Multiplex Fluorescence Based Experiment (MxFBE)
Cell DIVE
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.
This link lists the set of fields that are required in the OME TIFF file XML header.
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\/round_info_[^\/]+\.dat$ (example: raw/images/round_info_002.dat) |
Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. This is equivalent to the round_info_*.xml file that some systems generate. | |
raw\/images\/round_info_[^\/]+\.xml$ (example: raw/images/round_info_002.xml) |
Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. This is equivalent to the round_info_*.dat file that some systems generate. | |
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\/region_[^\/]+\/[^\/]+_region_[^\/]+\.ome\.(?:tif|tiff)$ (example: lab_processed/images/region_001/S20030092_region_011.ome.tif) |
✓ | OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077), organized into subdirectories based on their region. |
lab_processed\/images\/region_[^\/]+\/[^\/]*ome-tiff\.channels\.csv$ |
✓ | 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 |
lab_processed\/annotations\/.* |
✓ | This is a directory containing annotations. |
lab_processed\/annotations\/slide_list\.txt$ |
✓ | Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames. |
lab_processed\/transformations\/.* |
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). | |
lab_processed\/transformations\/[^\/]+\.txt$ |
Transformation matrices used to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). | |
lab_processed\/virtual_histology\/.* |
✓ | This is a directory containing annotations for virtual histology images |
lab_processed\/virtual_histology\/HandE_RGB_thumbnail\.jpg$ |
Virtual H&E RGB thumbnail | |
lab_processed\/virtual_histology\/HandE_RGB\.tif$ |
Virtual H&E RGB image | |
lab_processed\/virtual_histology\/[^\/]+_VHE_region_[^\/]+\.tif$ |
Virtual H&E image |
| 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\/round_info_[^\/]+\.dat$ (example: raw/images/round_info_002.dat) |
Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. This is equivalent to the round_info_*.xml file that some systems generate. | |
raw\/images\/round_info_[^\/]+\.xml$ (example: raw/images/round_info_002.xml) |
Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. This is equivalent to the round_info_*.dat file that some systems generate. | |
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\/region_[^\/]+\/[^\/]+_region_[^\/]+\.ome\.(?:tif|tiff)$ (example: lab_processed/images/region_001/S20030092_region_011.ome.tif) |
✓ | OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077), organized into subdirectories based on their region. |
lab_processed\/images\/region_[^\/]+\/[^\/]*ome-tiff\.channels\.csv$ |
✓ | 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 |
lab_processed\/annotations\/.* |
✓ | This is a directory containing annotations. |
lab_processed\/annotations\/slide_list\.txt$ |
✓ | Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames. |
lab_processed\/virtual_histology\/.* |
✓ | This is a directory containing annotations for virtual histology images |
lab_processed\/virtual_histology\/HandE_RGB_thumbnail\.jpg$ |
Virtual H&E RGB thumbnail | |
lab_processed\/virtual_histology\/HandE_RGB\.tif$ |
Virtual H&E RGB image | |
lab_processed\/virtual_histology\/[^\/]+_VHE_region_[^\/]+\.tif$ |
Virtual H&E image |
| 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\/round_info_[^\/]+\.dat$ (example: raw/images/round_info_002.dat) |
✓ | Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. |
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\/region_[^\/]+\/[^\/]+_region_[^\/]+\.ome\.(?:tif|tiff)$ (example: lab_processed/images/region_001/S20030092_region_011.ome.tif) |
✓ | OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077), organized into subdirectories based on their region. |
lab_processed\/images\/region_[^\/]+\/[^\/]*ome-tiff\.channels\.csv$ |
✓ | 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 |
lab_processed\/annotations\/.* |
✓ | This is a directory containing annotations. |
lab_processed\/annotations\/slide_list\.txt$ |
✓ | Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames. |
lab_processed\/virtual_histology\/.* |
✓ | This is a directory containing annotations for virtual histology images |
lab_processed\/virtual_histology\/HandE_RGB_thumbnail\.jpg$ |
Virtual H&E RGB thumbnail | |
lab_processed\/virtual_histology\/HandE_RGB\.tif$ |
Virtual H&E RGB image | |
lab_processed\/virtual_histology\/[^\/]+_VHE_region_[^\/]+\.tif$ |
Virtual H&E image |
| 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\/round_info_[^\/]+\.dat$ (example: raw/images/round_info_002.dat) |
