| --- |
| pretty_name: "OpenH-RF — eSAF Rotational 3D US Raw Channel Data (Medical FUSION Lab, WPI)" |
| license: cc-by-4.0 |
| task_categories: |
| - image-to-image |
| tags: |
| - ultrasound |
| - rf |
| - openh-rf |
| - 3d |
| - beamforming |
| - elevational-saf |
| language: |
| - en |
| size_categories: |
| - n<1K |
| --- |
| |
| # OpenH-RF Sub-Dataset — Rotational 3D US Raw Channel Data for Elevational SAF (Simulated + Measured Phantom) |
|
|
| ## Dataset Description |
| Synthetic rotational 3D ultrasound acquisitions of point, pair, and off-axis targets, captured |
| with an **elevation-focused 1D linear array** that is rotated 180° about its axial |
| axis (1° steps, 180 frames). Each acquisition stores the **raw per-element channel |
| RF** for a single normal plane-wave transmit at every rotation angle — i.e. the data |
| *before* in-plane beamforming — which is what enables flexible offline beamforming and |
| the **elevational Synthetic Aperture Focusing (eSAF)** method. The targets span a wide |
| depth range to capture the depth-dependent elevational beam thickness (the artifact |
| eSAF corrects). The release is **mostly simulated (Field II)**, complemented by a |
| small set of **real measured phantom** rotational scans acquired with the physical |
| Japan Probe 68-element array (same geometry as the simulation) over a shallow-to-focal |
| depth series (10–45 mm). **Simulated + measured phantom** data (no in-vivo / subjects). |
|
|
| ## Dataset Contributor(s) |
| Medical FUSION Laboratory, Worcester Polytechnic Institute. Contact: Ryo Murakami. |
|
|
| ## Dataset Creation Date |
| 06/15/2026. |
|
|
| ## License / Terms of Use |
| CC BY 4.0 (full text in `LICENSE`). The release contains **simulated (Field II) and |
| real measured phantom** rotational scans — inanimate phantom only, so there are no |
| IP, subject-consent, or IRB constraints. |
|
|
| **Citation.** When using this dataset, please cite: |
| > R. Murakami et al., "Elevational Synthetic Aperture Focusing for Rotated |
| > Array-Based Three-Dimensional Ultrasound Imaging," IEEE Access, 2025. |
|
|
| ## Intended Usage |
| Advanced beamforming and **elevational resolution recovery** for rotational 3D US |
| (eSAF), elevation-PSF / aperture-growth studies, and as a reproducible raw-channel-data |
| benchmark for rotational synthetic-aperture reconstruction. |
|
|
| ## Dataset Characterization |
| - **Data Collection Method:** synthetic, generated with **Field II** (Jensen) run in |
| **MATLAB**. The main release is a **probe × target grid** produced by |
| `sim/batch_sim_probe_target.m` (source) (with `sim/sim_probe_catalog.m` / |
| `sim/sim_target_catalog.m`, source): for each (probe type, target) it uses `xdc_focused_array` |
| + `calc_scat_multi` to produce the raw per-element channel RF at every rotation angle |
| (scatterer rotated about the axial axis, transducer fixed), then `sim/sim_dataset_to_zea.py` |
| (source) repackages every case into the zea format here. **10 probe types** span lateral aperture |
| (`n_el` 32/68/128, pitch 0.1/0.2/0.3 mm), elevation height `H` (4/8/12 mm), and elevation |
| focal depth `R` (25/45/90 mm + unfocused) — see the probe table in `data/manifest.json`. |
| (The earlier 18-acquisition set generated by `sim/batch_generate_fieldii.m` + |
| `sim/mat_to_zea.py` (source) remains available as a compatible alternative with the |
| identical schema.) |
| **Measured phantom acquisitions (5):** real rotational scans of the physical Japan |
| Probe 68-element array on a wire/point phantom, acquired with CPWC channel-RF capture |
| (`experiment/Ryo_SetUp_JP68_PWCompound_3D_ChannelRF.m`, source) and a Galil-controlled 180° |
