{
  "$defs": {
    "Acquisition": {
      "additionalProperties": false,
      "description": "When the acquisition was run and with what laser settings.\n\nEvery field is optional and left unset when the source does not\nreport it, so an absent field means \"not reported\", never \"none\".\nThe values are normalised: one timestamp format, one unit per\nquantity, where the raw ``uns[\"acquisition_params\"]`` dict keeps the\nvendor's own spelling and unit next to this block.",
      "properties": {
        "acquisition_datetime": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "When the acquisition started, as an ISO 8601 date and time (YYYY-MM-DDThh:mm:ss, optionally with fractional seconds). Carries a UTC offset when the source records one and none when it does not; no time zone is ever assumed.",
          "title": "Acquisition Datetime"
        },
        "laser_frequency_hz": {
          "anyOf": [
            {
              "exclusiveMinimum": 0,
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "IMS:1006000",
            "name": "repetition rate"
          },
          "default": null,
          "description": "Laser repetition rate in hertz.",
          "title": "Laser Frequency Hz"
        },
        "laser_power_percent": {
          "anyOf": [
            {
              "maximum": 100,
              "minimum": 0,
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Laser power as the percentage of the laser's range that the vendor's acquisition software shows, e.g. 70.0.",
          "title": "Laser Power Percent"
        },
        "method_file": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "File name of the acquisition method the run was recorded with, e.g. 'imaging_pos.m' or 'neg_FastDDA.EXP'. The name only, never a path.",
          "title": "Method File"
        },
        "shots_per_pixel": {
          "anyOf": [
            {
              "minimum": 1,
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "IMS:1006001",
            "name": "laser shots per spectrum"
          },
          "default": null,
          "description": "Laser shots summed into one pixel's spectrum.",
          "title": "Shots Per Pixel"
        }
      },
      "title": "Acquisition",
      "type": "object"
    },
    "Alignment": {
      "additionalProperties": false,
      "description": "How the source registers its raster onto an optical image.\n\nFacts about the source: which image the acquisition was planned on,\nand how that image was registered to the sample stage. Whether a\nconversion then placed the raster in that image's pixels is what the\nconversion did, and the store's ``coordinate_systems`` attribute says\nso.\n\nEvery field is optional and left unset when the source does not state\nit, and the section is absent when the source registers no image.",
      "properties": {
        "method": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "IMS:1006017",
            "name": "method used to align optical image"
          },
          "default": null,
          "description": "How the optical image was aligned with the raster, e.g. 'teaching points', the method flexImaging uses.",
          "title": "Method"
        },
        "optical_image_file": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "IMS:1006008",
            "name": "optical image location"
          },
          "default": null,
          "description": "File name of the optical image the registration is stated in, e.g. 'slide_0000.tif': the image whose pixels the teaching points name. The name only, never a path.",
          "title": "Optical Image File"
        },
        "teaching_points": {
          "description": "The points the optical image was registered to the stage with, in the order the source lists them; empty when it lists none. Their stage coordinates are in the frame the teaching was done in, which the positions an acquisition records its spectra at can be offset from: the points place the image on the target, not on those positions.",
          "items": {
            "$ref": "#/$defs/TeachingPoint"
          },
          "title": "Teaching Points",
          "type": "array"
        }
      },
      "title": "Alignment",
      "type": "object"
    },
    "Calibration": {
      "additionalProperties": false,
      "description": "How the source's m/z values were calibrated.\n\nFacts about the source, never about what Thyra did with it: which\ncalibration a conversion applied is a ``processing`` step bound to\nMS:1001485 (m/z calibration), because a converter can be told to\napply one the source does not consider current.\n\n\"The calibration\" is the one the source's m/z values rest on: the\nmost recent recalibration when the data were recalibrated after\nacquisition, otherwise the calibration the acquisition ran under.\nEvery field is optional and left unset when the source does not state\nit, and a value the vendor writes where it has nothing to state -- a\nstandard deviation of zero, over a fit with no residual to measure --\nis left unset too.",
      "properties": {
        "calibration_datetime": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "When the calibration was made, as an ISO 8601 date and time (YYYY-MM-DDThh:mm, optionally with seconds and fractional seconds, at the precision the source records). Carries a UTC offset when the source records one and none when it does not.",
          "title": "Calibration Datetime"
        },
        "lock_mass_corrected": {
          "anyOf": [
            {
