Imaging
Light Sheet
Related files:
-
🔬 Background doc: More details about this type.
- 📝 Excel template: For metadata entry.
- 📝 TSV template: Alternative for metadata entry.
Lightsheet uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For Lightsheet, the channel_id is the name of the fluorophore tag on the antibody. For an example of a lightsheet dataset & directory, see this example lightsheet dataset and click the Globus link.
Version 2 has 5 new fields for metadata describing the Z-dimension specifically relevant to lightsheet. These values provide the total number of image sections captured, the incremental value and unit of distance between the sections and the value and unit of the total distance captured.
The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation.
Metadata schema
Version 2 (use this one)
Shared by all types
version
Version of the schema to use when validating this metadata.
| constraint | value |
|---|---|
| enum | 2 |
| required | True |
description
Free-text description of this assay.
| constraint | value |
|---|---|
| required | True |
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |
| required | True |
execution_datetime
Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
assay_category
Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.
| constraint | value |
|---|---|
| enum | imaging |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | Light Sheet |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | protein |
| required | True |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
acquisition_instrument_vendor
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
| constraint | value |
|---|---|
| required | True |
acquisition_instrument_model
Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
| constraint | value |
|---|---|
| required | True |
Unique to this type
resolution_x_value
The width of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
resolution_x_unit
The unit of measurement of the width of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_x_value present |
resolution_y_value
The height of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
resolution_y_unit
The unit of measurement of the height of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_y_value present |
range_z_value
The total range of the z axis.
| constraint | value |
|---|---|
| type | number |
| required | True |
range_z_unit
The unit of range_z_value. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | range_z_value present |
step_z_value
The number of optical sections in z axis range.
| constraint | value |
|---|---|
| type | number |
| required | True |
increment_z_value
The distance between sequential optical sections.
| constraint | value |
|---|---|
| type | number |
| required | True |
increment_z_unit
The units of increment z value. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | increment_z_value present |
number_of_antibodies
Number of antibodies.
| constraint | value |
|---|---|
| type | integer |
| required | True |
number_of_channels
Number of fluorescent channels imaged during each cycle.
| constraint | value |
|---|---|
| type | integer |
| required | True |
antibodies_path
Relative path to file with antibody information for this dataset.
| constraint | value |
|---|---|
| required | True |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Version 1
Shared by all types
version
Version of the schema to use when validating this metadata.
| constraint | value |
|---|---|
| enum | 1 |
| required | True |
description
Free-text description of this assay.
| constraint | value |
|---|---|
| required | True |
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |
| required | True |
execution_datetime
Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
assay_category
Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.
| constraint | value |
|---|---|
| enum | imaging |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | Light Sheet |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | protein |
| required | True |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
acquisition_instrument_vendor
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
| constraint | value |
|---|---|
| required | True |
acquisition_instrument_model
Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
| constraint | value |
|---|---|
| required | True |
Unique to this type
resolution_x_value
The width of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
resolution_x_unit
The unit of measurement of the width of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_x_value present |
resolution_y_value
The height of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
resolution_y_unit
The unit of measurement of the height of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_y_value present |
resolution_z_value
The distance at which two objects along the detection z-axis can be distinguished (resolved as 2 objects).
| constraint | value |
|---|---|
| type | number |
| required | True |
resolution_z_unit
The unit of distance at which two objects along the detection z-axis can be distinguished (resolved as 2 objects). Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | mm, um, or nm |
| required | False |
| required if | resolution_z_value present |
number_of_antibodies
Number of antibodies.
| constraint | value |
|---|---|
| type | integer |
| required | True |
number_of_channels
Number of fluorescent channels imaged during each cycle.
| constraint | value |
|---|---|
| type | integer |
| required | True |
antibodies_path
Relative path to file with antibody information for this dataset.
| constraint | value |
|---|---|
| required | True |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Version 0
Shared by all types
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | ([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)? |
| required | True |
execution_datetime
Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
assay_category
Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.
| constraint | value |
|---|---|
| enum | imaging |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | Light Sheet |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | protein |
| required | True |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
acquisition_instrument_vendor
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
| constraint | value |
|---|---|
| required | True |
acquisition_instrument_model
Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
| constraint | value |
|---|---|
| required | True |
Unique to this type
resolution_x_value
The width of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
resolution_x_unit
The unit of measurement of the width of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_x_value present |
resolution_y_value
The height of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
resolution_y_unit
The unit of measurement of the height of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_y_value present |
resolution_z_value
The distance at which two objects along the detection z-axis can be distinguished (resolved as 2 objects).
