L1 ⚛ L1-127 ⊙ Testnet

MALDI-MSI — Matrix-Assisted Laser Desorption/Ionization Mass-Spec Imaging

Scientific Instrumentation · Laser-desorption mass-spec imaging of tissue

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⬇ L1-127.md

# ⚛ L1 Principle — MALDI-MSI — Matrix-Assisted Laser Desorption/Ionization Mass-Spec Imaging **ID:** `L1-127` · **Status:** ⊙ Testnet (genesis catalog) > **🌐 Domain:** Scientific Instrumentation — *Laser-desorption mass-spec imaging of tissue* > **🎯 Problem class:** linear inverse count · **🧮 Solution space:** molecular surface map > **📡 Carrier:** ion · **🌫 Noise:** shot poisson > **⚖ Difficulty (δ):** 3 · **⛓ Block:** 41554213 --- ## 🧠 1. Introduction **MALDI-MSI — Matrix-Assisted Laser Desorption/Ionization Mass-Spec Imaging** is a **linear inverse count** whose unknown lives in **molecular surface map** space, within the **Laser-desorption mass-spec imaging of tissue** sub-domain of **Scientific Instrumentation**. Measurements consist of ions detected after acceleration or extraction via a **matrix laser desorption** sensing mechanism. The forward operator applies, in order: S · desorb · laserMATRIX operator; L · disperse · mass operator; detector accumulates flux over the exposure window. Observations are corrupted by Poisson shot noise from quantum-limited detection. Counts-based Poisson noise; hot-spot variability and ion-suppression cause major between-pixel variance. Relative quantitation ok; absolute requires internal standards. ## ⚙ 2. Forward Model Physical chain: **x** → S · desorb · laserMATRIX → L · disperse · mass → Temporal integration → **y** (detector). ``` y = ∫_t dt `L.disperse.mass` `S.desorb.laserMATRIX` x, measurements ~ Poisson(αy) ``` **Measurement DAG:** | Primitive | What it does | |---|---| | `S.desorb.laserMATRIX` | S · desorb · lasermatrix operator | | `L.disperse.mass` | L · disperse · mass operator | | `int.temporal` | Detector accumulates flux over the exposure window | ## 🔬 3. Physics Fingerprint | Property | Value | |---|---| | Domain | Scientific Instrumentation | | Sub domain | Laser-desorption mass-spec imaging of tissue | | Carrier | ion | | Problem class | linear_inverse_count | | Solution space | molecular_surface_map | | Noise model | shot_poisson | | Integration axis | mass_and_spatial | | Difficulty delta | 3 | | L dag | 3 | ## 📡 4. Measurement Model Counts-based Poisson noise; hot-spot variability and ion-suppression cause major between-pixel variance. Relative quantitation ok; absolute requires internal standards. | Metric | Value | |---|---| | Metric | concentration_NMSE | | Secondary | spatial_resolution_um | ## 📏 5. Operating Range (Ω) **Center problem class:** `maldi_msi_mapping` · **Forward operator:** `maldi_msi_forward` **Center point:** | Parameter | Unit | Value | |---|---|---| | H | px | 300 | | K | — | 10 | | W | px | 300 | | N mz | — | 30000 | | R mass | — | 20000 | | Pixel um | µm | 50 | | Laser energy drift | — | 0.05 | | Matrix hot spot variability | — | 0.1 | **Allowed bounds:** | Parameter | Unit | Range | |---|---|---| | H | px | 32 – 2048 | | K | — | 1 – 50 | | W | px | 32 – 2048 | | N mz | — | 1000 – 200000 | | R mass | — | 2000 – 500000 | | Pixel um | µm | 5 – 200 | | Ion suppression | — | 0.0 – 0.5 | | Laser energy drift | — | 0.0 – 0.2 | | Tissue heterogeneity | — | 0.0 – 0.3 | | Mass calibration error | — | 0.0 – 50 | | Matrix hot spot variability | — | 0.0 – 0.5 | ## 🎯 6. Tolerance (ε) **Center tolerance:** NMSE 0.05 | Metric | Range | |---|---| | Nmse | 0.001 – 0.5 | ## ⚖ 7. Hardness Function Hardness scales as **`epsilon_fn`** on **concentration_NMSE**, with κ = `800` and δ = `3`. ## 💾 8. Reference Dataset - **primary** · weight 1.0 · IPFS _(not pinned yet)_ ## 9. On-chain Registration - **Chain hash:** `0x338a8be7f0b369d55fdb3dfebf969c9cd2aabc8003a9f786ce0d1f28e7691a4c` - **Chain tx hash:** `0x3d89a48c95d5fb3c12e49091a10c91c83c4177bb7fbdc2133e45502b6d1211e7` - **Chain block:** `41554213` --- ## File Mapping This bundle consists of: `L1-127.md`, `L1-127.json`. | File | Role | How to regenerate | |------|------|-------------------| | `L1-127.md` | Source of truth — edit this | Human or LLM | | `L1-127.json` | Structured metadata for the registry | LLM regenerates from the sections above | **Prompt for your LLM after editing this Markdown:** > Read the attached Markdown. Regenerate the sibling `.json` so every field matches. > Preserve the schema documented in the rows above. > Output each file in its own fenced code block tagged with the filename. > Output only the JSON object. _This Markdown was auto-synthesized from the catalog row for `L1-127`._ _Edit it, regenerate the JSON, and submit at [/submit](/submit) to claim the artifact._

