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 (https://celltypes.brain-map.org/cell_types_specimen_details.csv) 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)?
1 Like
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.
2 Likes
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!
2 Likes
Thank you very much! For some reason I thought those columns only have RNAseq labels.
This is perfect!