Is the absolute soma depth (in um) available for the neurons in the Cell Types database?

Technical
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1

Hi, I would like to have the absolute distance of the soma from pia for some of the neurons in the cell types database. Is this available? I’ve so far only found nomalised soma depth. From the Kalmbach et al Neuron 2018 paper however it seems that distance from pia was recorded for human supragranular neurons. Thanks

2

Hello @Thijs, absolute distance from pia can be available for only those cells with morphologies, is that still of interest to you?

-Rachel

3

Hi @racheld, thanks for your reply. Yes this would be tremendously valuable. I’m interested in the human L2/3 spiny neurons, would you have this available? Or have I missed this in the cell types database?

4

Hello @racheld, this is a kind reminder that I am still very eager to get the absolute distance from pia measures of the human L2/3 spiny cells with morphologies. Any chance I can get these?
Kind regards
Thijs

5

@Thijs Thanks for the reminder, message me your email and I can send you the csv.

6

Hi @racheld, my email is matthijs.verhoog@uct.ac.za. Thank you!

7

Dear @racheld hope you are well. I have a little follow-up question on the absolute/relative cell depths. For a subset of cells, I now have absolute and relative depth available. Am I right in that I can obtain the pia-white matter distance like this: absDepth/relDepth = pia-wm distance? Or was relative depth defined in a different way?

Further, I was wondering whether only pia-white matter distance was measured, or whether there is any more histological info available, particularly on the thickness of different human cortical layers from these patients/slices.

Thanks

8

Hello @Thijs, that is correct you could calculate the pia-wm distance the way you said. However, have you checked out this file (apologies for not pointing you to it earlier)? It also has depth within layer 2 & 3 that you might find helpful. Let me know if this doesn’t give you what you need. https://github.com/AllenInstitute/patchseq_human_L23/blob/3daf9f0803ea0c220a040ea523f23af5f93c56ac/data/human_IVSCC_excitatory_L23_consolidated_0131.csv

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Epic! thanks so much