Multiplex Fluorescence Based Experiment (MxFBE)
PhenoCycler
Prepare your metadata based on the latest metadata schema using one of the template files below. See the instructions in the Metadata Validation Workflow document for more information on preparing and validating your metadata.tsv file prior to submission.
Related files:
- 📝 Excel template: For metadata entry.
- 📝 TSV template: Alternative for metadata entry.
Metadata schema
Directory schemas
| pattern | required? | description |
|---|---|---|
extras\/.* |
✓ | Folder for general lab-specific files related to the dataset. [Exists in all assays] |
extras\/microscope_hardware\.json |
✓ | [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 help@hubmapconsortium.org if help is required in generating this document. |
extras\/microscope_settings\.json |
[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 help@hubmapconsortium.org if help is required in generating this document. | |
raw\/.* |
✓ | This is a directory containing raw data. |
raw\/images\/.* |
✓ | Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. |
raw\/images\/[^\/]+\.xpd |
✓ | Experimental set up of the Phenocycler-Fusion run. File includes cycle information, antibodies utilized, and the experimental design of the run |
raw\/images\/[^\/]+\.qptiff |
✓ | Final image file produced by the Phenocycler-Fusion |
raw\/images\/phenocycler\/.* |
✓ | 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. |
raw\/images\/phenocycler\/[^\/]+\.(?:qptiff\.raw|raw\.qptiff) |
✓ | Raw image files from the temp directory generated by the PhenoCycler. |
raw\/images\/phenocycler\/[^\/]+intermediate[^\/]+ |
Intermediate image files from the temp directory generated by the PhenoCycler. These files are not required. | |
raw\/images\/phenocycler\/(?:CombineInputs.txt|FocusMap.tif|FocusTable.txt|Label.tif|MarkerList.txt|OverviewBF.tif|SampleMask.tif) |
✓ | Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used. |
raw\/images\/phenocycler\/(?:CoverslipMask.tif|FlowCellOverview.tif|OverviewFL.tif|SampleValMask.tif) |
Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used. | |
lab_processed\/.* |
✓ | Experiment files that were processed by the lab generating the data. |
lab_processed\/images\/.* |
✓ | This is a directory containing processed image files |
lab_processed\/images\/[^\/]+tissue-boundary\.geojson |
[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”. | |
lab_processed\/images\/[^\/]*qptiff\.channels\.csv |
✓ | 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 |
| pattern | required? | description |
|---|---|---|
extras\/.* |
✓ | Folder for general lab-specific files related to the dataset. [Exists in all assays] |
extras\/microscope_hardware\.json |
✓ | [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 help@hubmapconsortium.org if help is required in generating this document. |
extras\/microscope_settings\.json |
[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 help@hubmapconsortium.org if help is required in generating this document. | |
raw\/.* |
✓ | This is a directory containing raw data. |
raw\/images\/.* |
✓ | Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. |
raw\/images\/[^\/]+\.xpd |
✓ | Experimental set up of the Phenocycler-Fusion run. File includes cycle information, antibodies utilized, and the experimental design of the run |
raw\/images\/[^\/]+\.qptiff |
✓ | Final image file produced by the Phenocycler-Fusion |
raw\/images\/phenocycler\/.* |
✓ | 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. |
raw\/images\/phenocycler\/[^\/]+\.qptiff\.raw |
✓ | Raw image files from the temp directory generated by the PhenoCycler. |
raw\/images\/phenocycler\/[^\/]+\.qptiff\.intermediate |
Intermediate image files from the temp directory generated by the PhenoCycler. These files are not required. | |
raw\/images\/phenocycler\/(?:CombineInputs.txt|FocusMap.tif|FocusTable.txt|Label.tif|MarkerList.txt|OverviewBF.tif|SampleMask.tif) |
✓ | Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used. |
raw\/images\/phenocycler\/(?:CoverslipMask.tif|FlowCellOverview.tif|OverviewFL.tif|SampleValMask.tif) |
Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used. | |
lab_processed\/.* |
✓ | Experiment files that were processed by the lab generating the data. |
lab_processed\/images\/.* |
✓ | This is a directory containing processed image files |
lab_processed\/images\/[^\/]+tissue-boundary\.geojson |
[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”. | |
lab_processed\/images\/[^\/]*qptiff\.channels\.csv |
✓ | 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 |