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Juranic/histology dirschema update #1314

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Mar 21, 2024
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Juranic/histology dirschema update #1314

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a36accf
Update histology-v2.yaml
j-uranic Mar 21, 2024
172cab3
Update CHANGELOG.md
j-uranic Mar 21, 2024
4f501b3
Docs: Update histology docs
Mar 21, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -21,6 +21,7 @@
- Update Histology with links
- Update GeoMx NGS directory schema
- Ported murine from SenNet
- Update Histology directory schema

## v0.0.17

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2 changes: 1 addition & 1 deletion docs/histology/current/index.md
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Expand Up @@ -37,7 +37,7 @@ Related files:
| <code>extras\/microscope_settings\.json</code> | | **[QA/QC]** A file generated by the micro-meta app that contains a description of the settings that were used to acquire the image data. Email HuBMAP Consortium Help Desk <[email protected]> if help is required in generating this document. | |
| <code>raw\/.*</code> | ✓ | Raw data files for the experiment. | |
| <code>raw\/images\/.*</code> | ✓ | Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file. | |
| <code>raw\/images\/[^\/]+\.(?:xml&#124;scn&#124;vsi&#124;ndpi&#124;svs&#124;czi&#124;tiff)</code> | ✓ | Raw microscope file for the experiment | |
| <code>raw\/images\/[^\/]+\.(?:xml&#124;scn&#124;vsi&#124;ndpi&#124;svs&#124;czi&#124;tiff&#124;qptiff)</code> | ✓ | Raw microscope file for the experiment | |
| <code>lab_processed\/.*</code> | ✓ | Experiment files that were processed by the lab generating the data. | |
| <code>lab_processed\/images\/.*</code> | ✓ | Processed image files | |
| <code>lab_processed\/images\/[^\/]+\.ome\.tiff</code> (example: <code>lab_processed/images/HBM892.MDXS.293.ome.tiff</code>) | ✓ | OME-TIFF files (multichannel, multi-layered) produced by the microscopy experiment. If compressed, must use loss-less compression algorithm. See the following link for the set of fields that are required in the OME TIFF file XML header. <https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0> | |
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2 changes: 1 addition & 1 deletion src/ingest_validation_tools/directory-schemas/histology-v2.yaml
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Expand Up @@ -22,7 +22,7 @@ files:
required: True
description: Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file.
-
pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff)
pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff|qptiff)
required: True
description: Raw microscope file for the experiment
is_qa_qc: False
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