seqFISH Metadata Attributes
Fields that are collected for seqFISH data, available at dataset.metadata.<attribute>
* indicates a required field
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| version * | Version of the schema to use when validating this metadata. | '1' |
|
| description | Free-text description of this assay. | ||
| donor_id | HuBMAP Display ID of the donor of the assayed tissue. | ||
| tissue_id | HuBMAP Display ID of the assayed tissue. | ||
| 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. | ||
| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | ||
| operator | Name of the person responsible for executing the assay. | ||
| operator_email | Email address for the operator. | ||
| pi | Name of the principal investigator responsible for the data. | ||
| pi_email | Email address for the principal investigator. | ||
| 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. | 'imaging' |
|
| assay_type | The specific type of assay being executed. | 'seqFISH' |
|
| analyte_class | Analytes are the target molecules being measured with the assay. | 'RNA' |
|
| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | 'Yes' 'No' |
|
| 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. | ||
| 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. | ||
| resolution_x_value | The width of a pixel. | ||
| resolution_x_unit | The unit of measurement of the width of a pixel. | 'nm' 'um' |
|
| resolution_y_value * | The height of a pixel | ||
| resolution_y_unit | The unit of measurement of the height of a pixel. | 'nm' 'um' |
|
| resolution_z_value | 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. | ||
| resolution_z_unit | The unit of incremental distance between image slices. | 'mm' 'um' 'nm' |
|
| preparation_instrument_vendor * | The manufacturer of the instrument used to prepare the sample for the assay. | ||
| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay | ||
| number_of_barcode_probes | Number of barcode probes targeting mRNAs (eg. 24,000 barcode probes = 24,000 mRNAs - 1 per mRNA of interest) | ||
| number_of_barcode_regions_per_barcode_probe | Number of barcode regions on each mRNA barcode probe (the paper describes mRNA probes with 4 barcoded regions) | ||
| number_of_readout_probes_per_channel | 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)) | ||
| number_of_pseudocolors_per_channel | Number of pseudocolors that can be assigned to each fluorescent channel (the paper describes 20 pseudocolors per channel (x 3 channels -> total = 60) | ||
| number_of_channels | Number of fluorescent channels (the paper describes 3 channels - for 3 fluorescent dyes) | ||
| number_of_cycles | 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) | ||
| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | ||
| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | ||
| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | ||
| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. |
Deprecated Attributes
* indicates a field that was previously required
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| donor_id | HuBMAP Display ID of the donor of the assayed tissue. | ||
| tissue_id | HuBMAP Display ID of the assayed tissue. | ||
| 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. | ||
| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | ||
| operator | Name of the person responsible for executing the assay. | ||
| operator_email | Email address for the operator. | ||
| pi | Name of the principal investigator responsible for the data. | ||
| pi_email | Email address for the principal investigator. | ||
| 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. | 'imaging' |
|
| assay_type | The specific type of assay being executed. | 'seqFISH' |
|
| analyte_class | Analytes are the target molecules being measured with the assay. | 'RNA' |
|
| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | 'Yes' 'No' |
|
| 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. | ||
| 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. | ||
| resolution_x_value | The width of a pixel. | ||
| resolution_x_unit | The unit of measurement of the width of a pixel. | 'nm' 'um' |
|
| resolution_y_value | The height of a pixel | ||
| resolution_y_unit | The unit of measurement of the height of a pixel. | 'nm' 'um' |
|
| resolution_z_value | 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. | ||
| resolution_z_unit | The unit of incremental distance between image slices. | 'mm' 'um' 'nm' |
|
| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | ||
| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay | ||
| number_of_barcode_probes | Number of barcode probes targeting mRNAs (eg. 24,000 barcode probes = 24,000 mRNAs - 1 per mRNA of interest) | ||
| number_of_barcode_regions_per_barcode_probe | Number of barcode regions on each mRNA barcode probe (the paper describes mRNA probes with 4 barcoded regions) | ||
| number_of_readout_probes_per_channel | 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)) | ||
| number_of_pseudocolors_per_channel | Number of pseudocolors that can be assigned to each fluorescent channel (the paper describes 20 pseudocolors per channel (x 3 channels -> total = 60) | ||
| number_of_channels | Number of fluorescent channels (the paper describes 3 channels - for 3 fluorescent dyes) | ||
| number_of_cycles | 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) | ||
| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | ||
| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | ||
| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | ||
| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. |