              "type": "boolean"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Whether the source's m/z values were corrected against a lock mass, a reference ion measured alongside the sample.",
          "title": "Lock Mass Corrected"
        },
        "mz_standard_deviation_ppm": {
          "anyOf": [
            {
              "exclusiveMinimum": 0,
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "How closely the reference peaks fit after the calibration: the square root of the summed squares of their m/z errors, in parts per million, over one less than the number of peaks. Never zero -- a fit with no residual has nothing to report -- and never without n_reference_peaks.",
          "title": "Mz Standard Deviation Ppm"
        },
        "n_reference_peaks": {
          "anyOf": [
            {
              "minimum": 1,
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "How many reference peaks the calibration was fitted to.",
          "title": "N Reference Peaks"
        },
        "original_calibration_datetime": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "When the calibration the acquisition ran under was made. Set only for recalibrated data, where calibration_datetime is the recalibration's; same format.",
          "title": "Original Calibration Datetime"
        },
        "recalibrated": {
          "anyOf": [
            {
              "type": "boolean"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Whether a calibration made after the acquisition is stored with the data, replacing the one the acquisition ran under.",
          "title": "Recalibrated"
        },
        "software": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "The software that made the calibration, in the source's own words, e.g. 'timsTOF'.",
          "title": "Software"
        },
        "software_version": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Version of the software that made the calibration.",
          "title": "Software Version"
        }
      },
      "title": "Calibration",
      "type": "object"
    },
    "Fragmentation": {
      "additionalProperties": false,
      "description": "Whether, and how, the acquisition fragmented its ions.\n\nAn MS/MS imaging run measures fragments, so the m/z axis of the table\nmeans fragment m/z. Nothing about the axis says so, which is why this\nblock exists: without it an MS/MS store is indistinguishable from an\nMS1 one.\n\nThe MSI table sums a frame that isolated several precursors into one\nspectrum. ``merges_precursors`` says when that has happened, so a\nconsumer knows the spectrum is a chimera rather than discovering it\nfrom the peaks, and ``resolved_table`` names the sibling table that\nholds those precursors split apart when one was written.",
      "properties": {
        "constant_across_pixels": {
          "default": true,
          "description": "Whether every pixel was fragmented on the same schedule. A scheduled method makes it so; a data-dependent one does not, and then the windows below are not a global precursor axis.",
          "title": "Constant Across Pixels",
          "type": "boolean"
        },
        "dissociation_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PSI-MS dissociation method, e.g. MS:1000133 (CID)."
        },
        "merges_precursors": {
          "default": false,
          "description": "Whether one stored spectrum sums fragments of more than one precursor, so its peaks cannot be attributed to a single one.",
          "title": "Merges Precursors",
          "type": "boolean"
        },
        "ms_level": {
          "cv": {
            "accession": "MS:1000511",
            "name": "ms level"
          },
          "description": "MS level of the stored spectra: 1 for a survey scan.",
          "minimum": 1,
          "title": "Ms Level",
          "type": "integer"
        },
        "present": {
          "description": "True when the stored spectra are fragment spectra.",
          "title": "Present",
          "type": "boolean"
        },
        "resolved_table": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Element key of the demultiplexed sibling table (pixels x (precursor, fragment)) written beside this summed table, when one was.",
          "title": "Resolved Table"
        },
        "windows": {
          "description": "The precursor schedule, empty when none was reported.",
          "items": {
            "$ref": "#/$defs/IsolationWindow"
          },
          "title": "Windows",
          "type": "array"
        }
      },
      "required": [
        "present",
        "ms_level"
      ],
      "title": "Fragmentation",
      "type": "object"
    },
    "IonMobility": {
      "additionalProperties": false,
      "description": "Whether, and how, the acquisition separated ions by mobility.\n\nWritten so a consumer can tell a spectrum that was *summed over* a\nmobility ramp (Bruker TDF, TIMS engaged) from one that never had a\nmobility dimension (TSF, imzML, most other sources).  The MSI table\nThyra writes collapses the ramp; the fields here describe what was\ncollapsed.  Mobility is a spectral coordinate, never a spatial one,\nso nothing about it appears in the store's coordinate systems.",
      "properties": {
        "grid": {
          "anyOf": [
            {
              "$ref": "#/$defs/MobilityGrid"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "The common mobility grid the resolved table was binned onto, when it was built from per-pixel mobility values."
