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metadata-schema.json
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{
"$defs": {
"Citation": {
"description": "Dataset citation.",
"properties": {
"title": {
"description": "Citation title",
"title": "Title",
"type": "string"
},
"contributors": {
"description": "Dataset contributors, listed alphabetically by name.",
"items": {
"$ref": "#/$defs/Contributor"
},
"title": "Contributors",
"type": "array"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"description": "Dataset DOI",
"title": "Doi"
},
"author_list": {
"description": "Author list. If citing this data, please use this authorship list in the order given",
"items": {
"type": "string"
},
"readOnly": true,
"title": "Author List",
"type": "array"
}
},
"required": ["title", "contributors", "doi", "author_list"],
"title": "Citation",
"type": "object"
},
"Contributor": {
"properties": {
"name": {
"title": "Name",
"type": "string"
},
"roles": {
"description": "Contributor role(s), following the Contributor Role Taxonomy (CReditT)",
"items": {
"enum": [
"Conceptualization",
"Data curation",
"Formal analysis",
"Funding acquisition",
"Investigation",
"Methodology",
"Project administration",
"Resources",
"Software",
"Supervision",
"Validation",
"Vlisualization",
"Writing - original draft",
"Writing - review & editing"
],
"type": "string"
},
"title": "Roles",
"type": "array"
}
},
"required": ["name", "roles"],
"title": "Contributor",
"type": "object"
},
"Data": {
"description": "Data metadata.",
"properties": {
"shape": {
"description": "Array shape for dataset.",
"maxItems": 3,
"minItems": 3,
"prefixItems": [
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"exclusiveMinimum": 0,
"type": "integer"
}
],
"title": "Shape",
"type": "array"
},
"voxel_size_um": {
"description": "Isotropic size of a single voxel, in micrometers.",
"exclusiveMinimum": 0.0,
"title": "Voxel size",
"type": "number"
}
},
"required": ["shape", "voxel_size_um"],
"title": "Data",
"type": "object"
},
"Donor": {
"additionalProperties": false,
"properties": {
"id": {
"description": "Unique donor ID.",
"title": "ID",
"type": "string"
},
"age": {
"anyOf": [
{
"minimum": 0,
"type": "integer"
},
{
"enum": ["<18", ">18"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Age in years at death.",
"title": "Age"
},
"sex": {
"anyOf": [
{
"enum": ["M", "F"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Sex"
},
"weight": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Weight in kg at death.",
"title": "Weight"
},
"height": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Height in cm at death.",
"title": "Height"
},
"cause_of_death": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Cause of death"
},
"date_of_death": {
"anyOf": [
{
"format": "date",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Date of death"
},
"medical_history": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Medical history"
},
"diabetes": {
"anyOf": [
{
"enum": ["Type 2", "No", "Yes"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Diabetes history"
},
"hypertension": {
"anyOf": [
{
"enum": ["Yes", "No"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Hypertension history"
},
"smoker": {
"anyOf": [
{
"enum": ["Never", "Yes"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Smoking history"
}
},
"required": ["id"],
"title": "Donor",
"type": "object"
},
"Proposal": {
"properties": {
"proposal_number": {
"description": "Proposal number.",
"enum": ["md1252", "md1290", "md1389"],
"title": "Proposal Number",
"type": "string"
},
"title": {
"description": "Proposal title.",
"title": "Title",
"type": "string"
},
"proposers": {
"description": "Proposal proposers.",
"items": {
"type": "string"
},
"title": "Proposers",
"type": "array"
}
},
"required": ["proposal_number", "title", "proposers"],
"title": "Proposal",
"type": "object"
},
"Registration": {
"description": "A set of registration parameters mapping array coordinates from\n`source_dataset` to `target_dataset`.\n\nThe transform is specified as (in order):\n\n1. Rotation anticlockwise about the z-axis\n2. Isotropic scaling\n3. Translation",
"properties": {
"source_dataset": {
"description": "Name of dataset that is registered (this dataset).",
"title": "Source Dataset",
"type": "string"
},
"target_dataset": {
"description": "Name of dataset that this dataset is registered to.",
"title": "Target Dataset",
"type": "string"
},
"translation": {
"description": "Translation vector.",
"maxItems": 3,
"minItems": 3,
"prefixItems": [
{
"type": "number"
},
{
"type": "number"
},
{
"type": "number"
}
],
"title": "Translation",
"type": "array"