| rotation. Each scan is time-tag-synced (frames → motor angles) and reduced to the |
| **single centre (normal) plane wave per angle** by `experiment/sync_channel_rf.m` (source) |
| (so the schema matches the simulation, n_tx = 1), then converted with the same |
| `sim/sim_dataset_to_zea.py` (source). They span a shallow-to-focal depth series (10, 20, 30, |
| 40, 45 mm nominal target depth). |
| - **Labeling Method:** synthetic ground truth (exact target positions known; in |
| `data/manifest.json`). |
| - **Acquisition system (simulated):** Japan Probe JP_Linear_68 — 68-element linear |
| array, pitch 0.2 mm, element width 0.15 mm, element height 8 mm, **elevational lens |
| focus 45 mm** (Field II `xdc_focused_array` with 500 elevation math sub-elements); |
| center frequency 10 MHz; sampling 40 MHz (NS200BW, 4 samples/wavelength); speed of |
| sound 1490 m/s; single normal plane-wave transmit per rotation angle; 180° rotation, |
| 1° step (180 frames). Parameters match the paper simulation. |
|
|
| ## Dataset Format |
| zea file format (HDF5), one file per acquisition, **single track**: the raw |
| channel RF + scan parameters live in the standard data/scan groups |
| (`tracks/track_0` on disk), and the paired eSAF label volume is stored as a |
| **zea custom field** in the `custom` group (`custom/saf_bmode`, read via |
| `zea.File.custom` — see below). The fused SAF volume is a single frame, so it |
| cannot share the data group with the ~180-frame `raw_data` (zea validates |
| `n_frames` across all fields of a data group); the `custom` group is the zea |
| mechanism for exactly such data, and keeping the file single-track avoids the |
| `track_schedule` warning a multi-track file would print on every load. |
| Pre-processing — *simulated:* none |
| beyond the forward model (raw RF, not demodulated/decimated); *measured:* time-tag |
| frame→angle synchronisation, per-angle dwell averaging, and centre-plane-wave selection |
| (still raw per-element RF, not demodulated/decimated; `scan/demodulation_frequency` |
| records the 10 MHz demodulation applied by the reference pipeline). The probe |
| rotation per frame is stored as the zea **`metadata/probe_pose`** trajectory |
| (`rotation_representation="euler_xyz"`, **radians**; the array rotates about its |
| axial axis, so the angle is the z Euler component and the translation is zero). |
| Note `probe_pose/sampling_frequency = 1.0 Hz` is a **nominal** one-pose-per-frame |
| value, not a physical acquisition rate. Every file is |
| written with `zea.File.create()` (`sim/sim_dataset_to_zea.py` + |
| `sim/pack_saf_labels.py`, source) and carries a |
| `zea_version` stamp, so zea loads it natively (not as a legacy file). |
| |
| **Paired pre-/post-SAF labels (the dataset's target output).** Each file also carries |
| the **elevational-SAF reconstructed 3D B-mode volume** as the custom field |
| **`custom/saf_bmode`**: `values` is `(1, z, x, y)` float32 in **dB** (log-compressed |
| normalized envelope, 0 dB = volume max, empty pixels −inf) and `coordinates` holds |
| the per-pixel `[x, y, z]` positions in **meters**, shape `(z, x, y, 3)`; both carry |
| `description`/`unit` attributes. This is |
| the *post*-SAF **output/label** paired with the *pre*-beamformed **input** |
| (`data/raw_data`): |
| the raw channel RF is back-projected through the published eSAF algorithm |
| (`matlab/saf/safrot_backproj.m`, source: in-plane DAS → `recon_3d` → `safrot_backproj`, |
| elevational focus 45 mm, f-number 45/8) into a 3D volume `B_SAF(x,y,z)`, generated by |
| `sim/make_saf_all.m` → `experiment/run_esaf_synced.m` (source) and written into the zea |
