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Juranic/phenocycler dirschema updates #1317

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Mar 27, 2024
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Juranic/phenocycler dirschema updates #1317

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de2619d
Update phenocycler-v2.yaml
j-uranic Mar 25, 2024
e39e00c
Update CHANGELOG.md
j-uranic Mar 25, 2024
2c2015d
Docs: Update phenocycler documentation
Mar 25, 2024
c9eb348
Update phenocycler-v2.yaml
j-uranic Mar 26, 2024
ff1679f
Docs: Update Phenocycler documentation and the example files for Phen…
Mar 27, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,7 @@

## v0.0.19 (in progress)
- Directory validation changes for "shared" uploads
- Update Phenocycler directory schema

## v0.0.18

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5 changes: 2 additions & 3 deletions docs/phenocycler/current/index.md
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Expand Up @@ -46,7 +46,6 @@ Related files:
| <code>raw\/images\/phenocycler\/(?:CoverslipMask.tif&#124;FlowCellOverview.tif&#124;OverviewFL.tif&#124;SampleValMask.tif)</code> | | Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used. |
| <code>lab_processed\/.*</code> | ✓ | Experiment files that were processed by the lab generating the data. |
| <code>lab_processed\/images\/.*</code> | ✓ | This is a directory containing processed image files |
| <code>lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson</code> | | **[QA/QC]** If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”. |
| <code>lab_processed\/images\/[^\/]+\.ome\.tiff</code> | ✓ | OME-TIFF file (multichannel, multi-layered) produced by the 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>. It is recommended that you confirm you're using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling. |
| <code>lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv</code> | ✓ | This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1xEJSb0xn5C5fB3k62pj1CyHNybpt4-YtvUs5SUMS44o/edit#gid=0> |
| <code>lab_processed\/images\/[^\/]+tissue-boundary\.geojson</code> | | **[QA/QC]** If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”. |
| <code>lab_processed\/images\/[^\/]*qptiff\.channels\.csv</code> | ✓ | This file provides essential documentation pertaining to each channel of the accommpanying QPTIFF. The file should contain one row per QPTIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1JikzRNyDErspgPSel4P9Y6gx6N_mrAGIMDcJZd8TucA/edit#gid=0> |

Empty file removed ...ec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome.tiff
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0 ...rocessed/images/OL9.ome-tiff.channels.csv → ..._processed/images/OL9.qptiff.channels.csv
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12 changes: 4 additions & 8 deletions src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml
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Expand Up @@ -60,16 +60,12 @@ files:
required: True
description: This is a directory containing processed image files
-
pattern: lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson
pattern: lab_processed\/images\/[^\/]+tissue-boundary\.geojson
required: False
description: If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”.
is_qa_qc: True
-
pattern: lab_processed\/images\/[^\/]+\.ome\.tiff
pattern: lab_processed\/images\/[^\/]*qptiff\.channels\.csv
required: True
description: OME-TIFF file (multichannel, multi-layered) produced by the 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>. It is recommended that you confirm you're using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling.
is_qa_qc: False
-
pattern: lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
required: True
description: This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1xEJSb0xn5C5fB3k62pj1CyHNybpt4-YtvUs5SUMS44o/edit#gid=0>
description: This file provides essential documentation pertaining to each channel of the accommpanying QPTIFF. The file should contain one row per QPTIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1JikzRNyDErspgPSel4P9Y6gx6N_mrAGIMDcJZd8TucA/edit#gid=0>

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