        },
        "num_scans": {
          "anyOf": [
            {
              "minimum": 1,
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Mobility scans per frame (the TIMS ramp length); the largest when frames differ.",
          "title": "Num Scans"
        },
        "present": {
          "description": "True when the source carries a mobility dimension, e.g. a Bruker TDF acquisition with TIMS engaged.",
          "title": "Present",
          "type": "boolean"
        },
        "range_lower": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Lower bound of the acquired mobility range.",
          "title": "Range Lower"
        },
        "range_upper": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Upper bound of the acquired mobility range.",
          "title": "Range Upper"
        },
        "resolved_table": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Element key of the mobility-resolved sibling table (pixels x (m/z, mobility)) written beside this summed table, when one was.",
          "title": "Resolved Table"
        },
        "separation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1002892",
            "name": "ion mobility attribute"
          },
          "default": null,
          "description": "The mobility quantity the instrument records, e.g. 'inverse reduced ion mobility' (TIMS) or 'ion mobility drift time'.",
          "title": "Separation"
        },
        "separation_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PSI-MS term for the quantity: MS:1002815 (inverse reduced ion mobility) or MS:1002476 (ion mobility drift time)."
        },
        "unit_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Unit of range_lower and range_upper, e.g. MS:1002814 volt-second per square centimeter for 1/K0."
        }
      },
      "required": [
        "present"
      ],
      "title": "IonMobility",
      "type": "object"
    },
    "IsolationWindow": {
      "additionalProperties": false,
      "description": "One precursor isolation, named the way mzPeak names it.\n\nThe window spans ``[target - lower_offset, target + upper_offset]``.\nOffsets rather than a single width is mzPeak's shape (and mzML's);\na source reporting one full width has it halved into two equal\noffsets, which is the reading every mzML writer for those\ninstruments takes.",
      "properties": {
        "collision_energy": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000045",
            "name": "collision energy"
          },
          "default": null,
          "description": "Collision energy in electronvolts (UO:0000266).",
          "title": "Collision Energy"
        },
        "lower_offset": {
          "anyOf": [
            {
              "minimum": 0,
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000828",
            "name": "isolation window lower offset"
          },
          "default": null,
          "description": "How far below the target the window reaches, in m/z.",
          "title": "Lower Offset"
        },
        "scan_begin": {
          "anyOf": [
            {
              "minimum": 0,
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "First mobility scan this window occupies, when the source separates its windows along the mobility ramp (Bruker PASEF).",
          "title": "Scan Begin"
        },
        "scan_end": {
          "anyOf": [
            {
              "minimum": 0,
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "One past the last mobility scan this window occupies.",
          "title": "Scan End"
        },
        "target": {
          "cv": {
            "accession": "MS:1000827",
            "name": "isolation window target m/z"
          },
          "description": "Isolation window target m/z.",
          "exclusiveMinimum": 0,
          "title": "Target",
          "type": "number"
        },
        "upper_offset": {
          "anyOf": [
            {
              "minimum": 0,
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000829",
            "name": "isolation window upper offset"
          },
          "default": null,
          "description": "How far above the target the window reaches, in m/z.",
          "title": "Upper Offset"
        }
      },
      "required": [
        "target"
      ],
      "title": "IsolationWindow",
      "type": "object"
    },
    "MSAnalysis": {
      "additionalProperties": false,
      "description": "How the data was acquired (METASPACE ``MS_Analysis``).\n\n``pixel_size_um`` is the one field that is always known at\nconversion time (conversion refuses to run without a pixel size),\nso it is the one required field of the section.",
      "properties": {
        "analyzer": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000443",
            "name": "mass analyzer type"
          },
          "default": null,
          "description": "E.g. 'TOF', 'Orbitrap', 'FTICR'.",
          "title": "Analyzer"
        },
        "analyzer_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PSI-MS mass analyzer type term."
        },
        "detector_resolving_power": {
          "anyOf": [
            {
              "$ref": "#/$defs/ResolvingPower"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000800",
            "name": "mass resolving power"
          },
          "default": null,
          "description": "Resolving power at a reference m/z."