| file by `sim/pack_saf_labels.py` (source). The stored volume covers |
| a thin depth window (±2 mm) about the target; per-case arc-FWHM before/after and gain |
| are in `data/manifest.json` and in the `description` attribute of |
| `custom/saf_bmode/values`. Read it with `zea.File`: |
|
|
| ```python |
| with zea.File("data/baseline_R45_H8__point_z080_r4.hdf5") as f: |
| saf = {e.name: e for e in f.custom} # custom/saf_bmode elements |
| volume_db = saf["values"].data # (1, z, x, y) float32 dB |
| coordinates = saf["coordinates"].data # (z, x, y, 3) float32 m |
| print(saf["values"].description) # axes + eSAF parameters + arc-FWHM |
| ``` |
|
|
| A **MATLAB `.mat` version** of the same raw channel data + metadata, plus a |
| **reference eSAF-beamformed** result and a `_ref.png` figure, is provided **per |
| acquisition** alongside the source grid as `sim_dataset_out/<probe>/<target>.mat` |
| and `..._ref.png` (each `.mat` holds the raw RF, the in-plane DAS, the metadata and |
| the eSAF output produced with the published algorithm `matlab/saf/safrot_backproj.m` |
| (source): in-plane DAS → `recon_3d` → `safrot_backproj`, f-number 45/8). A FWHM-vs-depth |
| overview across probes is `sim_dataset_out/dataset_overview_r4.png` |
| (`sim/dataset_overview.m`, source). The zea `.hdf5` acquisitions are **hosted on Hugging |
| Face** at <https://huggingface.co/datasets/RyoMurakami/OpenH-RF-eSAF> (git-LFS). |
| The MATLAB `.mat`/`_ref.png` intermediates are |
| reproducible from source and kept on lab storage. |
|
|
| ## Dataset Quantification |
|
|
| **Current OpenH-RF release:** 195 HDF5 files; 1.87 GB (1,870,462,976 bytes) stored; root `zea_version` **0.1.6**. Sizes include all HDF5 contents and use decimal units (MB = 10^6 bytes, GB = 10^9 bytes, TB = 10^12 bytes), not decoded-array memory or original-source download sizes. |
|
|
| - **Acquisitions:** **195** = **190 simulated** + **5 measured phantom**. |
| - *Simulated (190):* **10 probe types × 19 targets** (16 single points over depth |
| {20,45,80,130} mm × radial offset from the rotation centre {0,2,4,6} mm, plus 3 |
| pair/oblique cases). The probe and target axes are listed in `data/manifest.json`. (The |
| earlier compatible set has 18 acquisitions.) |
| - *Measured (5):* real rotational phantom scans at nominal depths {10,20,30,40,45} mm |
| (`experiment__acq_exp_*.hdf5`), centre plane wave, ~182 measured rotation angles |
| over ~180°. |
| - **Frames per acquisition:** simulated 180 (one per 1° step); measured ~182 (the |
| actual encoder angles are stored in `metadata/probe_pose` — z Euler component, |
| radians — not necessarily uniform). |
| - **Stored HDF5 size:** 1.87 GB (1,870,462,976 bytes), including the paired `saf_bmode` label volumes. |
| - **Train/val/test split:** N/A (benchmark / characterization set; the probe × depth × |
| radius axes are the intended study dimensions). |
| |
| ### Per-sample feature table |
| Shapes use placeholders because dimensions vary across the probe grid and between |
| simulated and measured scans: **`n_frames`** = 180 (simulated, one per 1° step) or |
| ~182 (measured encoder angles); **`n_el`** ∈ {32, 68, 128} (probe grid; 68 for the |
| baseline and all measured scans); **`n_ax`** = axial sample count (per case); |
| **`n_z`** = depth samples of the label volume (target ± ~2 mm window). |
|
|
| Paths below are inside each `.hdf5`; with `zea.File` use `f.data` / `f.scan` / |
| `f.metadata.probe_pose`, and `f.custom` for the SAF label volume. |
|
|
| | field (HDF5 path) | shape | dtype | units | description | |
| |-----------------------------------|--------------------------------|---------|-------|-------------| |
