Imaging

MxIF

Related files:

This schema is for multiplex immunofluorescence microscopy (MxIF).

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
number_of_channels
number_of_cycles
section_prep_protocols_io_doi
reagent_prep_protocols_io_doi
overall_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 MxIF
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 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

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. antibody application, 2. image capture, 3. antibody stripping.

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/

overall_protocols_io_doi

DOI for protocols.io for the overall process.

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

Shared by all types

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+)?
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 MxIF
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 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

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. antibody application, 2. image capture, 3. antibody stripping.

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/

overall_protocols_io_doi

DOI for protocols.io for the overall process.

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


Directory schemas

Version 0.0 (use this one)
pattern required? description
(Level0|level0)_raw\/cyc_[\d]+\.(tif|tiff) [QA/QC] MxiF raw tile data by cycle and channel.
(Level0|level0)_raw\/cyc_[\d]+\/tile_layout\.json MxiF tile layout in pixel coordinates in x and y.
(Level0|level0)_raw\/dataset\.json Additional specific metadata.
(Level1|level1)\/cyc_[\d]+\.ome\.(tif|tiff) Pre-processed stitched image files, but not registered across cycles.
(Level2|level2)\/ome\.(tif|tiff) [QA/QC] Full lab processed data, stitched, registered, and saved in pyramidal OME-TIFF.
(Level2|level2)_lab_final-processing\.pdf [QA/QC] Description of the lab-processed data.
extras\/.*   Folder for general lab-specific files related to the dataset. [Exists in all assays]