Imaging

CODEX / CODEX2

Related files:

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

This schema is for CO-Detection by indEXing (CODEX). CODEX uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For CODEX, in that TSV, the channel_id is a cycle#/channel# combination linked to a given image file (of the form Cycle[0-9]_CH[0-9]). Each TIF file in a CODEX dataset contains image data captured from a single channel in a single cycle, identified and connected to the channel_id by its location in the upload directory (of the form src_*/cyc*_reg*_*/*_*_Z*_CH*.tif). For an example of a CODEX dataset & directory, see this example CODEX dataset and click the Globus link. The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation.

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_antibodies
number_of_channels
number_of_cycles
section_prep_protocols_io_doi
reagent_prep_protocols_io_doi
antibodies_path
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`

`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.

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	`CODEX` or `CODEX2`
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 molecular mass.

constraint	value
enum	`Keyence` or `Zeiss`
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
enum	`BZ-X800`, `BZ-X710`, or `Axio Observer Z1`
required	`True`

Unique to this type

`resolution_x_value`

The width of a pixel. (Akoya pixel is 377nm square)

constraint	value
type	`number`
required	`True`

`resolution_x_unit`

The unit of measurement of width of a pixel.(nm) Leave blank if not applicable.

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

`resolution_y_value`

The height of a pixel. (Akoya pixel is 377nm square)

constraint	value
type	`number`
required	`True`

`resolution_y_unit`

The unit of measurement of height of a pixel. (nm) Leave blank if not applicable.

constraint	value
enum	`mm`, `um`, or `nm`
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
enum	`CODEX`
required	`True`

`preparation_instrument_model`

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

constraint	value
enum	`version 1 robot` or `prototype robot - Stanford/Nolan Lab`
required	`True`

`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`

`number_of_cycles`

Number of cycles of 1. oligo application, 2. fluor application, 3. washes.

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/`

`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