{
  "generated_from": "research/3dbrain/models.csv",
  "models": [
    {
      "benchmark": "Analytic sphere and cross-tool comparison",
      "compute": "CPU",
      "credibility": "research",
      "domains": [
        "eeg",
        "meg",
        "ecog",
        "seeg"
      ],
      "id": "3DB-M001",
      "inputs": [
        "anatomy",
        "conductivity",
        "sensor_geometry",
        "source_state"
      ],
      "intended_use": "Research forward and inverse comparison",
      "license": "BSD-3-Clause",
      "limitations": "Inverse non-unique and subject conductivity uncertain",
      "name": "MNE forward and inverse",
      "outputs": [
        "lead_field",
        "sensor_signal",
        "source_estimate"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S057",
        "3DB-S058"
      ],
      "uncertainty": "Conductivity geometry covariance and regularization sweeps",
      "version": "1.12.1"
    },
    {
      "benchmark": "Raw-intensity OD and haemoglobin stage checks",
      "compute": "CPU",
      "credibility": "research",
      "domains": [
        "fnirs"
      ],
      "id": "3DB-M002",
      "inputs": [
        "optode_geometry",
        "wavelength",
        "optical_density"
      ],
      "intended_use": "Metadata-complete fNIRS replay",
      "license": "BSD-3-Clause",
      "limitations": "Concentration requires calibrated extinction and DPF",
      "name": "MNE fNIRS observation",
      "outputs": [
        "HbO_HbR_or_OD"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S019",
        "3DB-S025"
      ],
      "uncertainty": "DPF coupling motion and systemic physiology",
      "version": "1.12.1"
    },
    {
      "benchmark": "Fixed-seed shape and finite-output test",
      "compute": "browser_or_CPU",
      "credibility": "demonstration",
      "domains": [
        "fmri"
      ],
      "id": "3DB-M003",
      "inputs": [
        "neural_drive",
        "HRF_parameters"
      ],
      "intended_use": "Demonstrate haemodynamic observation workflow",
      "license": "not_applicable",
      "limitations": "Not sequence-specific and not a patient BOLD predictor",
      "name": "Balloon-Windkessel observation",
      "outputs": [
        "normalized_BOLD_proxy"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S008"
      ],
      "uncertainty": "HRF drift physiology motion and model-form assumptions",
      "version": "platform-contract-1.0"
    },
    {
      "benchmark": "Analytic dipole reciprocity and timestep convergence",
      "compute": "CPU",
      "credibility": "demonstration",
      "domains": [
        "ecog",
        "seeg",
        "intracortical"
      ],
      "id": "3DB-M004",
      "inputs": [
        "cell_model",
        "electrode_geometry"
      ],
      "intended_use": "Research source-to-electrode hypothesis",
      "license": "GPL-3.0",
      "limitations": "Release candidate and morphology dependent",
      "name": "LFPy field generator",
      "outputs": [
        "LFP",
        "CSD",
        "EEG_MEG_estimate"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S014"
      ],
      "uncertainty": "Geometry conductivity morphology and timestep",
      "version": "v2.3.9rc2"
    },
    {
      "benchmark": "Timestep and mechanism regression",
      "compute": "CPU_MPI",
      "credibility": "demonstration",
      "domains": [
        "intracortical",
        "dbs",
        "cortical-stimulation"
      ],
      "id": "3DB-M005",
      "inputs": [
        "morphology",
        "mechanisms",
        "stimulus"
      ],
      "intended_use": "Cell and axon response hypothesis",
      "license": "manual_review",
      "limitations": "Mechanism and morphology specific with licence gap",
      "name": "NEURON compartment model",
      "outputs": [
        "voltage",
        "current",
        "spikes"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S009"
      ],
      "uncertainty": "Mechanism parameters morphology discretization and build",
      "version": "9.0.1"
    },
    {
      "benchmark": "Fixed graph seed thread and MPI regression",
      "compute": "CPU_MPI",
      "credibility": "demonstration",
      "domains": [
        "intracortical"
      ],
      "id": "3DB-M006",
      "inputs": [
        "network_graph",
        "neuron_parameters"
      ],
      "intended_use": "Large network workflow tests",
      "license": "GPL-2.0",
      "limitations": "Point neurons do not predict dendrites LFP or EEG",
      "name": "NEST point network",
      "outputs": [
        "spikes",
        "analog_state"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S010"
      ],
      "uncertainty": "Seed thread count connectivity and parameters",
      "version": "3.10"
    },
    {
      "benchmark": "Unit and generated-code parity",
      "compute": "CPU",
      "credibility": "demonstration",
      "domains": [
        "intracortical"
      ],
      "id": "3DB-M007",
      "inputs": [
        "unit_aware_equations",
        "network"
      ],
      "intended_use": "Rapid neural equation experiments",
      "license": "CeCILL-family",
      "limitations": "Convenient equations are not biological validation",
      "name": "Brian2 equation model",
      "outputs": [
        "spikes",
        "state",
        "generated_code"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S011"
      ],
      "uncertainty": "Equation priors compiler and code generation",
      "version": "2.10.1"
    },
    {
      "benchmark": "Fixed 68-node graph stability and rerun summaries",
      "compute": "CPU_GPU",
      "credibility": "research",
      "domains": [
        "eeg",
        "meg",
        "fmri"
      ],
      "id": "3DB-M008",
      "inputs": [
        "connectome",
        "delays",
        "regional_parameters"
      ],
      "intended_use": "Whole-brain hypothesis and sensitivity analysis",
      "license": "GPL-family",
      "limitations": "Parameter non-identifiability and atlas dependence",
      "name": "The Virtual Brain whole-brain dynamics",
      "outputs": [
        "regional_state",
        "optional_observations"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S008",
        "3DB-S055"
      ],
      "uncertainty": "Connectome atlas coupling delay solver and noise",