| | `tracks/track_0/data/raw_data` (`f.data.raw_data`) | (n_frames, 1, n_ax, n_el, 1) | float32 | a.u. | raw per-element channel RF; dims = (frame=rotation, tx, axial, element, ch) | |
| | `probe/probe_geometry` | (n_el, 3) | float32 | m | element positions (lateral x, 0, 0) | |
| | `tracks/track_0/scan/sampling_frequency` | scalar | float32 | Hz | 4.0e7 | |
| | `tracks/track_0/scan/center_frequency` | scalar | float32 | Hz | 1.0e7 | |
| | `tracks/track_0/scan/demodulation_frequency` | scalar | float32 | Hz | 1.0e7 (= center frequency; used by the reference pipeline's demodulate op) | |
| | `tracks/track_0/scan/sound_speed` | scalar | float32 | m/s | 1490 | |
| | `tracks/track_0/scan/initial_times` | (1,) | float32 | s | t0 (first-sample time) | |
| | `tracks/track_0/scan/t0_delays` | (1, n_el) | float32 | s | transmit delays (0; normal plane wave) | |
| | `tracks/track_0/scan/polar_angles` | (1,) | float32 | rad | transmit steering (0) | |
| | `metadata/probe_pose/rotation` | (n_frames, 3) | float32 | rad | probe pose per frame, `euler_xyz`; rotation about the axial (z) axis is the z component | |
| | `metadata/probe_pose/translation` | (n_frames, 3) | float32 | m | probe tip translation (all zero — pure rotation) | |
| | `metadata/probe_pose/sampling_frequency` | scalar | float32 | Hz | 1.0 — **nominal** one-pose-per-frame rate, not a physical value | |
| | `metadata/credit` (`f.metadata.credit`) | scalar | str | – | dataset credit / attribution (lab, contact, citation, license) | |
| | `metadata/subject/type` (`f.metadata.subject.type`) | scalar | str | – | `simulated phantom` (Field II sims) or `phantom` (measured `experiment__*` scans) | |
| | `custom/saf_bmode/values` (custom field, via `f.custom`) | (1, n_z, n_el, n_el) | float32 | dB | **paired label**: elevational-SAF reconstructed 3D B-mode volume, log-compressed normalized envelope (0 dB = max, empty pixels −inf); dims = (frame, z=depth, x=lateral, y=elevation) | |
| | `custom/saf_bmode/coordinates` | (n_z, n_el, n_el, 3) | float32 | m | per-pixel `[x, y, z]` positions of the label volume (target ± ~2 mm depth window) | |
| |
| ## Subject Metadata |
| No human or animal subjects / no PHI. Each file stores `metadata/subject/type`: |
| `simulated phantom` for the Field II simulations, `phantom` for the measured |
| `experiment__*` scans. Creator attribution is stored per file in `metadata/credit`. |
| |
| ## Data Validation |
| `reconstruct.py` (**runnable, verified** — official `zea` API, no fallback code) |
| loads one zea acquisition, reads its acquisition parameters via |
| `zea.Config.from_path('pipeline.yaml')` + `File.load_parameters`, beamforms the |
| rotation frame closest to ±90° rotation magnitude (the frame where an off-axis target |
| lies in-plane; this handles signed encoder angles too — measured scans run 0 → ~−180°) |
| with the native `zea.Pipeline` op chain **Cast → Demodulate → Beamform(delay_and_sum) → |
| EnvelopeDetect → Normalize → LogCompress** defined in `pipeline.yaml`, and writes a |
| two-panel PNG: the B-mode image, and the per-frame probe **rotation angle** |
| (from `metadata/probe_pose`, plotted in degrees) so downstream users know how to |
| interpret the frame axis — the special data this dataset adds: |
| ``` |
| python reconstruct.py --input data/baseline_R45_H8__point_z080_r4.hdf5 --output out.png |
| ``` |
| The rotational **eSAF** across frames — the contribution of this dataset — is implemented in |
| `matlab/saf` (source) (`recon_3d` → `safrot_backproj`); per-probe before/after eSAF reference |
| images and a FWHM-vs-depth overview accompany the MATLAB `.mat` release |
| (`sim/dataset_overview.m`, source), and the resulting paired SAF volume is stored as |
