# Donor mapping for MERFISH MEC/HPF specimens
**URL:** https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020
**Category:** General
**Tags:** transcriptomics, sea-ad
**Created:** [July 13, 2026, 2:52pm UTC](https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020 "2026-07-13T14:52:27Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@TamaraV](https://community.brain-map.org/u/TamaraV)
#### Post date: [July 13, 2026, 2:52pm UTC](https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020/1 "2026-07-13T14:52:27Z")
I’m working with two SEA-AD MERFISH files from the spatial-transcriptomics bucket: medial-entorhinal-cortex/combined\_anndata\_object/1444201261\_MEC\_mapped.h5ad andhippocampus/combined\_anndata\_object/1444211893\_HPF\_mapped.h5ad.
The `obs` in these combined objects contains only cell-type annotations and spatial coordinates — no `Donor ID` / `Specimen Barcode` / `Section` columns like the MTG MERFISH release has, and there’s no per-donor folder in the S3 path (unlike the caudate region). How do I map these specimens/cells to their donor(s) (`H20.33.xxx`)? Specifically: is each combined file a single donor, or are multiple donors pooled — and if pooled, where are the per-cell donor labels?
Thanks!
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### Author:  [@egelfan2](https://community.brain-map.org/u/egelfan2)
#### Post date: [July 21, 2026, 9:03pm UTC](https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020/2 "2026-07-21T21:03:45Z")
Hi @Tamarav,
Thanks for reaching out, and for your interest in our data! Each of these .h5ad files represents mapping for a single specimen/section. For each of these files, the Specimen Barcode is in the name - `1444201261` for 1444201261\_MEC\_mapped.h5ad, for example. However, the Donor ID for both of these files is `H24.30.005` - so same donor for both files, but different sections (the MEC\_mapped section comes from the MEC, etc).
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### Author:  [@TamaraV](https://community.brain-map.org/u/TamaraV)
#### Post date: [July 21, 2026, 10:54pm UTC](https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020/3 "2026-07-21T22:54:48Z")
Hi @egelfan2 !
Thank you — that resolved the specimen→donor mapping perfectly (barcode `1444201261` = MEC section, `1444211893` = HPF section, both donor `H24.30.005`).
I’m testing whether a cell-level phenotype I see in the entorhinal cortex tracks Alzheimer’s neuropathology, so it would be helpful to have the donor-level staging for the MERFISH data. Two things I couldn’t resolve on my end:
1. **Neuropathology + demographics for the MERFISH donors.** The `.h5ad` files carry no pathology fields, and `H24.30.005` isn’t in the SEA-AD MTG cohort metadata (the 84-donor `.33.` set) or in the Multiregion 10x donor set (81 donors, also `.33.`) — so the MERFISH donors appear to be a separate cohort. Is there a donor metadata table for the Multiregion MERFISH release giving, per donor: **Braak NFT stage, Thal phase, CERAD score, overall ADNC, APOE genotype, age at death, sex, and cognitive/dementia status**?
2. **Cohort composition.** How many donors (and sections/regions per donor) are in the Multiregion MERFISH release, and what pathology range does it span? Specifically, does it include **both low-/no-pathology (control) and high-pathology (AD) donors** — enough to compare across Braak stages?
If there’s a downloadable **specimen-barcode → donor-ID → neuropathology crosswalk** (analogous to the MTG cohort spreadsheet), that would be ideal — I can join everything from that myself.
Thanks a lot!
Tamara
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### Author:  [@kyle.travaglini](https://community.brain-map.org/u/kyle.travaglini)
#### Post date: [August 3, 2026, 5:49pm UTC](https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020/4 "2026-08-03T17:49:42Z")
Hi @TamaraV,
I will check with our spatial team on available metadata for this donor. We intended only to profile the MEC and HIP in a neurotypical context, so we could localize all of the transcriptionally defined types we found in the SEA-AD single nucleus -omics datasets from these regions. As a result, this donor is unlikely to have significant pathological burden.
We have not yet generated MEC and HIP data in aged individuals affected different levels of pathological burden.
Best, Kyle
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### Author:  [@TamaraV](https://community.brain-map.org/u/TamaraV)
#### Post date: [August 4, 2026, 8:44pm UTC](https://community.brain-map.org/t/donor-mapping-for-merfish-mec-hpf-specimens/5020/5 "2026-08-04T20:44:53Z")
Hi @kyle.travaglini ,
Thank you for your reply! I understand. It would be great if you could get more information on available metadata from the spatial team for this donor.
Best,
Tamara