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+# OpenH-RF Sub-Dataset: 2D Ring-Array USCT Waveforms from 2D- and 3D-k-Wave Simulations
+
+## Dataset Description
+
+This sub-dataset provides **pre-beamformed channel-domain radio-frequency
+ultrasound waveforms** from simulated ring-array **ultrasound computed
+tomography (USCT)** acquisitions of digital breast phantoms. All data are
+two-dimensional: each acquisition is a 2D channel tensor (transmit × time ×
+receiver) recorded at a 256-element ring as every element fires in turn, paired
+with 2D voxel-level ground-truth maps of **speed-of-sound (SOS)** and **acoustic
+attenuation** for a single breast cross-section.
+
+What distinguishes the two collections is **the k-Wave simulation used to
+generate the RF**:
+
+- **2D-sim** (2,149 acquisitions): RF computed with **2D** k-Wave
+  (`kspaceFirstOrder2D`) on the breast cross-section.
+- **3D-sim** (476 acquisitions): RF computed with **3D** k-Wave
+  (`kspaceFirstOrder3D`) on the full breast volume, then recorded at the ring
+  plane. The 3D simulation captures out-of-plane propagation and finite
+  focused-element behaviour that a 2D simulation cannot represent.
+
+Both collections are generated from the **same underlying digital breast
+phantoms** (derived from the open VICTRE breast model), enabling direct study of
+how 3D acoustic effects change the channel data relative to an idealized 2D
+simulation. All data are **synthetic (simulated)**; no human or animal subjects
+are involved.
+
+## Dataset Contributor(s)
+
+- **Contributing organizations:** Thayer School of Engineering, Dartmouth
+  College; University of Rochester Medical Center.
+- **Primary point of contact:** Yujia Wu — `yujia.wu.th@dartmouth.edu`
+- **PI:** Prof. Geoffrey P. Luke — `Geoffrey.P.Luke@dartmouth.edu`
+
+## Dataset Creation Date
+
+07/04/2026
+
+## License / Terms of Use
+
+**CC BY 4.0.** All contributed data are cleared for this license. The data are
+fully synthetic (no patient data, no consent or IRB requirements). The digital
+breast phantoms derive from the publicly available VICTRE model (U.S. FDA / NCI,
+public domain).
+
+## Intended Usage
+
+- **Sound-speed estimation / imaging** (quantitative SOS reconstruction).
+- **Acoustic-attenuation imaging.**
+- **Ultrasound computed tomography (USCT)** reconstruction from full-ring
+  channel data.
+- **Compressed sensing** — sub-sampling along the transmit
+  (Tx) or receive (Rx) axis and recovering missing channels.
+
+## Dataset Characterization
+
+- **Data Collection Method:** synthetic (k-Wave simulation).
+- **Labeling Method:** synthetic ground truth (voxel-level SOS and attenuation
+  maps are the exact simulation inputs; no annotation error).
+- **Acquisition system** (the label denotes the k-Wave simulation dimensionality;
+  the recorded data are 2D in both cases):
+
+**2D-sim** (RF from 2D k-Wave)
+
+| Parameter | Value |
+|---|---|
+| Simulation | `kspaceFirstOrder2D` |
+| Geometry | 256-element ring, point elements (no element directivity) |
+| Ring radius | 60 mm |
+| Grid spacing | 0.30 mm |
+| Center frequency | 1.0 MHz (Gaussian pulse, 0.75 fractional bandwidth) |
+| Sampling rate (saved) | 6.67 MHz (decimated 3× from 20 MHz native) |
+| Transmit events (Tx) | 256 (every element fires in turn) |
+| Receive elements (Rx) | 256 |
+| Time samples (T) | 867 |
+| Record length | 130 µs |
+
+**3D-sim** (RF from 3D k-Wave)
+
+| Parameter | Value |
+|---|---|
+| Simulation | `kspaceFirstOrder3D` |
+| Geometry | 256-element ring, PURE-calibrated positions; focused elements (0.558 mm × 19 mm, 75 mm elevation focus) |
+| Ring radius | 110.9 mm (PURE calibration) |
+| Grid spacing | 0.29 mm |
+| Center frequency | 1.5 MHz (5-cycle toneburst) |
+| Sampling rate (saved) | 12 MHz |
+| Transmit events (Tx) | 64 (every 4th element) |
+| Receive elements (Rx) | 256 |
+| Time samples (T) | 2161 |
+| Record length | ~180 µs |
+
+## Dataset Format
+
+All data are packaged in the **`zea` HDF5 file format** (one `.hdf5` file per
+acquisition), written entirely through `zea.File.create`. Each file stores the
+raw channel data under `tracks/track_0/data/raw_data`, the acquisition parameters
+under `tracks/track_0/scan`, the ring geometry under `probe` (in the **XZ imaging
+plane**, y = elevation), and the voxel-level ground truth as native zea map fields
+`tracks/track_0/data/sos_map` and `tracks/track_0/data/attenuation_map` (each with
+per-pixel `coordinates`). Tissue class is stored in `metadata/annotations`
+(`anatomy`, `label`); only fields with no standard spec home (z-plane indices,
+element focus) are zea `CustomElement`s under the top-level `custom/` group. Files
+are laid out by simulation type: `data/2d/` (2D-sim) and `data/3d/` (3D-sim),
+produced by
+[`convert_2d_to_zea.py`](convert_2d_to_zea.py) and
+[`convert_3d_to_zea.py`](convert_3d_to_zea.py) respectively.
