HOAMetadata

Type: object

root name

Name

Type: string

Unique name for dataset.

root organ

Organ

Type: enum (of string)

Organ name.

Must be one of:

  • "heart"
  • "kidney"
  • "lung"
  • "brain"
  • "spleen"

root scan_context

Scan Context

Type: enum (of string)

Must be one of:

  • "overview"
  • "zoom"

root organ_context

Organ Context


Context for location of the dataset within the whole organ. Only present for some zoom datasets.

root organ_context anyOf item 0
Type: string
root organ_context anyOf item 1
Type: null

root roi

Region of Interest

Type: string

Region of interest name.This is an arbitrary string that is unique within datasets taken from a given organ from a given donor.

root experiment_type

Experiment Type

Type: const
Specific value: "Tomography"

root technique

Experimental technique.

Type: const
Specific value: "Hierarchical Phase-Contrast Tomography (HiP-CT)"

root voxel_size_um

Voxel size

Type: number

Isotropic voxel size in micrometers.

root shape

Shape

Type: array

Shape of dataset.

Must contain a minimum of 3 items

Must contain a maximum of 3 items

No Additional Items

Tuple Validation

Item at 1 must be:
root shape shape item 0
Type: integer
Item at 2 must be:
root shape shape item 1
Type: integer
Item at 3 must be:
root shape shape item 2
Type: integer

root donor

Donor metadata

Type: object

Donor data model.

 No Additional Properties

root donor id

Id

Type: string

Donor ID

root donor age

Age

Default: null

Age in years at death.

root donor age anyOf item 0
Type: integer

Value must be greater or equal to 0

root donor age anyOf item 1
Type: enum (of string)

Must be one of:

  • "<18"
  • ">18"
root donor age anyOf item 2
Type: null

root donor sex

Sex

Default: null

root donor sex anyOf item 0
Type: enum (of string)

Must be one of:

  • "M"
  • "F"
root donor sex anyOf item 1
Type: null

root donor weight

Weight

Default: null

Weight in kg at death.

root donor weight anyOf item 0
Type: number

Value must be strictly greater than 0.0

root donor weight anyOf item 1
Type: null

root donor height

Height

Default: null

Height in cm at death.

root donor height anyOf item 0
Type: number

Value must be strictly greater than 0.0

root donor height anyOf item 1
Type: null

root donor cause_of_death

Cause of death

Default: null

root donor date_of_death

Date of death

Default: null

root donor date_of_death anyOf item 0
Type: stringFormat: date
root donor date_of_death anyOf item 1
Type: null

root donor medical_history

Medical history

Default: null

root donor diabetes

Diabetes history

Default: null

root donor diabetes anyOf item 0
Type: enum (of string)

Must be one of:

  • "Type 2"
  • "No"
  • "Yes"
root donor diabetes anyOf item 1
Type: null

root donor hypertension

Hypertension history

Default: null

root donor hypertension anyOf item 0
Type: enum (of string)

Must be one of:

  • "Yes"
  • "No"
root donor hypertension anyOf item 1
Type: null

root donor smoker

Smoking history

Default: null

root donor smoker anyOf item 0
Type: enum (of string)

Must be one of:

  • "Never"
  • "Yes"
root donor smoker anyOf item 1
Type: null

root scan

Scan metadata

Type: object

root scan dataset_name

Dataset Name

Type: string

root scan date

Date

Type: stringFormat: date

Date when the scan was performed.

root scan beamline

Beamline

Type: enum (of string)

ESRF beamline where scan was performed.

Must be one of:

  • "BM05"
  • "BM18"

root scan energy

Energy

Default: null

Energy used during the scan, measured in keV.

root scan energy anyOf item 0
Type: number

Value must be strictly greater than 0.0

root scan energy anyOf item 1
Type: null

root scan current_start

Current Start

Default: null

Current of the synchrotron at the start of the scan, measured in mA.

root scan current_start anyOf item 0
Type: number

Value must be strictly greater than 0.0

root scan current_start anyOf item 1
Type: null

root scan filling_mode

Filling Mode

Default: null

Mode of filling used in the synchrotron storage ring.

root scan filling_mode anyOf item 0
Type: enum (of string)

Must be one of:

