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* Create segmentation-mask-v2.2.yaml Add top-level "extras" directory * Create af-v2.1.yaml raw\/channel_layout\.tsv - make optional raw\/images\/[^\/]+\.(?:xml|nd2|oir|lif|czi|tiff|qptiff) - add qptiff * Create codex-v2.1.yaml Add .* to end of processed\/drv_[^\/]*\/ and raw\/src_[^\/]*\/ * Update CHANGELOG.md * Docs: Update dir schemas for af, seg-mask, and codex --------- Co-authored-by: Juan Puerto <=>
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@@ -28,7 +28,32 @@ This schema is for autofluorescence (AF). For an example of an AF dataset & dire | |
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| ## Directory schemas | ||
| <summary><b>Version 2.0 (use this one)</b></summary> | ||
| <summary><b>Version 2.1 (use this one)</b></summary> | ||
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| | pattern | required? | description | | ||
| | --- | --- | --- | | ||
| | <code>extras\/.*</code> | ✓ | Folder for general lab-specific files related to the dataset. [Exists in all assays] | | ||
| | <code>extras\/microscope_hardware\.json</code> | ✓ | **[QA/QC]** 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. | | ||
| | <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\/channel_layout\.tsv</code> | | Table that includes a dictionary for channel to moiety, which may be a protein given in an OMAP panel or captured in the ASCT+B table. | | ||
| | <code>raw\/images\/.*</code> | ✓ | Raw image files. Using this subdirectory allows for harmonization with other imaging assays. [This directory must include at least one raw file.] | | ||
| | <code>raw\/images\/[^\/]+\.(?:xml|nd2|oir|lif|czi|tiff|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> | | ||
| | <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\/transformations\/.*</code> | | This directory contains transformation matrices that capture how each modality is aligned with the other and can be used to visualize overlays of multimodal data. This is needed to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). In these cases data type may have different pixel sizes and slightly different orientations (i.e., one may be rotated relative to another). | | ||
| | <code>lab_processed\/transformations\/[^\/]+\.txt</code> | | Transformation matrices used to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). | | ||
| | <code>qa_qc\/.*</code> | ✓ | Directory containing QA and/or QC information. | | ||
| | <code>qa_qc\/resolution_report\/.*</code> | ✓ | Directory containing the results of resolution tests and/or vendor preventative maintenance reports. | | ||
| | <code>qa_qc\/resolution_report\/resolution\.txt</code> | | This file summarizes the results of resolution tests or vendor reports from preventative maintenance visits. | | ||
| | <code>qa_qc\/resolution_report\/[^\/]+\.pdf</code> | | This file is a pdf from a vendor preventative maintenance visit or resolution check tool demonstrating resolution. This file may include illumination test results. | | ||
| | <code>qa_qc\/illumination_report\/.*</code> | ✓ | Directory containing the results of illumination tests and/or vendor preventative maintenance reports. | | ||
| | <code>qa_qc\/illumination_report\/illumination.txt</code> | | This file summarizes the results of illumination tests or vendor reports from preventative maintenance visits. | | ||
| | <code>qa_qc\/illumination_report\/[^\/]+\.pdf</code> | | This file is a pdf from a vendor preventative maintenance visit or illumination check tool demonstrating illumination intensity. | | ||
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| <summary><b>Version 2.0</b></summary> | ||
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| | pattern | required? | description | | ||
| | --- | --- | --- | | ||
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| ## Directory schemas | ||
| <summary><b>Version 2.0 (use this one)</b></summary> | ||
| <summary><b>Version 2.1 (use this one)</b></summary> | ||
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| | pattern | required? | description | | ||
| | --- | --- | --- | | ||
| | <code>extras\/.*</code> | ✓ | Folder for general lab-specific files related to the dataset. [Exists in all assays] | | ||
| | <code>extras\/microscope_hardware\.json</code> | ✓ | **[QA/QC]** 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. | | ||
| | <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> | ✓ | This is a directory containing raw data. | | ||
| | <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> | | ||
| | <code>lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv</code> | ✓ | This file should describe any processing that was done to generate the images in each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. Two columns should be booleans "is this a channel to use for nuclei segmentation" and "is this a channel to use for cell segmentation". | | ||
| | <code>[^\/]*NAV[^\/]*\.tif</code> (example: <code>NAV.tif</code>) | | Navigational Image showing Region of Interest (Keyance Microscope only) | | ||
| | <code>[^\/]+\.pdf</code> (example: <code>summary.pdf</code>) | | **[QA/QC]** PDF export of Powerpoint slide deck containing the Image Analysis Report | | ||
| | <code>extras\/dir-schema-v2-with-dataset-json</code> | ✓ | Empty file whose presence indicates the version of the directory schema in use | | ||