      "version": "2.10.0"
    },
    {
      "benchmark": "Analytic fields mesh convergence and held-out measurements",
      "compute": "isolated_CPU_worker",
      "credibility": "research",
      "domains": [
        "tes",
        "tms"
      ],
      "id": "3DB-M009",
      "inputs": [
        "segmented_anatomy",
        "mesh",
        "montage_or_coil"
      ],
      "intended_use": "Research field comparison",
      "license": "GPL-3.0",
      "limitations": "Field is not neural activation efficacy safety or dose advice",
      "name": "SimNIBS FEM",
      "outputs": [
        "electric_field"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S026",
        "3DB-S028",
        "3DB-S029"
      ],
      "uncertainty": "Conductivity segmentation mesh pose waveform and measurement error",
      "version": "4.6.0"
    },
    {
      "benchmark": "Finite-output units and geometry contract only",
      "compute": "private_worker",
      "credibility": "demonstration",
      "domains": [
        "dbs"
      ],
      "id": "3DB-M010",
      "inputs": [
        "lead_geometry",
        "contacts",
        "conductivity",
        "waveform"
      ],
      "intended_use": "Define an auditable DBS worker interface",
      "license": "not_applicable",
      "limitations": "Lead-DBS and OSS-DBS version and licence audits unresolved",
      "name": "DBS FEM and axon interface",
      "outputs": [
        "field",
        "activation_proxy"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S001",
        "3DB-S009"
      ],
      "uncertainty": "Pose tissue encapsulation waveform axon orientation and threshold",
      "version": "interface-1.0"
    },
    {
      "benchmark": "Schema unit and failure-injection tests",
      "compute": "private_worker",
      "credibility": "demonstration",
      "domains": [
        "cortical-stimulation"
      ],
      "id": "3DB-M011",
      "inputs": [
        "contact_geometry",
        "return_path",
        "waveform"
      ],
      "intended_use": "Define cortical stimulation experiments",
      "license": "not_applicable",
      "limitations": "No device-specific clinical limits or activation validation",
      "name": "Cortical stimulation field interface",
      "outputs": [
        "field",
        "artifact_window"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S001",
        "3DB-S009"
      ],
      "uncertainty": "Contact area impedance interface tissue pose waveform and recovery",
      "version": "interface-1.0"
    },
    {
      "benchmark": "Same-input hash and finite-value regression",
      "compute": "browser",
      "credibility": "demonstration",
      "domains": [
        "eeg",
        "meg",
        "fnirs",
        "fmri",
        "ecog",
        "seeg",
        "intracortical",
        "tes",
        "tms",
        "dbs",
        "cortical-stimulation"
      ],
      "id": "3DB-M012",
      "inputs": [
        "duration_s",
        "sample_rate_hz",
        "noise_setting",
        "seed"
      ],
      "intended_use": "Test interaction provenance export and deterministic rerun",
      "license": "project_code",
      "limitations": "Synthetic normalized values have no physiological clinical or device meaning",
      "name": "Deterministic browser proxy",
      "outputs": [
        "normalized_signal",
        "uncertainty_band",
        "content_hash",
        "workflow_metrics"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S001"
      ],
      "uncertainty": "Seed and explicit scenario controls only",
      "version": "1.0.0"
    },
    {
      "benchmark": "Schema units finite values and blocked-kernel state",
      "compute": "private_worker",
      "credibility": "demonstration",
      "domains": [
        "focused-ultrasound"
      ],
      "id": "3DB-M013",
      "inputs": [
        "anatomy",
        "transducer_geometry",
        "acoustic_parameters"
      ],
      "intended_use": "Define typed worker and provenance boundaries",
      "license": "not_applicable",
      "limitations": "No pinned licensed kernel or exposure validation",
      "name": "Focused ultrasound extension interface",
      "outputs": [
        "acoustic_field",
        "thermal_proxy"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S001",
        "3DB-S048"
      ],
      "uncertainty": "Acoustic properties skull model transducer pose and thermal model",
      "version": "interface-1.0"
    },
    {
      "benchmark": "Timestep units and explicit nonhuman boundary",
      "compute": "private_worker",
      "credibility": "demonstration",
      "domains": [
        "optogenetics"
      ],
      "id": "3DB-M014",
      "inputs": [
        "cell_model",
        "opsin_model",
        "light_geometry"
      ],
      "intended_use": "Define preclinical cell-model experiments",
      "license": "not_applicable",
      "limitations": "No human clinical applicability and no validated optical kernel",
      "name": "Optogenetics extension interface",
      "outputs": [
        "cell_response_proxy"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S001",
        "3DB-S009"
      ],
      "uncertainty": "Opsin expression light transport cell type and model form",
      "version": "interface-1.0"
    },
    {
      "benchmark": "Schema parameter provenance and reversal tests",
      "compute": "private_worker",
      "credibility": "demonstration",
      "domains": [
        "pharmacology-pathology"
      ],
      "id": "3DB-M015",
      "inputs": [
        "baseline_model",
        "parameter_perturbation",
        "pathology_state"
      ],
      "intended_use": "Define hypothesis and sensitivity studies",
      "license": "not_applicable",
      "limitations": "Parameter changes are not drug effect disease prognosis or patient state",
      "name": "Pharmacology and pathology coupling interface",
      "outputs": [
        "sensitivity_distribution"
      ],
      "reviewed_at": "2026-07-26",
      "source_ids": [
        "3DB-S001",
        "3DB-S008",
        "3DB-S009"
      ],
      "uncertainty": "Prior population coupling identifiability and model form",
      "version": "interface-1.0"
    }
  ],
  "schema_version": "1.0"
}