Imaging Mass Spectrometry (IMS)

Imaging Mass Cytometry

Related files:

This schema is for imaging mass cytometry (IMC). IMC uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For IMC, the channel_id is the name of the metal tag on the corresponding antibody. 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

preparation_instrument_vendor
preparation_instrument_model
section_prep_protocols_io_doi
reagent_prep_protocols_io_doi
number_of_channels
ablation_distance_between_shots_x_value
ablation_distance_between_shots_x_units
ablation_distance_between_shots_y_value
ablation_distance_between_shots_y_units
ablation_frequency_value
ablation_frequency_unit
roi_description
roi_id
acquisition_id
dual_count_start
max_x_width_value
max_x_width_unit
max_y_height_value
max_y_height_unit
segment_data_format
signal_type
data_precision_bytes
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 mass_spectrometry_imaging
required True

assay_type

The specific type of assay being executed.

constraint value
enum Imaging Mass Cytometry
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

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

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/

number_of_channels

Number of mass channels measured.

constraint value
type integer
required True

ablation_distance_between_shots_x_value

x resolution. Distance between laser ablation shots in the X-dimension.

constraint value
type number
required True

ablation_distance_between_shots_x_units

Units of x resolution distance between laser ablation shots.

constraint value
enum um or nm
required True

ablation_distance_between_shots_y_value

y resolution. Distance between laser ablation shots in the Y-dimension.

constraint value
type number
required True

ablation_distance_between_shots_y_units

Units of y resolution distance between laser ablation shots.

constraint value
enum um or nm
required True

ablation_frequency_value

Frequency value of laser ablation (in Hz)

constraint value
type number
required True

ablation_frequency_unit

Frequency unit of laser ablation. Leave blank if not applicable.

constraint value
enum Hz
required False
required if ablation_frequency_value present

roi_description

A description of the region of interest (ROI) captured in the image.

constraint value
required True

roi_id

Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide.

constraint value
type integer
required True

acquisition_id

The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image.

constraint value
required True

dual_count_start

Threshold for dual counting.

constraint value
type number
required True

max_x_width_value

Image width value of the ROI acquisition.

constraint value
type number
required True

max_x_width_unit

Units of image width of the ROI acquisition. Leave blank if not applicable.

constraint value
enum um
required False
required if max_x_width_value present

max_y_height_value

Image height value of the ROI acquisition.

constraint value
type number
required True

max_y_height_unit

Units of image height of the ROI acquisition. Leave blank if not applicable.

constraint value
enum um
required False
required if max_y_height_value present

segment_data_format

This refers to the data type, which is a โ€œfloatโ€ for the IMC counts.

constraint value
enum float, integer, or string
required True

signal_type

Type of signal measured per channel (usually dual counts)

constraint value
enum dual count, pulse count, or intensity value
required True

data_precision_bytes

Numerical data precision in bytes.

constraint value
type number
required True

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 mass_spectrometry_imaging
required True

assay_type

The specific type of assay being executed.

constraint value
enum Imaging Mass Cytometry
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

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

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/

number_of_channels

Number of mass channels measured.

constraint value
type integer
required True

ablation_distance_between_shots_x_value

x resolution. Distance between laser ablation shots in the X-dimension.

constraint value
type number
required True

ablation_distance_between_shots_x_units

Units of x resolution distance between laser ablation shots.

constraint value
enum um or nm
required True

ablation_distance_between_shots_y_value

y resolution. Distance between laser ablation shots in the Y-dimension.

constraint value
type number
required True

ablation_distance_between_shots_y_units

Units of y resolution distance between laser ablation shots.

constraint value
enum um or nm
required True

ablation_frequency_value

Frequency value of laser ablation (in Hz)

constraint value
type number
required True

ablation_frequency_unit

Frequency unit of laser ablation. Leave blank if not applicable.

constraint value
enum Hz
required False
required if ablation_frequency_value present

roi_description

A description of the region of interest (ROI) captured in the image.

constraint value
required True

roi_id

Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide.

constraint value
type integer
required True

acquisition_id

The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image.

constraint value
required True

dual_count_start

Threshold for dual counting.

constraint value
type number
required True

end_datetime

Time stamp indicating end of ablation for ROI.

constraint value
type datetime
format %Y-%m-%d %H:%M
required True

max_x_width_value

Image width value of the ROI acquisition.

constraint value
type number
required True

max_x_width_unit

Units of image width of the ROI acquisition. Leave blank if not applicable.

constraint value
enum um
required False
required if max_x_width_value present

max_y_height_value

Image height value of the ROI acquisition.

constraint value
type number
required True

max_y_height_unit

Units of image height of the ROI acquisition. Leave blank if not applicable.

constraint value
enum um
required False
required if max_y_height_value present

segment_data_format

This refers to the data type, which is a โ€œfloatโ€ for the IMC counts.

constraint value
enum float, integer, or string
required True

signal_type

Type of signal measured per channel (usually dual counts)

constraint value
enum dual count, pulse count, or intensity value
required True

start_datetime

Time stamp indicating start of ablation for ROI.

constraint value
type datetime
format %Y-%m-%d %H:%M
required True

data_precision_bytes

Numerical data precision in bytes.

constraint value
type number
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
TODO โœ“ Directory structure not yet specified.
extras\/.* ย  Folder for general lab-specific files related to the dataset. [Exists in all assays]