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. SenNet 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)

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
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet 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

Version 0

Attribute Type Description Allowable Values Required
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet 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