✓ | Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. |
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\/region_[^\/]+\/[^\/]+_region_[^\/]+\.ome\.(?:tif|tiff)$ (example: lab_processed/images/region_001/S20030092_region_011.ome.tif) |
✓ | OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077), organized into subdirectories based on their region. |
lab_processed\/images\/region_[^\/]+\/[^\/]*ome-(?:tif|tiff)\.channels\.csv$ |
✓ | 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 |
lab_processed\/annotations\/.* |
✓ | This is a directory containing annotations. |
lab_processed\/annotations\/slide_list\.txt$ |
✓ | Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames. |
lab_processed\/virtual_histology\/.* |
✓ | This is a directory containing annotations for virtual histology images |
lab_processed\/virtual_histology\/HandE_RGB_thumbnail\.jpg$ |
Virtual H&E RGB thumbnail | |
lab_processed\/virtual_histology\/HandE_RGB\.(?:tif|tiff)$ |
Virtual H&E RGB image | |
lab_processed\/virtual_histology\/[^\/]+_VHE_region_[^\/]+\.(?:tif|tiff)$ |
Virtual H&E image |
| 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\/round_info_[^\/]+\.dat$ (example: raw/images/round_info_002.dat) |
✓ | Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. |
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\/region_[^\/]+\/[^\/]+_region_[^\/]+\.ome\.(?:tif|tiff)$ (example: lab_processed/images/region_001/S20030092_region_011.ome.tif) |
✓ | OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077), organized into subdirectories based on their region. |
lab_processed\/images\/region_[^\/]+\/[^\/]*ome-tiff\.channels\.csv$ |
✓ | 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 |
lab_processed\/annotations\/.* |
✓ | This is a directory containing annotations. |
lab_processed\/annotations\/slide_list\.txt$ |
✓ | Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames. |
lab_processed\/virtual_histology\/.* |
✓ | This is a directory containing annotations for virtual histology images |
lab_processed\/virtual_histology\/HandE_RGB_thumbnail\.jpg$ |
Virtual H&E RGB thumbnail | |
lab_processed\/virtual_histology\/HandE_RGB\.tif$ |
Virtual H&E RGB image | |
lab_processed\/virtual_histology\/[^\/]+_VHE_region_[^\/]+\.tif$ |
Virtual H&E image |
| 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\/round_info_[^\/]+\.dat$ (example: raw/images/round_info_002.dat) |
✓ | Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. |
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\/region_[^\/]+\/[^\/]+_region_[^\/]+\.ome\.(?:tif|tiff)$ (example: lab_processed/images/region_001/S20030092_region_011.ome.tif) |
✓ | OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077), organized into subdirectories based on their region. |
lab_processed\/images\/region_[^\/]+\/[^\/]*ome-tiff\.channels\.csv$ |
✓ | 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 |
lab_processed\/annotations\/.* |
✓ | This is a directory containing annotations. |
lab_processed\/annotations\/slide_list\.txt$ |
✓ | Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames. |
lab_processed\/virtual_histology\/.* |
✓ | This is a directory containing annotations for virtual histology images |
lab_processed\/virtual_histology\/HandE_RGB_thumbnail\.jpg$ |
✓ | Virtual H&E RGB thumbnail |
lab_processed\/virtual_histology\/HandE_RGB\.tif$ |
✓ | Virtual H&E RGB image |
lab_processed\/virtual_histology\/[^\/]+_VHE_region_[^\/]+\.tif$ |
✓ | Virtual H&E image |
| 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\/round_info_[^\/]+\.dat (example: raw/images/round_info_002.dat) |
✓ | Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle. |
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\/region_[^\/]+\/[^\/]+_region_[^\/]+\.ome\.(?:tif|tiff) (example: lab_processed/images/region_001/S20030092_region_011.ome.tif) |
✓ | OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077), organized into subdirectories based on their region. |
lab_processed\/images\/region_[^\/]+\/[^\/]*ome-tiff\.channels\.csv |
✓ | 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 |
lab_processed\/annotations\/.* |
✓ | This is a directory containing annotations. |
lab_processed\/annotations\/slide_list\.txt |
✓ | Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames. |
lab_processed\/virtual_histology\/.* |
✓ | This is a directory containing annotations for virtual histology images |
lab_processed\/virtual_histology\/HandE_RGB_thumbnail\.jpg |
✓ | Virtual H&E RGB thumbnail |
lab_processed\/virtual_histology\/HandE_RGB\.tif |
✓ | Virtual H&E RGB image |
lab_processed\/virtual_histology\/[^\/]+_VHE_region_[^\/]+\.tif |
✓ | Virtual H&E image |