  • "16 bunch"
  • "7/8 multibunch"
  • "uniform multibunch"
  • "28*12+1 bunch"
  • "4 bunch"
root scan filling_mode anyOf item 1
Type: null

root scan n_projections

N Projections

Default: null

Number of projection images acquired during the scan.

root scan n_projections anyOf item 0
Type: integer

Value must be strictly greater than 0

root scan n_projections anyOf item 1
Type: null

root scan n_ref

N Ref

Default: null

Number of reference images collected during the scan.

root scan n_ref anyOf item 0
Type: integer

Value must be greater or equal to 0

root scan n_ref anyOf item 1
Type: null

root scan n_dark

N Dark

Default: null

Number of dark images (without illumination) collected during the scan.

root scan n_dark anyOf item 0
Type: integer

Value must be greater or equal to 0

root scan n_dark anyOf item 1
Type: null

root scan latency_time

Latency Time

Default: null

Time delay between projections, measured in seconds.

root scan latency_time anyOf item 0
Type: number

Value must be strictly greater than 0.0

root scan latency_time anyOf item 1
Type: null

root scan exposure_time

Exposure Time

Default: null

Exposure time of each frame, measured in seconds.

root scan exposure_time anyOf item 0
Type: number

Value must be strictly greater than 0.0

root scan exposure_time anyOf item 1
Type: null

root scan accumulation_n_frames

Accumulation N Frames

Default: null

Number of frames accumulated per exposure.

root scan accumulation_n_frames anyOf item 0
Type: integer

Value must be strictly greater than 0

root scan accumulation_n_frames anyOf item 1
Type: null

root scan scan_type

Scan Type

Type: enum (of string)

Type of scan.

Must be one of:

  • "helical"
  • "zseries"

root scan scan_range

Scan Range

Type: number

Angular range of a single scan in degrees.

Value must be strictly greater than 0.0

root scan n_scans

N Scans

Default: null

Total number of scans. For a helical scan this is always 1. For a zseries this is the total number of scans concatenated to make the full data volume.

root scan n_scans anyOf item 0
Type: integer

Value must be strictly greater than 0

root scan n_scans anyOf item 1
Type: null

root scan acquisition

Acquisition

Default: null

Type of tomographic acquisition.

root scan acquisition anyOf item 0
Type: enum (of string)

Must be one of:

  • "half"
  • "quarter"
root scan acquisition anyOf item 1
Type: null

root scan z_step

Z Step

Default: null

Displacement in millimeters between scans.

root scan z_step anyOf item 0
Type: number
root scan z_step anyOf item 1
Type: null

root scan scan_time

Scan Time

Default: null

Total duration of a single scan in seconds.

root scan scan_time anyOf item 0
Type: number

Value must be strictly greater than 0.0

root scan scan_time anyOf item 1
Type: null

root scan filters

Filters

Default: null

List of filters used during the scan.

root scan filters anyOf item 0
Type: array of string
No Additional Items

Each item of this array must be:

root scan filters anyOf item 0 item 0 items
Type: string
root scan filters anyOf item 1
Type: null

root scan scintillator

Scintillator

Default: null

Scintillator used for converting X-rays to visible light.

root scan scintillator anyOf item 0
Type: enum (of string)

Must be one of:

  • "LuAG:Ce 1000um"
  • "LuAG:Ce 100um"
  • "LuAG:Ce 100um, reflective"
  • "LuAG:Ce 100um, lead glass meniscus"
  • "LuAG:Ce 2000um"
  • "LuAG:Ce 2000um, reflective"
  • "Multi LuAG:Ce 2000um, reflective"
  • "LuAG:Ce 200um"
  • "LuAG:Ce 250um"
  • "LuAG:Ce 25um"
  • "LuAG:Ce 50um"
  • "LuAG:Ce 50um, reflective"
  • "LuAG:Ce 500um"
  • "LySO:Ce 8.5um"
  • "LySO:Ce 23um"
  • "Gadox 60um"
root scan scintillator anyOf item 1
Type: null

root scan optic

Optic

Default: null

Optical components used during the scan

root scan optic anyOf item 0
Type: enum (of string)

Must be one of:

