seqFISH

NOTE: Several versions of this metadata schema have been created over time. The (Latest) version contains most attributes, but there may be some deprecated attributes in the older versions for which data has been collected. HuBMAP is in the process of creating a reference which combines all of these versions into a single view. That reference will be available here once completed.

Version 1 (no longer accepting data)

Attribute	Type	Description	Allowable Values	Required
version	Allowable Value	Version of the schema to use when validating this metadata.	[‘1’]	True
description	Textfield	Free-text description of this assay.		True
donor_id	Textfield	HuBMAP Display ID of the donor of the assayed tissue.		True
tissue_id	Textfield	HuBMAP Display ID of the assayed tissue.		True
execution_datetime	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.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	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.	[‘imaging’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘seqFISH’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘RNA’]	True
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.	[‘Yes’,’No’]	True
acquisition_instrument_vendor	Textfield	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.		True
acquisition_instrument_model	Textfield	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.		True
resolution_x_value	Numeric	The width of a pixel.		True
resolution_x_unit	Allowable Value	The unit of measurement of the width of a pixel.	[‘nm’, ‘um’]	False
resolution_y_value	Numeric	The height of a pixel		True
resolution_y_unit	Allowable Value	The unit of measurement of the height of a pixel.	[‘nm’, ‘um’]	False
resolution_z_value	Numeric	Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices (for Akoya, z-pitch=1.5um) ie. the microscope stage is moved up or down in increments of 1.5um to capture images of several focal planes. The best one will be used & the rest discarded. The thickness of the sample itself is sample metadata.		False
resolution_z_unit	Allowable Value	The unit of incremental distance between image slices.	[‘mm’, ‘um’, ‘nm’]	False
preparation_instrument_vendor	Textfield	The manufacturer of the instrument used to prepare the sample for the assay.		True
preparation_instrument_model	Textfield	The model number/name of the instrument used to prepare the sample for the assay		True
number_of_barcode_probes	Numeric	Number of barcode probes targeting mRNAs (eg. 24,000 barcode probes = 24,000 mRNAs - 1 per mRNA of interest)		True
number_of_barcode_regions_per_barcode_probe	Numeric	Number of barcode regions on each mRNA barcode probe (the paper describes mRNA probes with 4 barcoded regions)		True
number_of_readout_probes_per_channel	Numeric	Number of readout probes that can be interrogated per channel per cycle (the paper describes 20 readout probes per channel (x 3 channels -> total = 60))		True
number_of_pseudocolors_per_channel	Numeric	Number of pseudocolors that can be assigned to each fluorescent channel (the paper describes 20 pseudocolors per channel (x 3 channels -> total = 60)		True
number_of_channels	Numeric	Number of fluorescent channels (the paper describes 3 channels - for 3 fluorescent dyes)		True
number_of_cycles	Numeric	For each barcode region being interrogated, the number of cycles of 1. Hybridization of readout probes, 2. imaging, 3. Washes (the paper describes 1 readout probe per hyb cycle -> 20 readout probes = 20 hyb cycles)		True
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.		True
reagent_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing reagents for the assay.		True
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.		True

Version 0

Attribute	Type	Description	Allowable Values	Required
donor_id	Textfield	HuBMAP Display ID of the donor of the assayed tissue.		True
tissue_id	Textfield	HuBMAP Display ID of the assayed tissue.		True
execution_datetime	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.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	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.	[‘imaging’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘seqFISH’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘RNA’]	True
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.	[‘Yes’,’No’]	True
acquisition_instrument_vendor	Textfield	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.		True
acquisition_instrument_model	Textfield	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.		True
resolution_x_value	Numeric	The width of a pixel.		True
resolution_x_unit	Allowable Value	The unit of measurement of the width of a pixel.	[‘nm’, ‘um’]	False
resolution_y_value	Numeric	The height of a pixel		True
resolution_y_unit	Allowable Value	The unit of measurement of the height of a pixel.	[‘nm’, ‘um’]	False
resolution_z_value	Numeric	Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices (for Akoya, z-pitch=1.5um) ie. the microscope stage is moved up or down in increments of 1.5um to capture images of several focal planes. The best one will be used & the rest discarded. The thickness of the sample itself is sample metadata.		False
resolution_z_unit	Allowable Value	The unit of incremental distance between image slices.	[‘mm’, ‘um’, ‘nm’]	False
preparation_instrument_vendor	Textfield	The manufacturer of the instrument used to prepare the sample for the assay.		True
preparation_instrument_model	Textfield	The model number/name of the instrument used to prepare the sample for the assay		True
number_of_barcode_probes	Numeric	Number of barcode probes targeting mRNAs (eg. 24,000 barcode probes = 24,000 mRNAs - 1 per mRNA of interest)		True
number_of_barcode_regions_per_barcode_probe	Numeric	Number of barcode regions on each mRNA barcode probe (the paper describes mRNA probes with 4 barcoded regions)		True
number_of_readout_probes_per_channel	Numeric	Number of readout probes that can be interrogated per channel per cycle (the paper describes 20 readout probes per channel (x 3 channels -> total = 60))		True
number_of_pseudocolors_per_channel	Numeric	Number of pseudocolors that can be assigned to each fluorescent channel (the paper describes 20 pseudocolors per channel (x 3 channels -> total = 60)		True
number_of_channels	Numeric	Number of fluorescent channels (the paper describes 3 channels - for 3 fluorescent dyes)		True
number_of_cycles	Numeric	For each barcode region being interrogated, the number of cycles of 1. Hybridization of readout probes, 2. imaging, 3. Washes (the paper describes 1 readout probe per hyb cycle -> 20 readout probes = 20 hyb cycles)		True
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.		True
reagent_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing reagents for the assay.		True
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.		True