# Cell Taxonomies **URL:** https://community.brain-map.org/c/cell-taxonomies/11.md [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) --- ## [About the Cell Taxonomies category](https://community.brain-map.org/t/about-the-cell-taxonomies-category/223)
**Author:** [@amyb](https://community.brain-map.org/u/amyb)\ **Replies:** 0
The Allen Institute joins a wide community of researchers and analysts who seek to use measurable properties of individual cells to aid in biologically meaningful classification. Share your insights, suggestions and fe… --- ## [How to compare different taxonomies?](https://community.brain-map.org/t/how-to-compare-different-taxonomies/3220)
**Author:** [@rachel.hostetler](https://community.brain-map.org/u/rachel.hostetler)\ **Replies:** 2\ **Last updated:** [March 15, 2025, 3:31am UTC](https://community.brain-map.org/t/how-to-compare-different-taxonomies/3220 "2025-03-15T03:31:21Z")
Hi all, I am posting a question I received on whether or not a conversion table exists to compare clusters between the Gouwens 2020 (V1), Yao 2021 (whole cortex and hippocampus), and Yao 2023 (whole mouse brain) taxonom… --- ## [Mapmycell pipeline for user](https://community.brain-map.org/t/mapmycell-pipeline-for-user/3285)
**Author:** [@hansol](https://community.brain-map.org/u/hansol)\ **Replies:** 3\ **Last updated:** [May 1, 2024, 9:10pm UTC](https://community.brain-map.org/t/mapmycell-pipeline-for-user/3285 "2024-05-01T21:10:23Z")
dear Allen today I joined the talk about Maymycell i would like to apply and use this with my dataset however I could not well navigate it. may I ask your instruction about it? (the tutorial notebook link was broken as… --- ## [Common Cell Type Nomenclature (CCN) publication now available in eLife](https://community.brain-map.org/t/common-cell-type-nomenclature-ccn-publication-now-available-in-elife/882)
**Author:** [@amyb](https://community.brain-map.org/u/amyb)\ **Replies:** 0\ **Last updated:** [January 8, 2021, 11:22pm UTC](https://community.brain-map.org/t/common-cell-type-nomenclature-ccn-publication-now-available-in-elife/882 "2021-01-08T23:22:35Z")
"Common Cell Type Nomenclature for the Mammalian Brain" by Miller, et al. was published at the very end of 2020, in eLife. This article captures what is also described on the Allen Brain Map portal, with more information… --- ## [Clarification Needed on Reference Setup in HiCAT Tutorial](https://community.brain-map.org/t/clarification-needed-on-reference-setup-in-hicat-tutorial/3521)
**Author:** [@eko2](https://community.brain-map.org/u/eko2)\ **Replies:** 0\ **Last updated:** [July 24, 2024, 6:03am UTC](https://community.brain-map.org/t/clarification-needed-on-reference-setup-in-hicat-tutorial/3521 "2024-07-24T06:03:03Z")
I have completed the HiCAT tutorial for analyzing my 10x single-cell RNA sequencing data, but I am unclear about the need and purpose of comparing results with reference data. I would appreciate some clarity on the role … --- ## [Brain Data Standards Workshop, February 5, 2021 - Discussion thread](https://community.brain-map.org/t/brain-data-standards-workshop-february-5-2021-discussion-thread/928)
**Author:** [@kaitlync](https://community.brain-map.org/u/kaitlync)\ **Replies:** 0\ **Last updated:** [February 4, 2021, 10:29pm UTC](https://community.brain-map.org/t/brain-data-standards-workshop-february-5-2021-discussion-thread/928 "2021-02-04T22:29:04Z")
On February 5, the Allen Institute and the Brain Cell Data Center is holding a workshop with collaborators on the topic of cell type summaries and presentations. Topics include the annotation of cell types, use cases for… --- ## [Mouse brain scRNAseq: distribution of cells by cortical layers/brain subregions](https://community.brain-map.org/t/mouse-brain-scrnaseq-distribution-of-cells-by-cortical-layers-brain-subregions/240)
**Author:** [@ainej](https://community.brain-map.org/u/ainej)\ **Replies:** 5\ **Last updated:** [June 20, 2023, 3:40pm UTC](https://community.brain-map.org/t/mouse-brain-scrnaseq-distribution-of-cells-by-cortical-layers-brain-subregions/240 "2023-06-20T15:40:17Z")
Hello, Would anybody know why in the mouse brain scRNAseq from ALM and VISp cortex regions there appears to be more cells from deeper layers? Also, VISp seems to have more cells in L4 compared to ALM. Is the reason anat… --- ## [Experience with Cell Counterß](https://community.brain-map.org/t/experience-with-cell-counterss/1365)