},
"rotation": {
"description": "Rotation in degrees about z-axis",
"title": "Rotation",
"type": "number"
},
"scale": {
"description": "Isotropic scaling factor.",
"title": "Scale",
"type": "number"
}
},
"required": [
"source_dataset",
"target_dataset",
"translation",
"rotation",
"scale"
],
"title": "Registration",
"type": "object"
},
"Sample": {
"properties": {
"organ": {
"description": "Organ name.",
"enum": ["heart", "kidney", "lung", "brain", "spleen"],
"title": "Organ",
"type": "string"
},
"organ_context": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"description": "Human-readable context for location of the dataset within the whole organ. Only present for some zoom datasets.",
"examples": ["upper_lobe", "left", "tumor"],
"title": "Organ Context"
},
"post_mortem_interval_hours": {
"anyOf": [
{
"minimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Interval between death and fixation, in hours.",
"title": "Post-mortem interval"
},
"fixation_method": {
"anyOf": [
{
"enum": ["immersion", "perfusion"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Fixation preparation method.",
"title": "Fixation Method"
},
"fixation_medium": {
"anyOf": [
{
"const": "formalin",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Fixation medium",
"title": "Fixation Medium"
},
"organ_infilled": {
"anyOf": [
{
"type": "boolean"
},
{
"const": "n/a",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Organ Infilled"
},
"stabilisation_medium": {
"anyOf": [
{
"enum": ["agar cubes", "crushed agar", "beads"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Stabilisation Medium"
},
"degassing_method": {
"anyOf": [
{
"enum": ["inline", "vacuum", "vacuum+inline"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Degassing Method"
},
"scan_solvent": {
"anyOf": [
{
"enum": ["formalin", "ethanol"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Scan medium solvent.",
"title": "Scan Solvent"
},
"scan_solvent_concentration": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Scan medium solvent concentration in percent.",
"title": "Solvent concentration"
},
"scan_temperature": {
"anyOf": [
{
"const": "room temperature",
"type": "string"
},
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Temperature during scan, in degees celsius (if a number).",
"title": "Scan Temperature"
}
},
"required": ["organ", "organ_context"],
"title": "Sample",
"type": "object"
},
"Scan": {
"properties": {
"date": {
"description": "Date when the scan was performed.",
"format": "date",
"title": "Date",
"type": "string"
},
"beamline": {
"description": "ESRF beamline where scan was performed.",
"enum": ["BM05", "BM18"],
"title": "Beamline",
"type": "string"
},
"energy": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Energy used during the scan, measured in keV.",
"title": "Energy"
},
"current_start": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Current of the synchrotron at the start of the scan, measured in mA.",
"title": "Current Start"
},
"filling_mode": {
"anyOf": [
{
"enum": [
"16 bunch",
"7/8 multibunch",
"uniform multibunch",
"28*12+1 bunch",
"4 bunch"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Mode of filling used in the synchrotron storage ring.",
"title": "Filling Mode"
},
"n_projections": {
"anyOf": [
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of projection images acquired during the scan.",
"title": "Number of projections"
},
"n_ref": {
"anyOf": [
{
"minimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of reference images collected during the scan.",
"title": "Number of references"
},
"n_dark": {
"anyOf": [
{
"minimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of dark images (without illumination) collected during the scan.",
"title": "Number of darks"
},
"latency_time": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Time delay between projections, measured in seconds.",
"title": "Latency Time"
},
"exposure_time": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Exposure time of each frame, measured in seconds.",
"title": "Exposure Time"
},
"accumulation_n_frames": {
"anyOf": [
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of frames accumulated per exposure.",
"title": "Number of accumulation frames"
},
"scan_type": {
"description": "Type of scan.",
"enum": ["helical", "zseries"],
"title": "Scan Type",
"type": "string"
},
"scan_range": {
"description": "Angular range of a single scan in degrees.",
"exclusiveMinimum": 0.0,
"title": "Scan Range",
"type": "number"
},
"n_scans": {
"anyOf": [
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "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.",
