Matching Cell Type Nomenclature to Cells in the Cell Types Database

I am trying to analyze the morphology and electrophysiology data of individual cells in the Cell Types Database. I want to divide the cells based on cell types and have discovered that the Allen Brain Map is in an effort of standardizing the cell type nomenclature. However, the cell feature data ( only has cell specimen ID, but no cell set accession IDs or cell set aliases. Is there any ways of matching individual cells’ specimen ID to a reference cell type classification (either an ID or an alias)?

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Hi @Veritatem_Amo. Thank you for your interest–this is exactly the kind of use case we are targeting with the nomenclature efforts. This short answer is that it can be done currently through a two step process. First, cells were assigned to morphological and electrophysiological types in the associated manuscript (Classification of electrophysiological and morphological neuron types in the mouse visual cortex) and Supplementary Table 3 includes cell type calls for each cell (including Specimen ID to link back to the Allen Cell Type Database). Second, in our nomenclature manuscript (Common cell type nomenclature for the mammalian brain), we assigned aligned aliases to the associated ‘ME types’ from the above manuscript, which you can find in Additional File 1. Aligned aliases are also included for several other taxonomies, allowing you to link to other (primarily transcriptomics) studies.


Thank you very much @jeremyinseattle !
Sup table 3 of the Nature Neuroscience paper is very helpful, and I was able to align most cells of interest to me-types.
However, I couldn’t find alignment of nomenclature alias to me-type (I assume still looks like something along “ME_Exc_19”) in the eLife paper supplements. The closest thing I found is supplementary Table 3 of the Nature Neuroscience paper, which gives the description and relationship to previously described types of each me-type.

Within Additional File 1 there is a file called “cell_set_nomenclature.xlsx” that contains the following information:

cell_set_preferred_alias cell_set_ label cell_set_ aligned_alias cell_set_ additional_alias
ME_Inh_1 ME 01 Descending axon, bidirectional dendrites L2/3, L4
ME_Inh_2 ME 02 Descending axon, bidirectional dendrites L2/3
ME_Inh_3 ME 03 Descending axon, bidirectional dendrites
ME_Inh_4 ME 04 Descending axon, bidirectional dendrites L2/3, L4
ME_Inh_5 ME 05 Descending axon, bidirectional dendrites L2/3
ME_Inh_6 ME 06 Wide axon, large dendrites L6
ME_Inh_7 ME 07 Wide axon, large dendrites L6
ME_Inh_8 ME 08 Dense axon, intersecting dendrites L5, L4
ME_Inh_9 ME 09 Ascending axon L5, L6
ME_Inh_10 ME 10 Ascending axon
ME_Inh_11 ME 11 Ascending axon L5, L6
ME_Inh_12 ME 12 Small axon, intersecting dendrites
ME_Inh_13 ME 13 Ascending small axon L5, L4
ME_Inh_14 ME 14 Dense axon, intersecting dendrites L4, L2/3
ME_Inh_15 ME 15 L1-innervating ascending axon L2/3, L4
ME_Inh_16 ME 16 Descending dense, wide axon L2/3
ME_Inh_17 ME 17 Late-spiking L1 neurogliaform cells
ME_Inh_18 ME 18 Dense axon, large dendrites L1
ME_Inh_19 ME 19 Lamp5 Lhx6 Dense axon, small dendrites L6
ME_Inh_20 ME 20 Dense axon, small dendrites L2/3, L4
ME_Inh_21 ME 21 Chandelier Descending axon, small juxtaposed dendrites L2/3
ME_Inh_22 ME 22 Small axon, large dendrites L5, L6
ME_Inh_23 ME 23 Sst Chodl Wide axon, large dendrites L5, L6
ME_Inh_24 ME 24 Large ascending axon L5, L6
ME_Inh_25 ME 25 L1-innervating ascending axon L2/3, L4 & ascending large axon L5
ME_Inh_26 ME 26 Ascending small axon L5, L4
ME_Exc_7 ME 27 L2/3 IT Wide, short L2/3
ME_Exc_14 ME 28 Tufted (sparse) L4
ME_Exc_18 ME 29 Non-tufted L4
ME_Exc_13 ME 30 L5 IT Tufted L5
ME_Exc_1 ME 31 L5 CF Thick-tufted L5
ME_Exc_8 ME 32 L5 NP Tufted (sparse basal) L5
ME_Exc_6 ME 33 Wide, short L6a & tufted (large basal) L5
ME_Exc_11 ME 34 Inverted L6a, b
ME_Exc_2 ME 35 Narrow L6a
ME_Exc_4 ME 36 Narrow L6a
ME_Exc_9 ME 37 L6b Subplate L6b
GABAergic ME 01-26 GABAergic
Glutamatergic ME 27-37 Glutamatergic
Vip ME 01-05 Vip
Pvalb ME 06-14, 16, 21 Pvalb Fast spiking
Sst ME 15, 22-26 Sst
Lamp5 ME 17-20 Lamp5
L4 ME 28-29 L4
L6 IT ME 33-34 L6 IT
L6 CT ME 35-36 L6 CT
Sst (Martinotti) ME 15, 24-25 Martinotti
Sst (Non-Martinotti) ME 22-23 Deep non-Martinotti

Is this what you are looking for? If so, great! If not, please provide more details. Thanks!


Thank you very much! For some reason I thought those columns only have RNAseq labels.
This is perfect!