Clinical Imaging Modalities

Body CT

Related files:

This schema is for clinical imaging using body computed tomography (Body CT).

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
acquisition_instrument_vendor
acquisition_instrument_model

Shared by all clinical imaging assays

single_file_export_format
max_x_width_value
max_x_width_unit
max_y_height_value
max_y_height_unit
roi_description
roi_id
resolution_x_value
resolution_x_unit
resolution_y_value
resolution_y_unit
resolution_z_value
resolution_z_unit
pixel_size_z_value
pixel_size_z_unit
number_of_images

Unique to this type

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 clinical_imaging
required True

assay_type

The specific type of assay being executed.

constraint value
enum Body CT
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

Shared by all clinical imaging assays

single_file_export_format

The format in which each single imaging file will be exported. (Example: DICOM, tiff, avi, etc.)

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 or mm
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 or mm
required False
required if max_y_height_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. Leave blank if not applicable.

constraint value
type integer
required False
minimum 1

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, um, or mm
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, um, or mm
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, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. Leave blank if not applicable.

constraint value
type number
required False

resolution_z_unit

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

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

pixel_size_z_value

Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value). Leave blank if not applicable.

constraint value
type number
required False

pixel_size_z_unit

Depth unit of the pixel or voxel measurement. Leave blank if not applicable.

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

number_of_images

The total number of images in the dataset.

constraint value
type integer
required True

Unique to this type

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