Imaging

seqFISH

Related files:

🔬 Background doc: More details about this type.
📝 Excel template: For metadata entry.
📝 TSV template: Alternative for metadata entry.

This schema is for spatial sequencing by fluorescence in situ hybridization (seqFISH).

Metadata schema

Version 1 (use this one)

Shared by all types

version
description
donor_id
tissue_id
execution_datetime
protocols_io_doi
operator
operator_email
pi
pi_email
assay_category
assay_type
analyte_class
is_targeted
acquisition_instrument_vendor
acquisition_instrument_model

Unique to this type

resolution_x_value
resolution_x_unit
resolution_y_value
resolution_y_unit
resolution_z_value
resolution_z_unit
preparation_instrument_vendor
preparation_instrument_model
number_of_barcode_probes
number_of_barcode_regions_per_barcode_probe
number_of_readout_probes_per_channel
number_of_pseudocolors_per_channel
number_of_channels
number_of_cycles
section_prep_protocols_io_doi
reagent_prep_protocols_io_doi
contributors_path
data_path

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`

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	`seqFISH`
required	`True`

`analyte_class`

Analytes are the target molecules being measured with the assay.

constraint	value
enum	`RNA`
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`

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. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`resolution_z_unit`

The unit of incremental distance between image slices. Leave blank if not applicable.

constraint	value
enum	`mm`, `um`, or `nm`
required	`False`
required if	`resolution_z_value` present

`preparation_instrument_vendor`

The manufacturer of the instrument used to prepare the sample for the assay.

constraint	value
required	`True`

`preparation_instrument_model`

The model number/name of the instrument used to prepare the sample for the assay.

constraint	value
required	`True`

`number_of_barcode_probes`

Number of barcode probes targeting mRNAs (eg. 24,000 barcode probes = 24,000 mRNAs - 1 per mRNA of interest)

constraint	value
type	`integer`
required	`True`

`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)

constraint	value
type	`integer`
required	`True`

`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))

constraint	value
type	`integer`
required	`True`

`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)

constraint	value
type	`integer`
required	`True`

`number_of_channels`

Number of fluorescent channels (the paper describes 3 channels - for 3 fluorescent dyes)

constraint	value
type	`integer`
required	`True`

`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)

constraint	value
type	`integer`
required	`True`

`section_prep_protocols_io_doi`

DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.

constraint	value
required	`True`
pattern (regular expression)	`10\.17504/.*`
url	prefix: `https://dx.doi.org/`

`reagent_prep_protocols_io_doi`

DOI for protocols.io referring to the protocol for preparing reagents for the assay.

constraint	value
required	`True`
pattern (regular expression)	`10\.17504/.*`
url	prefix: `https://dx.doi.org/`

`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