Single-cycle Fluorescence Microscopy (SFM)

Light Sheet

Related files:

📝 Excel template: For metadata entry.
📝 TSV template: Alternative for metadata entry.

Metadata schema

Version 3 (use this one)

Version 2

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`

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`

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`

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`

constraint	value
required	`True`

`acquisition_instrument_model`

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`

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`

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`

constraint	value
required	`True`

`acquisition_instrument_model`

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

Version 2 (use this one) (draft - submission of data prepared using this schema will be supported by Sept. 30)

Version 1

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]

Version 0

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]