"title": "Number of scans"
},
"acquisition": {
"anyOf": [
{
"enum": ["half", "quarter"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Type of tomographic acquisition.",
"title": "Acquisition"
},
"z_step": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Displacement in millimeters between scans.",
"title": "Z Step"
},
"scan_time": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Total duration of a single scan in seconds.",
"title": "Scan Time"
},
"filters": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "List of filters used during the scan.",
"title": "Filters"
},
"scintillator": {
"anyOf": [
{
"enum": [
"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"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Scintillator used for converting X-rays to visible light.",
"title": "Scintillator"
},
"optic": {
"anyOf": [
{
"enum": [
"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",
"Fixed x10",
"Twinmic 5",
"Twinmic 10",
"Twinmic 20"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Optical components used during the scan",
"title": "Optic"
},
"distance_sample_detector": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Distance between the sample and the detector, measured in millimeters.",
"title": "Distance Sample Detector"
},
"sensor_name": {
"anyOf": [
{
"enum": ["PCO edge 4.2 CLHS", "Iris15"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Name of the sensor used during the scan.",
"title": "Sensor Name"
},
"sensor_mode": {
"anyOf": [
{
"enum": ["rolling shutter", "FFM"],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Operating mode of the sensor during the scan.",
"title": "Sensor Mode"
},
"sensor_magnification": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Magnification in the sensor setup.",
"title": "Sensor Magnification"
},
"sensor_roi_x_size": {
"anyOf": [
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of pixels in the x-dimension of the sensor's region of interest (ROI).",
"title": "Sensor Roi X Size"
},
"sensor_roi_y_size": {
"anyOf": [
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of pixels in the y-dimension of the sensor's region of interest (ROI).",
"title": "Sensor Roi Y Size"
},
"pixel_size": {
"description": "Size of a pixel at the source, measured in micrometers.",
"exclusiveMinimum": 0.0,
"title": "Pixel Size",
"type": "number"
},
"xray_magnification": {
"anyOf": [
{
"exclusiveMinimum": 0.0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Magnification of X-rays due to divergence between the source and detector.",
"title": "Xray Magnification"
},
"technique": {
"const": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
"default": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
"title": "Experimental technique.",
"type": "string"
},
"experiment_type": {
"default": "Tomography",
"title": "Experiment Type",
"type": "string"
}
},
"required": ["date", "beamline", "scan_type", "scan_range", "pixel_size"],
"title": "Scan",
"type": "object"
}
},
"additionalProperties": false,
"description": "Metadata for a Human Organ Atlas dataset.",
"properties": {
"name": {
"description": "Unique name for dataset.",
"title": "Name",
"type": "string"
},
"dataset_type": {
"description": "Type of dataset. Overview datasets contain the full sample. Zoom datasets contain a zoom into a particular volume of interest within the sample.",
"enum": ["overview", "zoom"],
"title": "Dataset Type",
"type": "string"
},
"voi": {
"description": "Volume of interest name. For zoom datasets this gives a unique identifier among zoom datasets taken within the same sample.",
"title": "Volume of Interest",
"type": "string"
},
"data": {
"$ref": "#/$defs/Data",
"description": "Data metadata"
},
"sample": {
"$ref": "#/$defs/Sample",
"description": "Sample metadata"
},
"donor": {
"$ref": "#/$defs/Donor",
"description": "Donor metadata"
},
"scan": {
"$ref": "#/$defs/Scan",
"description": "Scan metadata"
},
"proposal": {
"$ref": "#/$defs/Proposal",
"description": "Beamtime proposal metadata"
},
"registration": {
"anyOf": [
{
"$ref": "#/$defs/Registration"
},
{
"type": "null"
}
],
"description": "Metadata mapping high resolution volume of interest datasets to a full organ dataset. Not present for full organ datasets.",
"title": "Registration parameters"
},
"citation": {
"$ref": "#/$defs/Citation",
"title": "Dataset citation"
}
},
"required": [
"name",
"dataset_type",
"voi",
"data",
"sample",
"donor",
"scan",
"proposal",
"registration",
"citation"
],
"title": "HOAMetadata",
"type": "object",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://humanorganatlas.github.io/metadata-schemas/metadata-schema.json"
}