        },
        "fragmentation": {
          "anyOf": [
            {
              "$ref": "#/$defs/Fragmentation"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Whether the stored spectra are fragment spectra and, if so, of which precursors; unset when the source does not say."
        },
        "instrument_model": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000031",
            "name": "instrument model"
          },
          "default": null,
          "description": "Instrument model as reported by the source.",
          "title": "Instrument Model"
        },
        "ion_mobility": {
          "anyOf": [
            {
              "$ref": "#/$defs/IonMobility"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Whether the source separated ions by mobility and, if so, over what range; the MSI table is summed over that dimension."
        },
        "ionisation_source": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000008",
            "name": "ionization type"
          },
          "default": null,
          "description": "E.g. 'MALDI', 'DESI', 'SIMS'.",
          "title": "Ionisation Source"
        },
        "ionisation_source_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PSI-MS ionisation type term."
        },
        "manufacturer": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1001269",
            "name": "instrument vendor"
          },
          "default": null,
          "description": "Who built the instrument, in the source's own words, e.g. 'Bruker' or 'Waters'. Not normalised to a canonical list: vendors rename and merge, and the source's spelling is the fact it stated.",
          "title": "Manufacturer"
        },
        "n_spectra": {
          "anyOf": [
            {
              "minimum": 1,
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "How many spectra the source holds, as its reader counted them: the spectra actually present, not the positions the raster covers, and those of one region when only one was read. The table can have fewer rows, because a spectrum with nothing in it is not stored.",
          "title": "N Spectra"
        },
        "pixel_size_um": {
          "$ref": "#/$defs/PixelSizeUm"
        },
        "polarity": {
          "anyOf": [
            {
              "enum": [
                "positive",
                "negative"
              ],
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000465",
            "name": "scan polarity"
          },
          "default": null,
          "description": "Ion polarity mode.",
          "title": "Polarity"
        },
        "polarity_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PSI-MS scan polarity term (MS:1000130 / MS:1000129)."
        },
        "serial_number": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000529",
            "name": "instrument serial number"
          },
          "default": null,
          "description": "Serial number of the instrument that ran the acquisition. Identifies one physical machine, which is what makes it worth recording: calibration and detector response are properties of the machine, not of the model.",
          "title": "Serial Number"
        },
        "spectrum_representation": {
          "anyOf": [
            {
              "enum": [
                "profile",
                "centroid"
              ],
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000525",
            "name": "spectrum representation"
          },
          "default": null,
          "description": "Whether the stored spectra are profile or centroid, as the reader delivered them. Resampling does not change it: Thyra never peak-picks. Unset when the source does not state it and Thyra could only guess.",
          "title": "Spectrum Representation"
        },
        "spectrum_representation_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PSI-MS spectrum representation term (MS:1000128 / MS:1000127)."
        }
      },
      "required": [
        "pixel_size_um"
      ],
      "title": "MSAnalysis",
      "type": "object"
    },
    "MassAxisFingerprint": {
      "additionalProperties": false,
      "description": "The identity of a store's mass axis: a hash and a bin count.",
      "properties": {
        "n_bins": {
          "description": "The number of m/z values the hash covers (the axis length).",
          "minimum": 1,
          "title": "N Bins",
          "type": "integer"
        },
        "sha256": {
          "description": "SHA-256 (lower-case hex) of the m/z values of the store's MSI tables' var['mz'], taken as little-endian float64 bytes. Sibling tables (_mobility, _msms) carry the same value because their mz_index points into this axis, not because their own var['mz'] hashes to it. Two stores with equal values hold bin-for-bin identical axes.",
          "pattern": "^[0-9a-f]{64}$",
          "title": "Sha256",
          "type": "string"
        }
      },
      "required": [
        "sha256",
        "n_bins"
      ],
      "title": "MassAxisFingerprint",
      "type": "object"
    },
    "MobilityGrid": {
      "additionalProperties": false,
      "description": "The common mobility grid a mobility-resolved table was binned onto.\n\nDescribes the channels of a grid table (pixels x (m/z, mobility)\nbuilt from per-pixel mobility sources): the law the channel edges\nfollow, the range they span and how many there are. Absent until\nsuch a table is written; the store's ``uns[\"mobility_heatmap\"]`` uses\nthe same channel count and edges so the two align by index.",
