Clinical Imaging Modalities

Micro CT

Related files:

📝 Excel template: For metadata entry.
📝 TSV template: Alternative for metadata entry.

This schema is for clinical imaging using micro computed tomography (Micro 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

voltage_value
voltage_unit
current_value
current_unit
filter
imaging_threshold_value
imaging_threshold_unit_value
total_sections_analyzed
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`

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	`Micro 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

`voltage_value`

The voltage used to acquire images. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`voltage_unit`

The unit of the voltage used to acquire microCT images. Example: V. Leave blank if not applicable.

constraint	value
enum	`V` or `kV`
required	`False`
required if	`voltage_value` present

`current_value`

The current used to acquire microCT images. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`current_unit`

The unit of the current used to acquire microCT images. Example: mA. Leave blank if not applicable.

constraint	value
enum	`mA`, `microA`, or `A`
required	`False`
required if	`current_value` present

`filter`

The filter used to acquire microCT images. Leave blank if not applicable.

constraint	value
required	`False`

`imaging_threshold_value`

The threshold used for analyzing microCT images. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`imaging_threshold_unit_value`

The threshold unit used for analyzing microCT images (unitless) Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`total_sections_analyzed`

The number of sections used for analyzing microCT or OCT images. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`

`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`