HOAMetadata

Type: object

Metadata for a Human Organ Atlas dataset.

 No Additional Properties

root name

Name

Type: string

Unique name for dataset.

root dataset_type

Dataset Type

Type: enum (of string)

Type of dataset. Overview datasets contain the full sample. Zoom datasets contain a zoom into a particular volume of interest within the sample.

Must be one of:

  • "overview"
  • "zoom"

root voi

Volume of Interest

Type: string

Volume of interest name. For zoom datasets this gives a unique identifier among zoom datasets taken within the same sample.

root data

Data

Type: object

Data metadata

root data shape

Shape

Type: array

Array shape for 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 data shape shape item 0
Type: integer

Value must be strictly greater than 0

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

Value must be strictly greater than 0

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

Value must be strictly greater than 0

root data voxel_size_um

Voxel size

Type: number

Isotropic size of a single voxel, in micrometers.

Value must be strictly greater than 0

root data gcs_url

Google cloud storage URL

Type: string

URL to data in Google Cloud Storage. Starts with either n5:// or zarr:// to specify whether data is in N5 or OME-Zarr 0.4 format.

root sample

Sample

Type: object

Sample metadata

root sample organ

Organ

Type: enum (of string)

Organ name.

Must be one of:

  • "brain"
  • "breast"
  • "colon"
  • "eye"
  • "femaleGenitalia"
  • "kidney"
  • "liver"
  • "lung"
  • "heart"
  • "oesophagus"
  • "spinalCord"
  • "spine"
  • "spleen"
  • "heart+lungs"
  • "pancreas"
  • "placenta"
  • "prostate"
  • "testis"
  • "uterus"
  • "thoracicBlock"
  • "soleus"
  • "achillesTendon"
  • "knee"
  • "tibia"

root sample organ_context

Organ Context


Human-readable context for location of the dataset within the whole organ. Only present for some zoom datasets.
Examples:

"upper_lobe"

"left"

"tumor"

root sample post_mortem_interval_hours

Post-mortem interval

Default: null

Interval between death and fixation, in hours.

root sample post_mortem_interval_hours anyOf item 0
Type: number

Value must be greater or equal to 0

root sample post_mortem_interval_hours anyOf item 1
Type: null

root sample fixation_method

Fixation Method

Default: null

Fixation preparation method.

root sample fixation_method anyOf item 0
Type: enum (of string)

Must be one of:

  • "immersion"
  • "perfusion"
root sample fixation_method anyOf item 1
Type: null

root sample fixation_medium

Fixation Medium

Default: null

Fixation medium

root sample fixation_medium anyOf item 0
Type: const
Specific value: "formalin"
root sample fixation_medium anyOf item 1
Type: null

root sample organ_infilled

Organ Infilled

Default: null

root sample organ_infilled anyOf item 0
Type: boolean
root sample organ_infilled anyOf item 1
Type: const
Specific value: "n/a"
root sample organ_infilled anyOf item 2
Type: null

root sample stabilisation_medium

Stabilisation Medium

Default: null

root sample stabilisation_medium anyOf item 0
Type: enum (of string)

Must be one of:

  • "agar cubes"
  • "crushed agar"
  • "beads"
root sample stabilisation_medium anyOf item 1
Type: null

root sample degassing_method

Degassing Method

Default: null

root sample degassing_method anyOf item 0
Type: enum (of string)

Must be one of:

  • "inline"
  • "vacuum"
  • "vacuum+inline"
root sample degassing_method anyOf item 1
Type: null

root sample scan_solvent

Scan Solvent

Default: null

Scan medium solvent.

root sample scan_solvent anyOf item 0
Type: enum (of string)

Must be one of:

  • "formalin"
  • "ethanol"
root sample scan_solvent anyOf item 1
Type: null

root sample scan_solvent_concentration

Solvent concentration

Default: null

Scan medium solvent concentration in percent.

root sample scan_temperature

Scan Temperature

Default: "room temperature"

Temperature during scan, in degees celsius (if a number).

root sample scan_temperature anyOf item 0
Type: const
Specific value: "room temperature"
root sample scan_temperature anyOf item 1
Type: number

root donor

Donor

Type: object

Donor metadata

 No Additional Properties

root donor id

ID

Type: string

Unique 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

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

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

Type: object

Scan metadata

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

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

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_frames

Number of frames

Default: null

Number of frames acquired during the scan.

root scan n_frames anyOf item 0
Type: integer

Value must be strictly greater than 0

root scan n_frames anyOf item 1
Type: null

root scan n_ref

Number of references

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

Number of darks

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

Inactive time between active sensor times, measured in seconds.

root scan latency_time anyOf item 0
Type: number

Value must be strictly greater than 0

root scan latency_time anyOf item 1
Type: null

root scan exposure_time

Exposure Time

Default: null

Exposure time of a single frame, measured in seconds. This is the sub-frame time multiplied by the number of sub-frames.

