Open for (neuro)science symposium: Day 2, Allen Brain Observatory

Thanks for attending the webinar or viewing the video of the Open for (neuro)science symposium day 2: Allen Brain Observatory, featuring @saskiad, @joshs, @michaelbu, @jxiaoxuan, Peter Ledochowitsch, Yaniv Ziv, and Joel Zylberberg! The speakers discussed their research using the publicly available Allen Brain Observatory.

Please feel free to chime in here with additional questions or follow-up questions to those asked at the live symposium. You can find the recording of this symposium and accompanying tutorials here.

Additional questions to those answered during the symposium Q&A:

Question: No variation of contrast?
Saskia: if you’re interested, we have a paper about contrast tuning here and the data is available here.

Question: Saskia and Josh: for the cre lines you used for imaging, have you also done experiments where you silence one of those populations and either image or neuropixel record from another one?
Saskia: We haven’t done that. In the Neuropixels dataset there was optotagging done for the inhibitory Cre lines, but we have not done perturbations.

Question: Are any of the simultaneous ephys + ophys data publicly available?
Saskia: You can find the simultaneous ophys/ephys dataset here.

Question: I wonder if combining your comparative analyses with cell-type identity can yield quantitative estimates of cell-type (size, firing rate) sampling bias with ephys.
Josh: This is tricky to do, because we have limited access to cell type information in the ephys data. We have a handful of inhibitory cells (Pvalb, Sst, and Vip) that have been identified via optotagging, but for excitatory cells we only have information about what cortical layer they are in. We are currently taking a different approach to answering this question, which is to record with ultra-high density Neuropixels probes (6 µm spacing between sites). We can then downsample the data to determine which cells we would have missed in “standard” Neuropixels recordings.

Question: Is there any possibility to make neuron from stem cells?
Kaitlyn: The Allen Institute for Cell Science produces fluorescently tagged human induced pluripotent stem cell lines that can be differentiated into neurons, among other cell types. More info on the cell lines and how to obtain them here.

Question: Have you also presented olfactory cues simultaneously? Mice are very smell driven.
Michael: No, we haven’t. That would be interesting.

Question: I’m also puzzled how the index measures response to “surprise” as opposed to measuring how similar the D and U stimuli are after convolving by the cell’s RF.
Joel: That’s a key point, and a real confound when just looking at day 1 USIs. Here, the systematic change over days is important: if just changes in RF-stimulus organization, you wouldn’t expect to systematically see the responses to D and U become more similar over days (esp. since the D locations on day 2 aren’t the same as D locations on day 1).