| the `custom/saf_bmode` custom field of every `.hdf5` (see Dataset Format above). |
|
|
| ## Known Issues |
| - **Paired SAF label — on-axis targets (r0 = 0) do not narrow, by design.** eSAF |
| refocuses the *rotational elevation smear*; a target sitting on the rotation axis has |
| essentially no smear, so its `saf_bmode` label volume is not sharper than the input (arc-FWHM |
| gain ≈ 1). This is expected physics, not a defect — the 40 on-axis cases (median gain |
| 1.00×) are included so the pair covers the degenerate no-smear case. Off-axis targets |
| (n=120, median gain 1.75×, up to ~12×) and paired/oblique targets (n=30, median 3.71×) |
| improve clearly; targets at the focal depth (~45 mm) and weak-elevation-focus probes |
| (`efocus_deep_90`, `elev_unfocused`) have less smear to recover. Across all 195 cases, |
| median arc-FWHM gain is 1.36× (42 cases < 1×, mostly the on-axis/near-focus group above). |
| Arc-FWHM is measured on a **centred** reconstruction: the smear circle passes through both |
| the rotation axis and the target (not a circle centred on the rotation axis). The eSAF |
| back-projection uses a fixed elevational focus of 45 mm; per-depth focus tuning (see |
| `docs/eSAF_focus_depth_study_JP.md`, source) can further sharpen deep off-axis cases but was |
| not applied here (single as-designed focus). |
| - **Measured phantom depth window.** The real reflector bead sits **~4 mm off the rotation |
| axis** (not on-axis) and, for each scan, slightly deeper than the folder's nominal depth |
| label; labels are reconstructed over the interactively-identified reflector depth window |
| (not a naive nominal-depth ± 2 mm window), which matters because a mis-centred window can |
| pick up near-axis clutter instead of the actual bead. |
| - **Simulated** data (Field II spatial-impulse-response model): realistic transducer |
| field, but no tissue attenuation, aberration, multiple scattering, or electronic |
| noise. Not a substitute for measured data. |
| - Speed of sound is 1490 m/s, matching the paper Table 1 and the experiment. |
| - A single normal plane-wave transmit per rotation angle is simulated (the dataset |
| stores n_tx = 1); multi-angle compounding is left to downstream users. |
| - **Measured scans:** acquired as 7-angle CPWC; only the **centre (0°) plane wave** is |
| kept here to match the n_tx = 1 schema. The dwell frames per angle are averaged before |
| storage (noise reduction). Real reflectors are not ideal point scatterers — expect |
| reverberation/clutter near the surface and specular layering; rotation angles are the |
| measured encoder values (slightly non-uniform, full span ≈ 180°, sign per encoder |
| direction). The elevational lens focus is the nominal 45 mm, but the effective |
| back-projection focus for eSAF is depth-dependent on real data (see |
| `docs/eSAF_focus_depth_study_JP.md`, source). |
|
|
| ## Raw Source Data |
| The raw, pre-conversion acquisition/simulation outputs that were processed into the |
| zea `.hdf5` files above are archived (same CC BY 4.0 license) at |
| <https://huggingface.co/datasets/RyoMurakami/OpenH-RF-eSAF-raw>: the raw Verasonics |
| per-line channel-RF captures (`RFdata_line*.mat` + encoder logs) for the 5 measured |
| acquisitions, and the per-case MATLAB intermediates (raw RF, in-plane DAS, eSAF |
| output) for the 190 simulated cases. See that repository's README for how each |
| maps to `data/*.hdf5` here. |
|
|
| ## Ethical Considerations |
| None. The data is either fully synthetic (Field II) or measured on an **inanimate |
| phantom** — no human or animal subjects, no PHI, no consent/IRB constraints. |
|
|
