L1 ⚛ L1-092 ⊙ Testnet

Cryo-Electron Tomography (cryoET) — in-situ 3D biology at nm scale

Electron Microscopy · In-situ structural biology via cryo tilt-series

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⬇ principle.md ⬇ principle.json

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⬇ L1-092.md ⬇ L1-092.json

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You are helping me submit a MODIFICATION of L1-092 (Cryo-Electron Tomography (cryoET) — in-situ 3D biology at nm scale) to the PWM Protocol — a Principle (L1) artifact.

I will paste a Markdown template (or the current L1-092.md).
1. Rewrite the Markdown so the science is correct and clearly explained for my change.
2. Regenerate the sibling L1-092.json so EVERY field matches the Markdown.
3. Keep the schema in the "File Mapping" footer at the bottom of the MD.
4. Keep the parent reference unchanged unless I ask otherwise.
Rules: the Markdown is the source of truth; use SI units; do NOT invent benchmark scores.
Output each file in its own fenced code block tagged with the filename.

Here is my template:
[PASTE THE .md HERE]

⚙ Forward Model

y = ∫dΩ `L.subtomogram_average` R(θ) `L.transmit_sample` x,    measurements ~ Poisson(αy)

world state x (3D density)

→

L · transmit sample `L.transmit_sample`

→

Angular scan R(θ)

→

L · subtomogram average `L.subtomogram_average`

→

Angular integration ∫dΩ

→

observation y (electron detector)

Noise: Poisson shot noise from quantum-limited detection

Solver / auxiliary components (1)

L.backproject — spreads measurements back along source rays (adjoint operator)