      "properties": {
        "law": {
          "description": "How channel edges are spaced across the range, e.g. 'linear' (equal width in the axis unit).",
          "minLength": 1,
          "title": "Law",
          "type": "string"
        },
        "lower": {
          "description": "Lower edge of the first channel.",
          "title": "Lower",
          "type": "number"
        },
        "n_channels": {
          "description": "Number of mobility channels.",
          "minimum": 1,
          "title": "N Channels",
          "type": "integer"
        },
        "upper": {
          "description": "Upper edge of the last channel.",
          "title": "Upper",
          "type": "number"
        }
      },
      "required": [
        "law",
        "lower",
        "upper",
        "n_channels"
      ],
      "title": "MobilityGrid",
      "type": "object"
    },
    "OntologyTerm": {
      "additionalProperties": false,
      "description": "A controlled-vocabulary reference: CURIE accession plus label.",
      "properties": {
        "accession": {
          "description": "CURIE identifier, e.g. 'MS:1000075', 'NCBITaxon:10090', 'UBERON:0002107' or 'CHEBI:90695'.",
          "pattern": "^[A-Za-z_][A-Za-z0-9_]*:\\S+$",
          "title": "Accession",
          "type": "string"
        },
        "name": {
          "description": "The term's primary label in its ontology.",
          "minLength": 1,
          "title": "Name",
          "type": "string"
        }
      },
      "required": [
        "accession",
        "name"
      ],
      "title": "OntologyTerm",
      "type": "object"
    },
    "PixelSizeUm": {
      "additionalProperties": false,
      "description": "In-plane raster pitch in micrometres.",
      "properties": {
        "x": {
          "cv": {
            "accession": "IMS:1000046",
            "name": "pixel size (x)"
          },
          "description": "Pixel size along x in micrometres.",
          "exclusiveMinimum": 0,
          "title": "X",
          "type": "number"
        },
        "y": {
          "cv": {
            "accession": "IMS:1000047",
            "name": "pixel size y"
          },
          "description": "Pixel size along y in micrometres.",
          "exclusiveMinimum": 0,
          "title": "Y",
          "type": "number"
        }
      },
      "required": [
        "x",
        "y"
      ],
      "title": "PixelSizeUm",
      "type": "object"
    },
    "ProcessingStep": {
      "additionalProperties": false,
      "description": "One processing action between the raw data and this store.\n\nModeled on mzQC provenance: an ordered list of steps, each naming\nthe software that performed it and the parameters it ran with.  The\nconverter records its own steps (conversion, mass axis resampling);\ndownstream tools append theirs (normalisation, peak picking,\nannotation) when they modify the store.",
      "properties": {
        "action_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "The PSI-MS data processing action the step is, when one exists, e.g. MS:1001485 (m/z calibration)."
        },
        "name": {
          "description": "What was done, e.g. 'conversion', 'm/z calibration', 'mass axis resampling', 'normalisation', 'peak picking', 'annotation'.",
          "minLength": 1,
          "title": "Name",
          "type": "string"
        },
        "parameters": {
          "additionalProperties": {
            "anyOf": [
              {
                "type": "string"
              },
              {
                "type": "integer"
              },
              {
                "type": "number"
              },
              {
                "type": "boolean"
              }
            ]
          },
          "description": "The parameters the step ran with.",
          "title": "Parameters",
          "type": "object"
        },
        "software": {
          "$ref": "#/$defs/SoftwareRef",
          "description": "The software that did it."
        }
      },
      "required": [
        "name",
        "software"
      ],
      "title": "ProcessingStep",
      "type": "object"
    },
    "Provenance": {
      "additionalProperties": false,
      "description": "Who wrote the block and from what.\n\nDeliberately small: the store's ``uns[\"essential_metadata\"]`` already\nrecords the source's dimensions, mass range and spectrum type, and the\nspectrum representation is also a field of ``ms_analysis``.  This\nsection records only what is needed to interpret the *metadata block\nitself*, and contains no timestamps so that two conversions of the\nsame input produce an identical block (the uns parity tests rely on this).  The mass axis\nfingerprint keeps that true: it is a hash of the axis, so the same\naxis gives the same block.",
      "properties": {
        "mass_axis": {
          "anyOf": [
            {
              "$ref": "#/$defs/MassAxisFingerprint"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "A SHA-256 of the store's m/z axis and its bin count, written for every conversion whether or not it resampled. Absent from stores written before 0.11.0 and from a standalone document, which has no axis."
