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Jpuerto/xenium release #1375

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Oct 14, 2024
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Jpuerto/xenium release #1375

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29dfb98
General: Add Xenium
Oct 14, 2024
92d62e6
Docs: Add Xenium
Oct 14, 2024
984ea4b
General: Add Xenium
Oct 14, 2024
8b36214
Merge branch 'main' into jpuerto/xenium-release
jpuerto-psc Oct 14, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@
- Update Phenocycler directory schema
- Update GeoMx NGS directory schema
- Update shared upload check
- Release Xenium

## v0.0.26
- Update GeoMx NGS directory schema
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12 changes: 8 additions & 4 deletions docs/xenium/current/index.md
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Expand Up @@ -3,21 +3,25 @@ title: Xenium
schema_name: xenium
category: Spatial Transcriptomics
all_versions_deprecated: False
exclude_from_index: True
exclude_from_index: False
layout: default

---
Prepare your metadata based on the latest metadata schema using one of the template files below. See the instructions in the [Metadata Validation Workflow](https://docs.google.com/document/d/1lfgiDGbyO4K4Hz1FMsJjmJd9RdwjShtJqFYNwKpbcZY) document for more information on preparing and validating your metadata.tsv file prior to submission.

Related files:

Excel and TSV templates for this schema will be available when the draft next-generation schema, to be used in all future submissions, is finalized (no later than Sept. 30).

[This link](https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0) lists the set of fields that are required in the OME TIFF file XML header.
- [📝 Excel template](https://raw.githubusercontent.com/hubmapconsortium/dataset-metadata-spreadsheet/main/xenium/latest/xenium.xlsx): For metadata entry.
- [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/dataset-metadata-spreadsheet/main/xenium/latest/xenium.tsv): Alternative for metadata entry.




## Metadata schema


<summary><a href="https://docs.google.com/spreadsheets/d/1kd1UQ2il-eW-MTM4iEotyAxa8M_hcwn8yQJTU_II-F8"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30)</a></summary>
<summary><a href="https://openview.metadatacenter.org/templates/https:%2F%2Frepo.metadatacenter.org%2Ftemplates%2Fc83b9743-ea76-4eb3-97f1-7325331936ea"><b>Version 2 (use this one)</b></a></summary>



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5 changes: 1 addition & 4 deletions src/ingest_validation_tools/table-schemas/assays/xenium-v2.yaml
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@@ -1,10 +1,7 @@
exclude_from_index: True
description_md: '[This link](https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0) lists the set of fields that are required in the OME TIFF file XML header.'
draft: true
fields:
- name: is_cedar
description: 'Identifies whether the version is hosted by CEDAR'
example: 'https://docs.google.com/spreadsheets/d/1kd1UQ2il-eW-MTM4iEotyAxa8M_hcwn8yQJTU_II-F8'
example: 'https://openview.metadatacenter.org/templates/https:%2F%2Frepo.metadatacenter.org%2Ftemplates%2Fc83b9743-ea76-4eb3-97f1-7325331936ea'
- name: assay_category
constraints:
enum:
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