  • "Zoom"
  • "DZoom"
  • "10x 0.4NA reflective optic"
  • "Hasselblad tandem optic 100mm/300mm"
  • "Hasselblad revolved 100 100"
  • "LAFIP2 optic with canon 50mm"
  • "Fixed x1"
  • "Fixed x0.125"
  • "Fixed x0.1"
  • "Fixed x2.85"
  • "Twinmic 5"
  • "Twinmic 10"
  • "Twinmic 20"
root scan optic anyOf item 1
Type: null

root scan distance_sample_detector

Distance Sample Detector

Default: null

Distance between the sample and the detector, measured in millimeters.

root scan distance_sample_detector anyOf item 0
Type: number

Value must be strictly greater than 0.0

root scan distance_sample_detector anyOf item 1
Type: null

root scan sensor_name

Sensor Name

Default: null

Name of the sensor used during the scan.

root scan sensor_name anyOf item 0
Type: enum (of string)

Must be one of:

  • "PCO edge 4.2 CLHS"
  • "Iris15"
root scan sensor_name anyOf item 1
Type: null

root scan sensor_mode

Sensor Mode

Default: null

Operating mode of the sensor during the scan.

root scan sensor_mode anyOf item 0
Type: enum (of string)

Must be one of:

  • "rolling shutter"
  • "FFM"
root scan sensor_mode anyOf item 1
Type: null

root scan sensor_magnification

Sensor Magnification

Default: null

Magnification in the sensor setup.

root scan sensor_magnification anyOf item 0
Type: number

Value must be strictly greater than 0.0

root scan sensor_magnification anyOf item 1
Type: null

root scan sensor_roi_x_size

Sensor Roi X Size

Default: null

Number of pixels in the x-dimension of the sensor's region of interest (ROI).

root scan sensor_roi_x_size anyOf item 0
Type: integer

Value must be strictly greater than 0

root scan sensor_roi_x_size anyOf item 1
Type: null

root scan sensor_roi_y_size

Sensor Roi Y Size

Default: null

Number of pixels in the y-dimension of the sensor's region of interest (ROI).

root scan sensor_roi_y_size anyOf item 0
Type: integer

Value must be strictly greater than 0

root scan sensor_roi_y_size anyOf item 1
Type: null

root scan pixel_size

Pixel Size

Type: number

Size of a pixel at the source, measured in micrometers.

Value must be strictly greater than 0.0

root scan xray_magnification

Xray Magnification

Default: null

Magnification of X-rays due to divergence between the source and detector.

root scan xray_magnification anyOf item 0
Type: number

Value must be strictly greater than 0.0

root scan xray_magnification anyOf item 1
Type: null

root proposal

Beamtime proposal metadata

Type: object

root proposal proposal_number

Proposal Number

Type: string

Proposal number.

root proposal title

Title

Type: string

Proposal title.

root proposal proposers

Proposers

Type: array of string

Proposal proposers.

 No Additional Items

Each item of this array must be:

root proposal proposers proposers items
Type: string

root registration

Registration parameters


Metadata mapping high resolution volume of interest datasets to a full organ dataset. Not present for full organ datasets.

root registration anyOf Registration

Registration

Type: object

A set of registration parameters mapping array coordinates from
'sourcedatase' to 'targetdataset'.

The transform is specified as (in order):

  1. Rotation anticlockwise about the z-axis
  2. Isotropic scaling
  3. Translation

root registration anyOf Registration source_dataset

Source Dataset

Type: string

Dataset that is registered

root registration anyOf Registration target_dataset

Target Dataset

Type: string

Dataset that source_dataset is registered to.

root registration anyOf Registration translation

Translation

Type: array

Must contain a minimum of 3 items

Must contain a maximum of 3 items

No Additional Items

Tuple Validation

Item at 1 must be:
root registration anyOf Registration translation translation item 0
Type: number
Item at 2 must be:
root registration anyOf Registration translation translation item 1
Type: number
Item at 3 must be:
root registration anyOf Registration translation translation item 2
Type: number

root registration anyOf Registration rotation

Rotation

Type: number

Rotation in degrees about z-axis

root registration anyOf Registration scale

Scale

Type: number

Isotropic scaling factor
root registration anyOf item 1
Type: null

root citation

Dataset citation

Type: object

Dataset citation.

root citation title

Title

Type: string

Citation title.

root citation authors

Authors

Type: array of string

Dataset authors.

 No Additional Items

Each item of this array must be:

root citation authors authors items
Type: string

root citation doi

Doi


Dataset DOI.

root citation doi anyOf item 0
Type: string
root citation doi anyOf item 1
Type: null