Markdown — human-readable source of truth

⚙ auto-generated

⬇ L1-092.md

# ⚛ L1 Principle — Cryo-Electron Tomography (cryoET) — in-situ 3D biology at nm scale **ID:** `L1-092` · **Status:** ⊙ Testnet (genesis catalog) > **🌐 Domain:** Electron Microscopy — *In-situ structural biology via cryo tilt-series* > **🎯 Problem class:** linear inverse · **🧮 Solution space:** 3D density > **📡 Carrier:** electron · **🌫 Noise:** shot poisson > **⚖ Difficulty (δ):** 10 · **⛓ Block:** 41554185 --- ## 🧠 1. Introduction **Cryo-Electron Tomography (cryoET) — in-situ 3D biology at nm scale** is a **linear inverse problem** whose unknown lives in **3D density** space, within the **In-situ structural biology via cryo tilt-series** sub-domain of **Electron Microscopy**. Measurements consist of electrons collected by an electron detector via a **cryo electron transmission** sensing mechanism. The forward operator applies, in order: L · transmit sample operator; rotates source / detector to acquire different projections; spreads measurements back along source rays (adjoint operator); L · subtomogram average operator; integration over the solid angle of incidence/emission. Observations are corrupted by Poisson shot noise from quantum-limited detection. Existence of the recovered 3D density is guaranteed within the declared Omega bounds. Uniqueness holds on the measurement-supported subspace; out-of-support modes are controlled by the declared priors. Stability is moderately conditioned (kappa_eff ~= 35); tilt_angle_error dominates the stability cliff; CTF_per_tilt and the remaining mismatch parameters contribute higher-order bias terms. Photon-shot-noise-limited (poisson counting) sets the irreducible data-fidelity floor, while TV / wavelet-sparsity / deep priors stabilise recovery at the ill-conditioned end of Omega. ## ⚙ 2. Forward Model Physical chain: **x** → L · transmit sample → Angular scan → L · subtomogram average → Angular integration → **y** (detector). ``` y = ∫dΩ `L.subtomogram_average` R(θ) `L.transmit_sample` x, measurements ~ Poisson(αy) ``` **Measurement DAG:** | Primitive | What it does | |---|---| | `L.transmit_sample` | L · transmit sample operator | | `S.scan.angular` | Rotates source / detector to acquire different projections | | `L.subtomogram_average` | L · subtomogram average operator | | `int.angular` | Integration over the solid angle of incidence/emission | **🛠 Solver components** _(used inside the solver, not in the forward equation)_: | Primitive | What it does | |---|---| | `L.backproject` | Spreads measurements back along source rays (adjoint operator) | ## 🔬 3. Physics Fingerprint | Property | Value | |---|---| | Domain | Electron Microscopy | | Sub domain | In-situ structural biology via cryo tilt-series | | Carrier | electron | | Problem class | linear_inverse | | Solution space | 3D_density | | Noise model | shot_poisson | | Integration axis | angular | | Difficulty delta | 10 | | L dag | 4.5 | ## 📡 4. Measurement Model Existence of the recovered 3D density is guaranteed within the declared Omega bounds. Uniqueness holds on the measurement-supported subspace; out-of-support modes are controlled by the declared priors. Stability is moderately conditioned (kappa_eff ~= 35); tilt_angle_error dominates the stability cliff; CTF_per_tilt and the remaining mismatch parameters contribute higher-order bias terms. Photon-shot-noise-limited (poisson counting) sets the irreducible data-fidelity floor, while TV / wavelet-sparsity / deep priors stabilise recovery at the ill-conditioned end of Omega. | Metric | Value | |---|---| | Metric | PSNR_dB | | Secondary | SSIM | ## 📏 5. Operating Range (Ω) **Center problem class:** `cryoet_tilt_series` · **Forward operator:** `cryoet_tilt_series_forward` **Center point:** | Parameter | Unit | Value | |---|---|---| | H | px | 4096 | | W | px | 4096 | | Z | — | 256 | | Kv | — | 300 | | N tilts | — | 61 | | Beam damage | — | 0.2 | | Total dose e | — | 60 | | Missing wedge | — | 0.33 | | Tilt range deg | deg | 60 | | Tilt angle error | — | 0 | **Allowed bounds:** | Parameter | Unit | Range | |---|---|---| | H | px | 1024 – 8192 | | W | px | 1024 – 8192 | | Z | — | 64 – 1024 | | Kv | — | 300 – 300 | | N tilts | — | 20 – 200 | | Beam damage | — | 0.0 – 0.8 | | Total dose e | — | 20 – 200 | | Missing wedge | — | 0.1 – 0.5 | | Dose weighting | — | 0.0 – 1.0 | | Tilt range deg | deg | 40 – 80 | | Tilt angle error | — | 0.0 – 0.3 | ## 🎯 6. Tolerance (ε) **Center tolerance:** 22.0 | Metric | Range | |---|---| | Psnr db | 10.0 – 40.0 | ## ⚖ 7. Hardness Function Hardness scales as **`epsilon_fn`** on **PSNR_dB**, with κ = `700` and δ = `10`. ## 💾 8. Reference Dataset - **primary** · weight 1.0 · IPFS _(not pinned yet)_ ## 9. On-chain Registration - **Chain hash:** `0x0dbf3b1a3249338f26ada5f995e0eff81af86c94902cebc8b873a412a75666d1` - **Chain tx hash:** `0x2b24a247c36da2878087519cc99e669d3cb0cc60ad41af578be47e17fbc2f306` - **Chain block:** `41554185` --- ## File Mapping This bundle consists of: `L1-092.md`, `L1-092.json`. | File | Role | How to regenerate | |------|------|-------------------| | `L1-092.md` | Source of truth — edit this | Human or LLM | | `L1-092.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 `L1-092`._ _Edit it, regenerate the JSON, and submit at [/submit](/submit) to claim the artifact._

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L2-092-001 Cryo-Electron Tomography (cryoET) — in-situ 3D biology at nm scale Mismatch-Only Spec