| constraint | value |
|---|---|
| type | number |
| required | True |
resolution_z_unit
The unit of distance at which two objects along the detection z-axis can be distinguished (resolved as 2 objects). Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | mm, um, or nm |
| required | False |
| required if | resolution_z_value present |
number_of_antibodies
Number of antibodies.
| constraint | value |
|---|---|
| type | integer |
| required | True |
number_of_channels
Number of fluorescent channels imaged during each cycle.
| constraint | value |
|---|---|
| type | integer |
| required | True |
antibodies_path
Relative path to file with antibody information for this dataset.
| constraint | value |
|---|---|
| required | True |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Directory schemas
| pattern | required? | description |
|---|---|---|
Level0/Channel[^/]+/[^/]+\.csv |
✓ | [QA/QC] Contains metadata and channel info. |
Level0/Channel[^/]+/[^/]+\.czi |
Zeiss raw image file. | |
Level0/Merged/MergedChannel[^/]+/[^/]+\.czi |
Merged Zeiss raw image file. | |
Level0/Channel[^/]+/[^/]+\.ome.tiff |
✓ | Raw image file. |
Level0/Merged/MergedChannel[^/]+/[^/]+\.ome.tiff |
✓ | Merged raw image file. |
Level1/Channel[^/]+/[^/]+\.tif |
Stitched image. | |
Level1/Merged/MergedChannel[^/]+/[^/]+\.tif |
Merged stitched image. | |
Level1/Channel[^/]+/[^/]+\.mp4 |
Stitched image. | |
Level2/Channel[^/]+/[^/]+\.csv |
[QA/QC] Contains file, parent and bounds. Required when level 2 is populated. File is optional. | |
Level2/Channel[^/]+/[^/]+\.obj |
Segmentation mask. | |
Level2/Channel[^/]+/[^/]+\.stl |
Segmentation mask. | |
Level2/Channel[^/]+/[^/]+\.ome.tiff |
Segmentation mask. | |
Level2/Merged/MergedChannel[^/]+/[^/]+\.ome.tiff |
Merged segmentation mask. | |
Level3/Channel[^/]+/[^/]+\.csv |
[QA/QC] Contains file, parent and bounds. Required when level 3 is populated. File is optional. | |
Level3/Channel[^/]+/[^/]+\.obj |
Annotation file. | |
Level3/Channel[^/]+/[^/]+\.stl |
Annotation file. | |
Level3/Channel[^/]+/[^/]+\.ome.tiff |
Image file. | |
Level3/Merged/MergedChannel[^/]+/[^/]+\.ome.tiff |
Merged image file. | |
extras\/.* |
Folder for general lab-specific files related to the dataset. [Exists in all assays] |
| pattern | required? | description |
|---|---|---|
Level0/Channel[^/]+/[^/]+\.csv |
✓ | [QA/QC] Contains metadata and channel info. |
Level0/Channel[^/]+/[^/]+\.czi |
Zeiss raw image file. File is optional. | |
Level0/Channel[^/]+/[^/]+\.ome.tiff |
✓ | Raw image file. |
Level1/Channel[^/]+/[^/]+\.tif |
Stitched image. File is optional. | |
Level1/Channel[^/]+/[^/]+\.mp4 |
Stitched image. File is optional. | |
Level2/Channel[^/]+/[^/]+\.csv |
[QA/QC] Contains file, parent and bounds. Required when level 2 is populated. File is optional. | |
Level2/Channel[^/]+/[^/]+\.obj |
Segmentation mask. File is optional. | |
Level2/Channel[^/]+/[^/]+\.stl |
Segmentation mask. File is optional. | |
Level2/Channel[^/]+/[^/]+\.ome.tiff |
Segmentation mask. File is optional. | |
Level3/Channel[^/]+/[^/]+\.csv |
[QA/QC] Contains file, parent and bounds. Required when level 3 is populated. File is optional. | |
Level3/Channel[^/]+/[^/]+\.obj |
Annotation file. File is optional. | |
Level3/Channel[^/]+/[^/]+\.stl |
Annotation file. File is optional. | |
Level3/Channel[^/]+/[^/]+\.ome.tiff |
Annotation file. File is optional. | |
extras\/.* |
Folder for general lab-specific files related to the dataset. [Exists in all assays] |