Where's the data for spike width, and what are all these features?

Hi all!

In the documentation for the Cell Types Database, there’s a mention of spike width as a derived metric for single spikes, however I don’t see it on the website or when I pull the data from the SDK. Is this metric hiding? Or is it simply not in the cell features any longer? It would be great to have. :slight_smile:

Related, is there any documentation that clearly maps all of the metrics available via get_ephys_features to what each of these are actually capturing (e.g., fast trough vs slow trough)? I can piece it together from the documentation, but it is kind of dense to tease apart.

Thanks!
Ashley

Hi Ashley,
You’re correct that spike width is not among the spike features included in the cell features summary. However, you can use AllenSDK to calculate it easily - see https://allensdk.readthedocs.io/en/latest/_static/examples/nb/cell_types.html#Computing-Electrophysiology-Features.
Regarding documentation, it looks like you already found the ephys whitepaper (help.brain-map.org/display/celltypes/Documentation), which is the best source currently. Note that the AP features included as cell features are in Table 3. I know there are a few aspects of the whitepaper that are out of date (e.g. AP height from trough is no longer calculated at all), so if you have any specific suggestions for clarity there let us know, as it’s due for an update soon.

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Thank you, I didn’t know about the EphysSweepFeatureExtractor – that’s useful!

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