**Author:** [@Tiho](https://community.brain-map.org/u/Tiho)\ **Replies:** 0\ **Last updated:** [November 28, 2021, 6:30pm UTC](https://community.brain-map.org/t/experience-with-cell-counterss/1365 "2021-11-28T18:30:36Z")
Hi guys, I wanted to ask if by any chance someone has experience with this cell counter ? And if not, with any other cell counter? Thanks! :slight\_smile: --- ## [Fastq file availability from human SMARTseq data](https://community.brain-map.org/t/fastq-file-availability-from-human-smartseq-data/1891)
**Author:** [@jkniehaus](https://community.brain-map.org/u/jkniehaus)\ **Replies:** 1\ **Last updated:** [October 19, 2022, 3:28pm UTC](https://community.brain-map.org/t/fastq-file-availability-from-human-smartseq-data/1891 "2022-10-19T15:28:35Z")
Hello, First off, thank you for your atlases! I am interested in reanalyzing the SMARTseq human cortex data and was wondering if there was a repository where I could download this from. I see that the count matrices ar… --- ## [Average Firing Rate of a Cell](https://community.brain-map.org/t/average-firing-rate-of-a-cell/1160)
**Author:** [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Replies:** 1\ **Last updated:** [July 7, 2021, 6:39pm UTC](https://community.brain-map.org/t/average-firing-rate-of-a-cell/1160 "2021-07-07T18:39:36Z")
I have downloaded a file cell\_types\_specimen\_details.csv from the cell type database, which has a column “ef\_\_avg\_firing\_rate”. From the electrophysiology white paper, it seems like “cell-wide spike train features were b… --- ## [Regional cell taxonomy](https://community.brain-map.org/t/regional-cell-taxonomy/3746)
**Author:** [@scanchi](https://community.brain-map.org/u/scanchi)\ **Replies:** 3\ **Last updated:** [October 15, 2024, 5:51pm UTC](https://community.brain-map.org/t/regional-cell-taxonomy/3746 "2024-10-15T17:51:05Z")
Hello All, Thank you for providing the community with both the resources and tools for taxonomy assignment. Our lab is interested in developing region specific reference for our analysis purposes. I have been using the … --- ## [Open questions from recent workshops on cell ontology and taxonomy](https://community.brain-map.org/t/open-questions-from-recent-workshops-on-cell-ontology-and-taxonomy/226)
**Author:** [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\ **Replies:** 5\ **Last updated:** [August 20, 2019, 8:45pm UTC](https://community.brain-map.org/t/open-questions-from-recent-workshops-on-cell-ontology-and-taxonomy/226 "2019-08-20T20:45:31Z")
The Allen Institute recently hosted two workshops on Cell Ontology & Taxonomy, which brought together scientists studying brain cell types with subject matter experts in ontology building. In my opinion, these workshop … --- ## [NeMO atac-seq barcoding](https://community.brain-map.org/t/nemo-atac-seq-barcoding/2140)
**Author:** [@jkniehaus](https://community.brain-map.org/u/jkniehaus)\ **Replies:** 2\ **Last updated:** [April 21, 2023, 8:36pm UTC](https://community.brain-map.org/t/nemo-atac-seq-barcoding/2140 "2023-04-21T20:36:06Z")
Hello, I’m interested in analyzing mouse snATAC-seq data posted on the NeMO data portal. The compressed files contain read1 and read2 fastq files with what appears to be cell barcodes/UMIs in the fastq headers. However… --- ## [MapMyCells marker genes of classes](https://community.brain-map.org/t/mapmycells-marker-genes-of-classes/3150)
**Author:** [@mbatiuk](https://community.brain-map.org/u/mbatiuk)\ **Replies:** 2\ **Last updated:** [March 19, 2024, 10:03am UTC](https://community.brain-map.org/t/mapmycells-marker-genes-of-classes/3150 "2024-03-19T10:03:45Z")
Thanks for developing MapMyCells, it is very useful to annotate our data with Allen taxonomy. We got class/subclass predictions from mapmycells, and now we’re trying to validate those with marker gene expression. Curre… --- ## [Decode MapMyCell Abbreviations](https://community.brain-map.org/t/decode-mapmycell-abbreviations/3974)
