Google Drive > Colab Notebooks folder. 3) Re-open the file with Google Colab!

Question: Where can we find information about the location of the cell during the recording (e.g., region, layer, position on the CCF, etc.)
Kaitlyn: This is included in the cell metadata! It should be pulled in when you create that dataframe or view the data on our website.

Please feel free to post additional/follow-up questions below!