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phenocycler-v2.yaml
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phenocycler-v2.yaml
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files:
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pattern: extras\/.*
required: True
description: Folder for general lab-specific files related to the dataset. [Exists in all assays]
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pattern: extras\/microscope_hardware\.json
required: True
description: A file generated by the micro-meta app that contains a description of the hardware components of the microscope. Email HuBMAP Consortium Help Desk <[email protected]> if help is required in generating this document.
is_qa_qc: True
-
pattern: extras\/microscope_settings\.json
required: False
description: 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.
is_qa_qc: True
-
pattern: raw\/.*
required: True
description: This is a directory containing raw data.
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pattern: raw\/images\/.*
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.
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pattern: raw\/images\/[^\/]+\.xpd
required: True
description: Experimental set up of the Phenocycler-Fusion run. File includes cycle information, antibodies utilized, and the experimental design of the run
is_qa_qc: False
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pattern: raw\/images\/[^\/]+\.qptiff
required: True
description: Final image file produced by the Phenocycler-Fusion
is_qa_qc: False
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pattern: raw\/images\/phenocycler\/.*
required: True
description: These are the files from the temp directory generated by the PhenoCycler. The dataset should include all files from this directory except the "qptiff.intermediate" files.
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pattern: raw\/images\/phenocycler\/[^\/]+\.qptiff\.raw
required: True
description: Raw image files from the temp directory generated by the PhenoCycler.
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pattern: raw\/images\/phenocycler\/[^\/]+\.qptiff\.intermediate
required: False
description: Intermediate image files from the temp directory generated by the PhenoCycler. These files are not required.
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pattern: raw\/images\/phenocycler\/(?:CombineInputs.txt|FocusMap.tif|FocusTable.txt|Label.tif|MarkerList.txt|OverviewBF.tif|SampleMask.tif)
required: True
description: Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used.
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pattern: raw\/images\/phenocycler\/(?:CoverslipMask.tif|FlowCellOverview.tif|OverviewFL.tif|SampleValMask.tif)
required: False
description: Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used.
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pattern: lab_processed\/.*
required: True
description: Experiment files that were processed by the lab generating the data.
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pattern: lab_processed\/images\/.*
required: True
description: This is a directory containing processed image files
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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
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pattern: lab_processed\/images\/[^\/]+\.ome\.tiff
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>
is_qa_qc: False
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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>