**Author:** [@reck999](https://community.brain-map.org/u/reck999)\ **Replies:** 7\ **Last updated:** [December 19, 2024, 8:50pm UTC](https://community.brain-map.org/t/decode-mapmycell-abbreviations/3974 "2024-12-19T20:50:52Z")
I really like the MapMyCell tool! I would like to ensure I am correctly decoding the provided cell class and subclass abbreviations . There appears to be a table for this: Cell type references - brain-map.org. But the cu… --- ## [Matching Cell Type Nomenclature to Cells in the Cell Types Database](https://community.brain-map.org/t/matching-cell-type-nomenclature-to-cells-in-the-cell-types-database/1128)
**Author:** [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Replies:** 4\ **Last updated:** [June 14, 2021, 9:03pm UTC](https://community.brain-map.org/t/matching-cell-type-nomenclature-to-cells-in-the-cell-types-database/1128 "2021-06-14T21:03:51Z")
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… --- ## [Scrattch.hicat tutorial](https://community.brain-map.org/t/scrattch-hicat-tutorial/999)
**Author:** [@enh008](https://community.brain-map.org/u/enh008)\ **Replies:** 1\ **Last updated:** [April 2, 2021, 11:06pm UTC](https://community.brain-map.org/t/scrattch-hicat-tutorial/999 "2021-04-02T23:06:21Z")
Hello, I followed the scrattch.hicat tutorial found here (https://taxonomy.shinyapps.io/scrattch\_tutorial/#section-overview) with my scRNAseq dataset (instead of the tasic et al data) and the results says that my data h… --- ## [Neurons/Glia nuclei sizes for single nuclear RNAseq](https://community.brain-map.org/t/neurons-glia-nuclei-sizes-for-single-nuclear-rnaseq/280)
**Author:** [@ainej](https://community.brain-map.org/u/ainej)\ **Replies:** 4\ **Last updated:** [September 23, 2019, 10:47pm UTC](https://community.brain-map.org/t/neurons-glia-nuclei-sizes-for-single-nuclear-rnaseq/280 "2019-09-23T22:47:27Z")
Dear Community, I’m looking for quantitative estimates on sizes of nuclei of neurons (including subtypes) and glia in human brain. I haven’t found a comprehensive study of this in the literature and was wondering if the… --- ## [Top Leaf classification possible for Mouse Whole Cortex and Hippocampus (SMART-seq) RNAseq data?](https://community.brain-map.org/t/top-leaf-classification-possible-for-mouse-whole-cortex-and-hippocampus-smart-seq-rnaseq-data/1828)
**Author:** [@AnnaGalakhova](https://community.brain-map.org/u/AnnaGalakhova)\ **Replies:** 1\ **Last updated:** [October 4, 2022, 4:02am UTC](https://community.brain-map.org/t/top-leaf-classification-possible-for-mouse-whole-cortex-and-hippocampus-smart-seq-rnaseq-data/1828 "2022-10-04T04:02:17Z")
Hello everyone. I am trying to get RNAseq data from Mouse Whole Cortex and Hippocampus (SMART-seq) database. My interest is to look at the differential expression of a gene between three major excitatory subclasses in … --- ## [Invitation to Preview and Test Patch-seq Data Exploration Tool](https://community.brain-map.org/t/invitation-to-preview-and-test-patch-seq-data-exploration-tool/778)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 5\ **Last updated:** [February 1, 2021, 9:07pm UTC](https://community.brain-map.org/t/invitation-to-preview-and-test-patch-seq-data-exploration-tool/778 "2021-02-01T21:07:27Z")
In early 2021, we’re releasing new data exploration and visualization functionality for patch-seq data (detailed below). Initially this functionality will be enabled for the Allen Institute’s mouse datasets from visual a… --- ## [Transcriptomics-based classification and nomenclature of neocortical cell types](https://community.brain-map.org/t/transcriptomics-based-classification-and-nomenclature-of-neocortical-cell-types/294)
**Author:** [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\ **Replies:** 3\ **Last updated:** [December 1, 2020, 6:49pm UTC](https://community.brain-map.org/t/transcriptomics-based-classification-and-nomenclature-of-neocortical-cell-types/294 "2020-12-01T18:49:20Z")
In a recent submission to arXiv several prominent investigators of brain cell types (from the Allen Institute and across the world) presented a position piece that proposes to use a transcriptomics-based system for cell …