Brain region specific mapping taxonomy files

[siennasage18]

Hi there! As it says in the mapping_cells.md file, I'm filing this to see if it is possible to get allen brain atlas taxonomy mapping files that are not currently available/supported by the online tool. I have a dataset of mouse single cell hippocampus sequencing that I'd like to annotate specifically to the ABA mouse hippocampus annotated cells (from the HPF/hippocampus regions) instead of the whole mouse brain. Are these files something that exists/could be easily generated and shared?

Thanks for your help!
Sienna

If you are an internal Allen Institute user and just want to map to one of the taxonomies currently supported by the MapMyCells online app, email Scott Daniel, and he can provide you with the appropriate files. If you are an external user and want to map to one of the MapMyCells-supported taxonomies and the online MapMyCells app is for some reason insufficient for your purposes, please file an issue on this repository and we can discuss how to get you the relevant files.

[danielsf]

Hi @siennasage18

To answer the question you asked: unfortunately, no. The files listed here represent the only taxonomies for which we have precomputed reference files.

However, depending on what data you do have, this repository contains the functionality you need to create the necessary reference files for mapping to a different taxonomy.

Do you mind posting a link to the data that you want to map to? I get the sense that you are referring to a dataset that predates my term here at the Allen Institute, and I'm not sure off the top of my head what data we have made available for download from that dataset.

[siennasage18]

Hi Daniel, I'm sorry if my question was unclear. The way I understand the ABA single-cell objects that were used for creating the mouse whole brain atlas (that then was used to generate the taxonomies for mapping) is that there were various experiments micro dissecting different regions of the mouse brain, these were all annotated and merged to generate the mouse brain atlas. My data is just of the mouse hippocampus, and therefore it would make more sense to me to map to the subset of the data that was generated from the hippocampus experiments, rather than the whole mouse brain. However, I'm not sure how to generate the taxonomies, or whether these might already be generated and available on your end. Here are the nemo archive folder for the subset of the data that I would prefer to map to: NeMO Data Archive Assets <https://assets.nemoarchive.org/dat-iye7gkp> I am unsure whether there is a way to either subset the whole brain atlas json/taxonomies file that is already available on the git to just the data from the hippocampus/isocortex, or how to generate a new taxonomy file out of the subset of raw data from the NeMO archive. I hope that is more clear, thanks for getting back to me and for any help you can provide! Warmly, Sienna

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On Wed, 4 Dec 2024 at 17:29, danielsf ***@***.***> wrote: Hi @siennasage18 <https://github.com/siennasage18> To answer the question you asked: unfortunately, no. The files listed here <https://github.com/AllenInstitute/cell_type_mapper/blob/main/docs/input_data_files/running_online_taxonomies_locally.md> represent the only taxonomies for which we have precomputed reference files. *However*, depending on what data you do have, this repository contains the functionality you need to create the necessary reference files for mapping to a different taxonomy. Do you mind posting a link to the data that you want to map to? I get the sense that you are referring to a dataset that predates my term here at the Allen Institute, and I'm not sure off the top of my head what data we have made available for download from that dataset. — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOISJ7JSIFKFCZWKDTJBVUD2D565TAVCNFSM6AAAAABSQ22ST2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMJYGY4DSOJUGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[danielsf]

Hi @siennasage18

Thank you for your patience. I took the opportunity of your question to put together an example Jupyter notebook I've been meaning to write which I think will address your question.

For now, you are going to need to clone and work off this branch

https://github.com/AllenInstitute/cell_type_mapper/tree/rc/v1.4.0

of the repository (I hope to have it merged into main by early 2025). This notebook ought to show you how to

• download a subset of the Whole Mouse Brain single cell sequencing data
• create the files needed to define a taxonomy limited to that subset of the data
• map your data to that taxonomy

That being said: there may be an easier and equally effective way to do the mapping you want. See section (8) of the notebook.

Sidebar: you may benefit from reading over the conversation in this issue as it seems almost identical to what you are asking.

Let me know if anything is unclear or does not work for you.

Good luck,

Scott (Daniel is my surname; I probably should have picked a different GitHub handle...)

[siennasage18]

Sorry about the misnaming Scott! Thanks so much for all your help, I'll take a look at the Jupyter notebook. I had looked at that previous asked question before, but I was stuck at the earlier step of generating taxonomy files based on the subset of data, but I'll look it over again with the notebook in hand and see if I understand the issues better. Warmly, Sienna

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On Wed, 11 Dec 2024 at 17:34, danielsf ***@***.***> wrote: Hi @siennasage18 <https://github.com/siennasage18> Thank you for your patience. I took the opportunity of your question to put together an example Jupyter notebook I've been meaning to write which I *think* will address your question. For now, you are going to need to clone and work off this branch https://github.com/AllenInstitute/cell_type_mapper/tree/rc/v1.4.0 of the repository (I hope to have it merged into main by early 2025). This notebook <https://github.com/AllenInstitute/cell_type_mapper/blob/rc/v1.4.0/examples/mapping_to_subset_of_abc_atlas_data.ipynb> ought to show you how to - download a subset of the Whole Mouse Brain single cell sequencing data - create the files needed to define a taxonomy limited to that subset of the data - map your data to that taxonomy That being said: there may be an easier and equally effective way to do the mapping you want. See section (8) of the notebook. Sidebar: you may benefit from reading over the conversation in this issue <#23> as it seems almost identical to what you are asking. Let me know if anything is unclear or does not work for you. Good luck, Scott (Daniel is my surname; I probably should have picked a different GitHub handle...) — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOISJ7MU4IDAUY2LFGSSR3L2FC4WVAVCNFSM6AAAAABSQ22ST2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZXGMZTSOBTHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>