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📋 JSON metadata

{
  "artifact_id": "L1-092",
  "chain_block": 41554185,
  "chain_hash": "0x0dbf3b1a3249338f26ada5f995e0eff81af86c94902cebc8b873a412a75666d1",
  "chain_tx_hash": "0x2b24a247c36da2878087519cc99e669d3cb0cc60ad41af578be47e17fbc2f306",
  "domain": "Electron Microscopy",
  "hardness_fn": {
    "delta": 10,
    "kappa": 700,
    "metric": "PSNR_dB",
    "type": "epsilon_fn"
  },
  "initiator_dataset": [
    {
      "ipfs_cid": null,
      "license_hash": null,
      "name": "primary",
      "weight": 1.0
    }
  ],
  "layer": "L1",
  "observable_profile": {
    "metric": "PSNR_dB",
    "regime": "Existence of the recovered 3D density is guaranteed within the declared Omega bounds. Uniqueness holds on the measurement-supported subspace; out-of-support modes are controlled by the declared priors. Stability is moderately conditioned (kappa_eff ~= 35); tilt_angle_error dominates the stability cliff; CTF_per_tilt and the remaining mismatch parameters contribute higher-order bias terms. Photon-shot-noise-limited (poisson counting) sets the irreducible data-fidelity floor, while TV / wavelet-sparsity / deep priors stabilise recovery at the ill-conditioned end of Omega.",
    "secondary": "SSIM"
  },
  "physics_fingerprint": {
    "L_DAG": 4.5,
    "carrier": "electron",
    "difficulty_delta": 10,
    "domain": "Electron Microscopy",
    "integration_axis": "angular",
    "noise_model": "shot_poisson",
    "primitives": [
      "L.transmit_sample",
      "S.scan.angular",
      "L.backproject",
      "L.subtomogram_average",
      "int.angular"
    ],
    "problem_class": "linear_inverse",
    "sensing_mechanism": "cryo_electron_transmission",
    "solution_space": "3D_density",
    "sub_domain": "In-situ structural biology via cryo tilt-series",
    "title": "Cryo-Electron Tomography (cryoET) \u2014 in-situ 3D biology at nm scale"
  },
  "size_tiers": {
    "allowed_forward_operators": [
      "cryoet_tilt_series_forward"
    ],
    "allowed_omega_dimensions": [
      "H",
      "W",
      "Z",
      "N_tilts",
      "tilt_range_deg",
      "kV",
      "total_dose_e",
      "tilt_angle_error",
      "missing_wedge",
      "beam_damage",
      "tilt_angle_error",
      "CTF_per_tilt",
      "beam_damage",
      "missing_wedge",
      "dose_weighting"
    ],
    "allowed_problem_classes": [
      "cryoet_tilt_series"
    ],
    "center_spec": {
      "epsilon_fn_center": "22.0",
      "forward_operator": "cryoet_tilt_series_forward",
      "input_format": "measurement_only",
      "omega": {
        "H": 4096,
        "N_tilts": 61,
        "W": 4096,
        "Z": 256,
        "beam_damage": 0.2,
        "kV": 300,
        "missing_wedge": 0.33,
        "tilt_angle_error": 0.0,
        "tilt_range_deg": 60,
        "total_dose_e": 60
      },
      "problem_class": "cryoet_tilt_series"
    },
    "epsilon_bounds": {
      "psnr_db": [
        10.0,
        40.0
      ]
    },
    "omega_bounds": {
      "H": [
        1024,
        8192
      ],
      "N_tilts": [
        20,
        200
      ],
      "W": [
        1024,
        8192
      ],
      "Z": [
        64,
        1024
      ],
      "beam_damage": [
        0.0,
        0.8
      ],
      "dose_weighting": [
        0.0,
        1.0
      ],
      "kV": [
        300,
        300
      ],
      "missing_wedge": [
        0.1,
        0.5
      ],
      "tilt_angle_error": [
        0.0,
        0.3
      ],
      "tilt_range_deg": [
        40,
        80
      ],
      "total_dose_e": [
        20,
        200
      ]
    }
  },
  "staked_pwm": 0.0,
  "status": "testnet",
  "sub_domain": "In-situ structural biology via cryo tilt-series",
  "title": "Cryo-Electron Tomography (cryoET) \u2014 in-situ 3D biology at nm scale"
}

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