root scan exposure_time anyOf item 0
Type: number

Value must be strictly greater than 0

root scan exposure_time anyOf item 1
Type: null

root scan subframe_time

Subframe Time

Default: null

Exposure time of a single sub-frame, measured in seconds.

root scan subframe_time anyOf item 0
Type: number

Value must be strictly greater than 0

root scan subframe_time anyOf item 1
Type: null

root scan n_subframes

Number of sub-frames

Default: null

Number of frames accumulated per exposure.

root scan n_subframes anyOf item 0
Type: integer

Value must be strictly greater than 0

root scan n_subframes 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

root scan n_scans

Number of 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

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 250um, reflective"
  • "LuAG:Ce 25um"
  • "LuAG:Ce 50um"
  • "LuAG:Ce 50um, reflective"
  • "LuAG:Ce 500um"
  • "LySO:Ce 8.5um"
  • "LySO:Ce 23um"
  • "LySO:Ce 2000um, reflective"
  • "Gadox 60um"
  • "CSI trixell structured 650um, 5um pitch"
  • "GGG 8um"
  • "GGG 20um"
  • "GAGG 1000um, reflective"
  • "GAGG 100um, reflective"
  • "Dual LySO:Ce 5000um, reflective"
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 x2"
  • "Fixed x1"
  • "Fixed x0.125"
  • "Fixed x0.1"
  • "Fixed x2.85"
  • "Fixed x10"
  • "Twinmic 5"
  • "Twinmic 10"
  • "Twinmic 20"
  • "Triplemic 10"
root scan optic anyOf item 1
Type: null

root scan optic_magnification

Optic Magnification

Default: null

Magnification in the optical setup.

root scan optic_magnification anyOf item 0
Type: number

Value must be strictly greater than 0

root scan optic_magnification anyOf item 1
Type: null

root scan distance_source_sample

Source-sample distance

Default: null

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

root scan distance_source_sample anyOf item 0
Type: number

Value must be strictly greater than 0

root scan distance_source_sample anyOf item 1
Type: null

root scan distance_sample_detector

Sample-detector distance

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

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_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 sensor_binning

Sensor Binning

Default: null

Pixel binning on the sensor.

root scan sensor_binning anyOf item 0
Type: array

Must contain a minimum of 2 items

Must contain a maximum of 2 items

No Additional Items

Tuple Validation

Item at 1 must be:
root scan sensor_binning anyOf item 0 item 0 item 0
Type: integer

Value must be strictly greater than 0

Item at 2 must be:
root scan sensor_binning anyOf item 0 item 0 item 1
Type: integer

Value must be strictly greater than 0

root scan sensor_binning anyOf item 1
Type: null

root scan pixel_size

Pixel Size

Type: number

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

Value must be strictly greater than 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

root scan xray_magnification anyOf item 1
Type: null

root scan technique

Experimental technique.

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

root scan experiment_type

Experiment Type

Type: string Default: "Tomography"

root proposal

Proposal

Type: object

Beamtime proposal metadata

root proposal proposal_number

Proposal Number

Type: enum (of string)

Proposal number.

Must be one of:

  • "md1252"
  • "md1290"
  • "md1389"

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
source_dataset to target_dataset.

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

Name of dataset that is registered (this dataset).

root registration anyOf Registration target_dataset

Target Dataset

Type: string

Name of dataset that this dataset is registered to.

root registration anyOf Registration translation

Translation

Type: array

Translation vector.

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 contributors

Contributors

Type: array

Dataset contributors, listed alphabetically by name.

 No Additional Items

Each item of this array must be:

root citation contributors Contributor

Contributor

Type: object

root citation contributors Contributor first_name

First Name

Type: string

root citation contributors Contributor last_name

Last Name

Type: string

root citation contributors Contributor orcid

Orcid

Default: null

ORCID iD

root citation contributors Contributor orcid anyOf item 0
Type: string
Must match regular expression: ^\d{4}-\d{4}-\d{4}-\d{3}[0-9X]{1}$
root citation contributors Contributor orcid anyOf item 1
Type: null

root citation contributors Contributor roles

Roles

Type: array of enum (of string)

Contributor role(s), following the Contributor Role Taxonomy (CReditT)

 No Additional Items

Each item of this array must be:

root citation contributors Contributor roles roles items
Type: enum (of string)

Must be one of:

  • "Conceptualization"
  • "Data curation"
  • "Formal analysis"
  • "Funding acquisition"
  • "Investigation"
  • "Methodology"
  • "Project administration"
  • "Resources"
  • "Software"
  • "Supervision"
  • "Validation"
  • "Vlisualization"
  • "Writing - original draft"
  • "Writing - review & editing"

root citation doi

Doi


Dataset DOI

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

root citation author_list

Author List

Type: array of string

Author list. If citing this data, please use this authorship list in the order given

 No Additional Items

Each item of this array must be:

root citation author_list author_list items
Type: string

root metadata_version

Metadata Version

Type: const Default: "1.0"

Version of this metadata file.

Specific value: "1.0"