Imaging Mass Spectrometry (IMS)

3D Imaging Mass Cytometry

Related files:

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

This schema is for 3 dimensional imaging mass cytometry (IMC 3D). 3D IMC uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For 3D 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
number_of_sections
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
max_x_width_value
max_x_width_unit
max_y_height_value
max_y_height_unit
segment_data_format
signal_type
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	`3D 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`

`number_of_sections`

Number of sections.

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`

`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 “float” 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`

`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