+
+**Pre-processing applied before packaging:**
+- 2D-sim: temporal decimation by 3× (20 MHz → 6.67 MHz native simulation rate).
+  3D-sim: saved at the native 12 MHz, no decimation.
+- Time-zero is carried in `scan/initial_times`; the per-sample time vector is
+  `initial_times[tx] + n / sampling_frequency`. In **both** sets `t = 0` is the
+  emission centroid: `initial_times = -2.15e-6` (2D-sim) and `-1.625e-6` (3D-sim,
+  the 5-cycle toneburst centroid). The 3D simulation saved its time vector from
+  the pulse onset, so this centroid offset is applied during conversion.
+- Single-element transmit events are described by `scan/tx_apodizations` with zero
+  `scan/t0_delays`. **2D-sim:** all 256 elements fire (identity matrix).
+  **3D-sim:** 64 events fire every 4th element (a `(64, 256)` stride-4 matrix).
+- Per-acquisition channel data stored as `float32` (zea's `raw_data` spec allows
+  only `float32` or `int16`). The 2D-sim RF was decimated and intermediately
+  cached at fp16 precision, so its stored `float32` is bit-faithful to that source
+  rather than carrying extra precision; the 3D-sim RF is the native `float32`
+  simulation output.
+- No demodulation or beamforming is applied — data are raw RF channel signals.
+
+## Dataset Quantification
+
+- **Number of acquisitions:** **2,149 (2D-sim)** (1,859 dense + 290 fatty) +
+  **476 (3D-sim)** = **2,625 acquisitions**.
+- **Single-Tx channel-capture frames:** 2,149 × 256 (2D-sim) + 476 × 64 (3D-sim)
+  ≈ **5.8 × 10⁵ frames**.
+- **Train / val / test split:** suggested 80 / 10 / 10 by **source phantom**
+  (so slices/z-planes from one phantom never cross splits — prevents leakage).
+- **Total size on disk:** ~395 GB float32 — ~333 GB (2D-sim, ~160 MB/acq) +
+  ~62 GB (3D-sim, ~140 MB/acq).