        },
        "pixel_size_source": {
          "anyOf": [
            {
              "enum": [
                "default",
                "manual",
                "automatic"
              ],
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "How the pixel size was determined: read from the source metadata ('automatic'), supplied by the user ('manual'), or the 1.0 um fallback ('default').",
          "title": "Pixel Size Source"
        },
        "source_format": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Detected input format, e.g. 'imzml', 'bruker', 'phi'.",
          "title": "Source Format"
        },
        "source_path": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Where the source data was read from. A block inside a store carries the path it was converted from; a standalone document carries the source's name only, because a document is written to be sent somewhere the path means nothing.",
          "title": "Source Path"
        },
        "thyra_version": {
          "description": "Thyra version that wrote the block.",
          "minLength": 1,
          "title": "Thyra Version",
          "type": "string"
        }
      },
      "required": [
        "thyra_version"
      ],
      "title": "Provenance",
      "type": "object"
    },
    "ResolvingPower": {
      "additionalProperties": false,
      "description": "Mass resolving power quoted at a reference m/z.",
      "properties": {
        "at_mz": {
          "description": "The m/z the value is quoted at.",
          "exclusiveMinimum": 0,
          "title": "At Mz",
          "type": "number"
        },
        "value": {
          "description": "Resolving power (FWHM definition).",
          "exclusiveMinimum": 0,
          "title": "Value",
          "type": "number"
        }
      },
      "required": [
        "value",
        "at_mz"
      ],
      "title": "ResolvingPower",
      "type": "object"
    },
    "SampleInformation": {
      "additionalProperties": false,
      "description": "What the sample is (METASPACE ``Sample_Information``).\n\nEvery field is user-supplied. ``sample_id`` and ``sample_name`` are set\nonly from what the user gives the conversion, never read from the\nsource: a vendor sample name can be a patient identifier, so Thyra\ndoes not carry one into a store on its own.",
      "properties": {
        "condition": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "E.g. 'wildtype', 'diseased'.",
          "title": "Condition"
        },
        "organism": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Species, e.g. 'Mus musculus'.",
          "title": "Organism"
        },
        "organism_part": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Organ or organism part, e.g. 'liver'.",
          "title": "Organism Part"
        },
        "organism_part_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "UBERON term for the organism part."
        },
        "organism_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "NCBITaxon term for the organism."
        },
        "sample_growth_conditions": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "E.g. intervention or treatment.",
          "title": "Sample Growth Conditions"
        },
        "sample_id": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000001",
            "name": "sample number"
          },
          "default": null,
          "description": "The user's identifier for the sample, to tell it apart from the others in a study. Supplied by the user, never read from the source. One conversion stamps the same value on every region it converts.",
          "title": "Sample Id"
        },
        "sample_name": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "cv": {
            "accession": "MS:1000002",
            "name": "sample name"
          },
          "default": null,
          "description": "The user's name for the sample, to tell it apart from the others in a study. Supplied by the user, never read from the source. One conversion stamps the same value on every region it converts.",
          "title": "Sample Name"
        }
      },
      "title": "SampleInformation",
      "type": "object"
    },
    "SamplePreparation": {
      "additionalProperties": false,
      "description": "How the sample was prepared (METASPACE ``Sample_Preparation``).",
      "properties": {
        "matrix": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "MALDI matrix, e.g. '2,5-dihydroxybenzoic acid (DHB)'. 'none' for matrix-free techniques (DESI, SIMS).",
          "title": "Matrix"
        },
        "matrix_application": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Matrix application device or protocol.",
          "title": "Matrix Application"
        },
        "matrix_term": {
          "anyOf": [
            {
              "$ref": "#/$defs/OntologyTerm"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "CHEBI term for the matrix compound."