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Prompt to give your LLM

Read the attached Markdown (L1-127.md).
Regenerate L1-127.json so every field matches the Markdown.
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Output each file in its own fenced code block tagged with the filename.

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L2-127-001 MALDI-MSI Mapping Spec (tissue lipid family)

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📋 JSON metadata

{
  "artifact_id": "L1-127",
  "chain_block": 41554213,
  "chain_hash": "0x338a8be7f0b369d55fdb3dfebf969c9cd2aabc8003a9f786ce0d1f28e7691a4c",
  "chain_tx_hash": "0x3d89a48c95d5fb3c12e49091a10c91c83c4177bb7fbdc2133e45502b6d1211e7",
  "domain": "Scientific Instrumentation",
  "hardness_fn": {
    "delta": 3,
    "kappa": 800,
    "metric": "concentration_NMSE",
    "type": "epsilon_fn"
  },
  "initiator_dataset": [
    {
      "ipfs_cid": null,
      "license_hash": null,
      "name": "primary",
      "weight": 1.0
    }
  ],
  "layer": "L1",
  "observable_profile": {
    "metric": "concentration_NMSE",
    "regime": "Counts-based Poisson noise; hot-spot variability and ion-suppression cause major between-pixel variance. Relative quantitation ok; absolute requires internal standards.",
    "secondary": "spatial_resolution_um"
  },
  "physics_fingerprint": {
    "L_DAG": 3.0,
    "carrier": "ion",
    "difficulty_delta": 3,
    "domain": "Scientific Instrumentation",
    "integration_axis": "mass_and_spatial",
    "noise_model": "shot_poisson",
    "primitives": [
      "S.desorb.laserMATRIX",
      "L.disperse.mass",
      "int.temporal"
    ],
    "problem_class": "linear_inverse_count",
    "sensing_mechanism": "matrix_laser_desorption",
    "solution_space": "molecular_surface_map",
    "sub_domain": "Laser-desorption mass-spec imaging of tissue",
    "title": "MALDI-MSI \u2014 Matrix-Assisted Laser Desorption/Ionization Mass-Spec Imaging"
  },
  "size_tiers": {
    "allowed_forward_operators": [
      "maldi_msi_forward",
      "desorption_electrospray_forward"
    ],
    "allowed_omega_dimensions": [
      "H",
      "W",
      "N_mz",
      "pixel_um",
      "R_mass",
      "K",
      "matrix_hot_spot_variability",
      "laser_energy_drift",
      "mass_calibration_error",
      "ion_suppression",
      "tissue_heterogeneity"
    ],
    "allowed_problem_classes": [
      "maldi_msi_mapping",
      "maldi_classification",
      "maldi_lipid_identification"
    ],
    "center_spec": {
      "epsilon_fn_center": "NMSE 0.05",
      "forward_operator": "maldi_msi_forward",
      "input_format": "ion_count_cube",
      "omega": {
        "H": 300,
        "K": 10,
        "N_mz": 30000,
        "R_mass": 20000,
        "W": 300,
        "laser_energy_drift": 0.05,
        "matrix_hot_spot_variability": 0.1,
        "pixel_um": 50
      },
      "problem_class": "maldi_msi_mapping"
    },
    "epsilon_bounds": {
      "nmse": [
        0.001,
        0.5
      ]
    },
    "omega_bounds": {
      "H": [
        32,
        2048
      ],
      "K": [
        1,
        50
      ],
      "N_mz": [
        1000,
        200000
      ],
      "R_mass": [
        2000,
        500000
      ],
      "W": [
        32,
        2048
      ],
      "ion_suppression": [
        0.0,
        0.5
      ],
      "laser_energy_drift": [
        0.0,
        0.2
      ],
      "mass_calibration_error": [
        0.0,
        50
      ],
      "matrix_hot_spot_variability": [
        0.0,
        0.5
      ],
      "pixel_um": [
        5,
        200
      ],
      "tissue_heterogeneity": [
        0.0,
        0.3
      ]
    }
  },
  "staked_pwm": 0.0,
  "status": "testnet",
  "sub_domain": "Laser-desorption mass-spec imaging of tissue",
  "title": "MALDI-MSI \u2014 Matrix-Assisted Laser Desorption/Ionization Mass-Spec Imaging"
}

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