+
+**Per-sample feature table — 2D-sim** (HDF5 keys per `.hdf5` acquisition):
+
+| Key | Shape | Dtype | Units | Description |
+|---|---|---|---|---|
+| `tracks/track_0/data/raw_data` | `(1, 256, 867, 256, 1)` | float32 | a.u. (pressure) | Raw channel data, axis order `(n_frames, n_tx, n_ax, n_el, n_ch)` |
+| `tracks/track_0/scan/sampling_frequency` | scalar | float32 | Hz | 6.67e6 |
+| `tracks/track_0/scan/center_frequency` | scalar | float32 | Hz | 1.0e6 |
+| `tracks/track_0/scan/sound_speed` | scalar | float32 | m/s | Reference (water) sound speed, 1500 |
+| `tracks/track_0/scan/initial_times` | `(256,)` | float32 | s | First-sample time per Tx (`-2.15e-6`; `t=0` at pulse centroid) |
+| `tracks/track_0/scan/tx_apodizations` | `(256, 256)` | float32 | – | Identity: transmit event *i* fires element *i* |
+| `tracks/track_0/scan/t0_delays` | `(256, 256)` | float32 | s | Transmit delays (zeros — single-element transmits) |
+| `tracks/track_0/scan/transmit_origins` | `(256, 3)` | float32 | m | Firing-element position per Tx |
+| `probe/probe_geometry` | `(256, 3)` | float32 | m | Ring element coordinates `(x, y=0, z)` in the XZ plane, 60 mm radius |
+| `tracks/track_0/data/sos_map/values` | `(1, 230, 230)` | float32 | m/s | Ground-truth SOS map |
+| `tracks/track_0/data/sos_map/coordinates` | `(230, 230, 3)` | float32 | m | Per-pixel `[x, y=0, z]` (dx = 0.30 mm, centred on ring; x=cols, z=rows) |
+| `tracks/track_0/data/attenuation_map/values` | `(1, 230, 230)` | float32 | dB/m/Hz | Ground-truth attenuation coefficient α₀ |
+| `tracks/track_0/data/attenuation_map/gamma` | scalar | float32 | – | Power-law exponent γ (1.01; α(f)=α₀·fᵞ) |
+| `metadata/annotations` | – | str | – | `anatomy="breast"`, `label="dense"`/`"fatty"` |
+| `custom/z_slice` | scalar | int | – | Phantom z-slice index |
+
+Attenuation is stored in the zea base unit **dB/m/Hz** (`1 dB/cm/MHz = 1e-4
+dB/m/Hz`); the `sos_map`/`attenuation_map` `coordinates` carry the physical grid
+(so `dx` is implicit), and `scan/sound_speed` holds the water reference.
+
+**Per-sample feature table — 3D-sim** (HDF5 keys per `.hdf5` acquisition):
+
+| Key | Shape | Dtype | Units | Description |
+|---|---|---|---|---|
+| `tracks/track_0/data/raw_data` | `(1, 64, 2161, 256, 1)` | float32 | a.u. (pressure) | Raw channel data, `(n_frames, n_tx, n_ax, n_el, n_ch)` |
+| `tracks/track_0/scan/sampling_frequency` | scalar | float32 | Hz | 12e6 |
+| `tracks/track_0/scan/center_frequency` | scalar | float32 | Hz | 1.5e6 |
+| `tracks/track_0/scan/sound_speed` | scalar | float32 | m/s | Reference (water) sound speed, ≈1500 |
+| `tracks/track_0/scan/initial_times` | `(64,)` | float32 | s | First-sample time per Tx (`-1.625e-6`; `t=0` at toneburst centroid) |
+| `tracks/track_0/scan/tx_apodizations` | `(64, 256)` | float32 | – | Stride-4 selection: transmit event *k* fires element `4k` |
+| `tracks/track_0/scan/t0_delays` | `(64, 256)` | float32 | s | Transmit delays (zeros — single-element transmits) |
+| `tracks/track_0/scan/transmit_origins` | `(64, 3)` | float32 | m | Firing-element position per Tx |
+| `probe/probe_geometry` | `(256, 3)` | float32 | m | PURE-calibrated ring positions `(x, y=0, z)` in the XZ plane, 110.9 mm radius |
+| `probe/element_width`, `probe/element_height` | scalar | float32 | m | 0.558 mm × 19 mm focused element |
+| `tracks/track_0/data/sos_map/values` | `(1, 800, 800)` | float32 | m/s | Ground-truth SOS slice (sim-grid in-plane cross-section at the ring) |
+| `tracks/track_0/data/sos_map/coordinates` | `(800, 800, 3)` | float32 | m | Per-pixel `[x, y=0, z]` (dx = 0.29 mm, centred on ring; x=cols, z=rows) |
+| `tracks/track_0/data/attenuation_map/values` | `(1, 800, 800)` | float32 | dB/m/Hz | Ground-truth attenuation coefficient α₀ |
+| `tracks/track_0/data/attenuation_map/gamma` | scalar | float32 | – | Power-law exponent γ (1.01) |
+| `metadata/annotations` | – | str | – | `anatomy="breast"` (no dense/fatty label for the 3D set) |
+| `custom/z_off`, `custom/phantom_z_idx`, `custom/element_focus` | scalar | int / float | – / m | Ring z-offset, phantom z-slice index, element focus (0.075 m) |
+
+Attenuation is in the zea base unit **dB/m/Hz**; the map `coordinates` carry the
+physical grid (XZ plane, y = 0).