| | <code>processed\/drv_[^\/]*\/.*</code> | ✓ | Processed files produced by the Akoya software or alternative software. | | ||
| | <code>raw\/cyc[^\/]*_reg[^\/]*\/.*</code> | ✓ | Intermediary directory | | ||
| | <code>raw\/src_[^\/]*\/.*</code> | ✓ | Intermediary directory | | ||
| | <code>raw\/cyc[^\/]*_reg[^\/]*\/[^\/]*_z[^\/]*_CH[^\/]*\.tif</code> | ✓ | TIFF files produced by the experiment. General folder format: Cycle(n)_Region(n)_date; General file format: name_tileNumber(n)_zplaneNumber(n)_channelNumber(n) | | ||
| | <code>raw\/src_[^\/]*\/cyc[^\/]*_reg[^\/]*_[^\/]*\/[^\/]+\.gci</code> | | Group Capture Information File (Keyance Microscope only) | | ||
| | <code>raw\/dataset\.json</code> (example: <code>raw/dataset.json</code>) | ✓ | Data processing parameters file. This will include additional CODEX specific metadata needed for the HIVE processing workflow. | | ||
| | <code>raw\/reg_[^\/]*\.png</code> (example: <code>raw/reg_00.png</code>) | | Region overviews | | ||
| | <code>raw\/experiment\.json</code> (example: <code>raw/experiment.json</code>) | | JSON file produced by the Akoya software which contains the metadata for the experiment, including the software version used, microscope parameters, channel names, pixel dimensions, etc. (required for HuBMAP pipeline) | | ||
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| <summary><b>Version 2.0</b></summary> | ||
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| | pattern | required? | description | | ||
| | --- | --- | --- | | ||
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src/ingest_validation_tools/directory-schemas/af-v2.1.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| files: | ||
| - | ||
| pattern: extras\/.* | ||
| required: True | ||
| description: Folder for general lab-specific files related to the dataset. [Exists in all assays] | ||
| - | ||
| 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: Raw data files for the experiment. | ||
| - | ||
| pattern: raw\/channel_layout\.tsv | ||
| required: False | ||
| description: Table that includes a dictionary for channel to moiety, which may be a protein given in an OMAP panel or captured in the ASCT+B table. | ||
| is_qa_qc: False | ||
| - | ||
| pattern: raw\/images\/.* | ||
| required: True | ||
| description: Raw image files. Using this subdirectory allows for harmonization with other imaging assays. [This directory must include at least one raw file.] | ||
| - | ||
| pattern: raw\/images\/[^\/]+\.(?:xml|nd2|oir|lif|czi|tiff|qptiff) | ||
| required: True | ||
| description: Raw microscope file for the experiment | ||
| is_qa_qc: False | ||
| - | ||
| pattern: lab_processed\/.* | ||
| required: True | ||
| description: Experiment files that were processed by the lab generating the data. | ||
| - | ||
| pattern: lab_processed\/images\/.* | ||
| required: True | ||
| description: Processed image files | ||
| - | ||
| pattern: lab_processed\/images\/[^\/]+\.ome\.tiff | ||
| required: True | ||
| description: 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> | ||
| is_qa_qc: False | ||
| example: lab_processed/images/HBM892.MDXS.293.ome.tiff | ||
| - | ||
| 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> | ||
| is_qa_qc: False | ||
| - | ||
| pattern: lab_processed\/transformations\/.* | ||
| required: False | ||
| description: This directory contains transformation matrices that capture how each modality is aligned with the other and can be used to visualize overlays of multimodal data. This is needed to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). In these cases data type may have different pixel sizes and slightly different orientations (i.e., one may be rotated relative to another). | ||
| - | ||
| pattern: lab_processed\/transformations\/[^\/]+\.txt | ||
| required: False | ||
| description: Transformation matrices used to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). | ||
| is_qa_qc: False | ||
| - | ||
| pattern: qa_qc\/.* | ||
| required: True | ||
| description: Directory containing QA and/or QC information. | ||
| - | ||
| pattern: qa_qc\/resolution_report\/.* | ||
| required: True | ||
| description: Directory containing the results of resolution tests and/or vendor preventative maintenance reports. | ||
| - | ||
| pattern: qa_qc\/resolution_report\/resolution\.txt | ||
| required: False | ||
| description: This file summarizes the results of resolution tests or vendor reports from preventative maintenance visits. | ||
| - | ||
| pattern: qa_qc\/resolution_report\/[^\/]+\.pdf | ||
| required: False | ||
| description: This file is a pdf from a vendor preventative maintenance visit or resolution check tool demonstrating resolution. This file may include illumination test results. | ||
| - | ||
| pattern: qa_qc\/illumination_report\/.* | ||
| required: True | ||
| description: Directory containing the results of illumination tests and/or vendor preventative maintenance reports. | ||
| - | ||
| pattern: qa_qc\/illumination_report\/illumination.txt | ||
| required: False | ||
| description: This file summarizes the results of illumination tests or vendor reports from preventative maintenance visits. | ||
| - | ||
| pattern: qa_qc\/illumination_report\/[^\/]+\.pdf | ||
| required: False | ||
| description: This file is a pdf from a vendor preventative maintenance visit or illumination check tool demonstrating illumination intensity. |
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