        },
        "sample_stabilisation": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Preservation method, e.g. 'fresh frozen'.",
          "title": "Sample Stabilisation"
        },
        "solvent": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Solvent used.",
          "title": "Solvent"
        },
        "tissue_modification": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Chemical modification, e.g. 'derivatised'.",
          "title": "Tissue Modification"
        }
      },
      "title": "SamplePreparation",
      "type": "object"
    },
    "SoftwareRef": {
      "additionalProperties": false,
      "description": "A software agent, the way mzQC records analysis software.",
      "properties": {
        "name": {
          "description": "Software name, e.g. 'thyra'.",
          "minLength": 1,
          "title": "Name",
          "type": "string"
        },
        "uri": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Homepage or repository URL.",
          "title": "Uri"
        },
        "version": {
          "description": "Software version.",
          "minLength": 1,
          "title": "Version",
          "type": "string"
        }
      },
      "required": [
        "name",
        "version"
      ],
      "title": "SoftwareRef",
      "type": "object"
    },
    "TeachingPoint": {
      "additionalProperties": false,
      "description": "One point the optical image was registered to the sample stage with.\n\nThe operator marks a feature in the image and brings the stage to the\nsame feature; three such pairs fix the affine map from the image's\npixels to the stage.",
      "properties": {
        "image_x_px": {
          "description": "Column of the point in the optical image, in pixels from its left edge.",
          "title": "Image X Px",
          "type": "number"
        },
        "image_y_px": {
          "description": "Row of the point in the optical image, in pixels from its top edge.",
          "title": "Image Y Px",
          "type": "number"
        },
        "stage_x_um": {
          "description": "Stage x of the same feature, in micrometres.",
          "title": "Stage X Um",
          "type": "number"
        },
        "stage_y_um": {
          "description": "Stage y of the same feature, in micrometres.",
          "title": "Stage Y Um",
          "type": "number"
        }
      },
      "required": [
        "image_x_px",
        "image_y_px",
        "stage_x_um",
        "stage_y_um"
      ],
      "title": "TeachingPoint",
      "type": "object"
    }
  },
  "$id": "https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/schema/0.14.0/msi_metadata.schema.json",
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false,
  "description": "The versioned MSI metadata document.\n\n``sample`` and ``preparation`` cannot be auto-populated from raw\nfiles and default to empty; Thyra fills ``sample.sample_id`` and\n``sample.sample_name`` only when the conversion was given them;\n``ms_analysis`` and ``provenance`` are written by the converter for\nevery store; ``acquisition``, ``calibration`` and ``alignment`` are\neach written when the reader reports at least one of their facts and\nare absent -- not empty -- otherwise.\n\nThe emitted JSON Schema carries ``$id`` and ``$schema`` so that the\ncommitted artifact names its own published address; they are added\nhere, on the root model, rather than pasted into the file, so the\nsync test that compares the file with ``model_json_schema()`` keeps\nholding.",
  "properties": {
    "acquisition": {
      "anyOf": [
        {
          "$ref": "#/$defs/Acquisition"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "When the acquisition was run and with what laser settings; auto-populated from the vendor metadata where a reader has the facts, absent when it has none of them."
    },
    "alignment": {
      "anyOf": [
        {
          "$ref": "#/$defs/Alignment"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Which optical image the source registers its raster onto, and how; auto-populated from the vendor metadata where a reader has the facts, absent when it has none of them."
    },
    "calibration": {
      "anyOf": [
        {
          "$ref": "#/$defs/Calibration"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "How the source's m/z values were calibrated; auto-populated from the vendor metadata where a reader has the facts, absent when it has none of them."
    },
    "ms_analysis": {
      "$ref": "#/$defs/MSAnalysis",
      "description": "How the data was acquired; auto-populated where possible."
    },
    "preparation": {
      "$ref": "#/$defs/SamplePreparation",
      "description": "How the sample was prepared; user-supplied."
    },
    "processing": {
      "description": "Ordered processing history, oldest first (mzQC-style).",
      "items": {
        "$ref": "#/$defs/ProcessingStep"
      },
      "title": "Processing",
      "type": "array"
    },
    "provenance": {
      "$ref": "#/$defs/Provenance",
      "description": "Who wrote this block and from what source."
    },
    "sample": {
      "$ref": "#/$defs/SampleInformation",
      "description": "What the sample is; user-supplied. Thyra fills its id and name only when the conversion was given them."
    },
    "schema_version": {
      "default": "0.14.0",
      "description": "Semantic version of the schema this document conforms to.",
      "pattern": "^\\d+\\.\\d+\\.\\d+$",
      "title": "Schema Version",
      "type": "string"
    }
  },
  "required": [
    "ms_analysis",
    "provenance"
  ],
  "title": "MSIMetadata",
  "type": "object"
}