+
+## Subject Metadata
+
+Not applicable — all data are synthetic. Aggregate phantom statistics:
+
+- **Anatomical region:** breast cross-sections. The 3D-sim set samples several
+  z-planes per phantom (one 2D cross-section each).
+- **Tissue classes represented:** fat, glandular, skin/connective, with
+  continuous SOS/attenuation/density assignments.
+- **No PHI.**
+
+## Data Validation
+
+A single reference reconstruction, [`reconstruct.py`](reconstruct.py), serves
+**both** sub-datasets. It builds a `zea.Pipeline` whose beamforming stage is
+zea's dedicated `zea.ops.USCTReflectivityDAS` — a round-trip time-of-flight
+Delay-And-Sum that, for every pixel, coherently sums over all transmit/receive
+pairs, rejects the direct through-transmission arrival, and apodizes to keep only
+backscatter geometries. The pipeline is saved to [`pipeline.yaml`](pipeline.yaml).
+
+The same code reconstructs the 2D-sim (256 transmits) and 3D-sim (64 transmits)
+files because everything it needs is read **back from the zea file**: element
+positions (`probe/probe_geometry`), the transmit selection (`scan/tx_apodizations`),
+sampling rate (`scan/sampling_frequency`), time-zero (`scan/initial_times`), and
+the imaging grid (from the ground-truth `coordinates`). The ring is stored in the
+XZ imaging plane, so `zea.File.load_parameters` + `pipeline.prepare_parameters`
+drive the reconstruction directly. A resulting image whose bright skin boundary
+traces the ground-truth contour confirms the geometry, timing, and transmit
+parameters were recorded correctly.
+
+```
+python reconstruct.py --input data/2d/phantom_xxx.hdf5
+python reconstruct.py --input data/3d/phantom_xxx.hdf5
+```
+
+## Known Issues
+
+- **2D-sim vs 3D-sim differ in geometry and sampling** — 60 mm vs 110.9 mm ring;
+  256 vs 64 transmits; 867 @ 6.67 MHz (130 µs) vs 2161 @ 12 MHz (~180 µs); 230²
+  (0.30 mm) vs 800² (0.29 mm) GT maps. Users combining both must resample to a
+  common grid.
+- **2D-sim point elements vs 3D-sim focused elements:** the 2D-sim set idealizes
+  elements as points (no element directivity), while the 3D-sim set models finite
+  focused elements (0.558 mm × 19 mm, 75 mm elevation focus) and out-of-plane
+  propagation.
+- **Attenuation units:** stored in the zea base unit `dB/m/Hz` (converted from the
+  simulation's `dB/cm/MHz`; `1 dB/cm/MHz = 1e-4 dB/m/Hz`). The k-Wave `alpha_power`
+  is the `attenuation_map/gamma` field (α(f)=α₀·fᵞ, γ=1.01).
+- **Time-zero convention:** in both sets `t = 0` is the emission centroid (carried
+  in `scan/initial_times`), not the first recorded sample — important for
+  time-of-flight methods.
+
+## Ethical Considerations
+
+Fully synthetic dataset. No human or animal subjects; no consent, IRB, or
+de-identification requirements apply. The VICTRE breast phantoms are publicly
+released by the U.S. FDA/NCI. No usage caveats beyond the CC BY 4.0 attribution
+requirement.
+
+---
+
+### Provenance / Citation
+
+If you use this sub-dataset, please cite:
+
+- Badano A, Graff CG, Badal A, Sharma D, Zeng R, Samuelson FW, Glick SJ,
+  Myers KJ. *Evaluation of Digital Breast Tomosynthesis as Replacement of
+  Full-Field Digital Mammography Using an In Silico Imaging Trial.*
+  JAMA Network Open. 2018;1(7):e185474. doi:10.1001/jamanetworkopen.2018.5474
+- Treeby BE, Cox BT. *k-Wave: MATLAB toolbox for the simulation and
+  reconstruction of photoacoustic wave fields.* J Biomed Opt. 2010;15(2):021314.