| --- |
| 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) |
|
|
| > One `.hdf5` per acquisition, zea file format. Raw **per-element channel data** |
| > (pre-beamforming). See `manifest.json` for the full list and `../reconstruct.py` |
| > + `../pipeline.yaml` for the reference reconstruction. |
|
|
| ## 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 (see `LICENSE`). Simulated data — no IP/consent constraints. |
|
|
| ## 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` (with `../sim/sim_probe_catalog.m` / |
| `../sim/sim_target_catalog.m`): 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` |
| 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 `manifest.json`. |
| (The earlier 18-acquisition set generated by `../sim/batch_generate_fieldii.m` + |
| `../sim/mat_to_zea.py`, and a pure-Python analytic forward model `../sim/forward_sim.py`, |
| remain available as compatible alternatives 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`) 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` |
| (so the schema matches the simulation, n_tx = 1), then converted with the same |
| `../sim/sim_dataset_to_zea.py`. 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 |
| `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 (`makeslices_field2.m`). |
|
|
| ## Dataset Format |
| zea file format (HDF5), one file per acquisition. 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). Rotation angle per frame is |
| stored as a zea **custom** element at `custom/scan/rotation_angles_deg`. Every file is |
| written with `zea.File.create()` (`../sim/sim_dataset_to_zea.py`) 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** at |
| `custom/labels/saf_bmode_volume` (with `custom/labels/saf_{x,y,z}_mm` axes). 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`: 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` and written into the zea |
| file by `../sim/pack_saf_labels.py`. The stored volume is the normalized envelope over |
| a thin depth window (±2 mm) about the target; per-case arc-FWHM before/after and gain |
| are in `manifest.json` and on the dataset (`arc_fwhm_before_after_mm` attribute). |
|
|
| 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`: |
| 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`). The zea `.hdf5` acquisitions are **hosted on Hugging |
| Face** at <https://huggingface.co/datasets/RyoMurakami/OpenH-RF-eSAF> (git-LFS; not |
| committed to the GitHub code repo). The MATLAB `.mat`/`_ref.png` intermediates are |
| reproducible from source and kept on lab storage. |
|
|
| ## Dataset Quantification |
| - **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 `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 `custom/scan/rotation_angles_deg`, not necessarily |
| uniform). |
| - **Total size on disk:** simulated ~0.6–5 MB per case (zea gzip; point-target RF is |
| sparse), measured ~80–92 MB per case (dense tissue RF); **~1.5 GB** for the full set |
| (including the paired `saf_bmode_volume` labels). |
| - **Train/val/test split:** N/A (benchmark / characterization set; the probe × depth × |
| radius axes are the intended study dimensions). |
| |
| ### Per-sample feature table |
| | field (HDF5 path) | shape | dtype | units | description | |
| |-----------------------------------|--------------------------------|---------|-------|-------------| |
| | `data/raw_data` | (180, 1, n_ax, 68, 1) | float32 | a.u. | raw per-element channel RF; dims = (frame=rotation, tx, axial, element, ch) | |
| | `scan/probe_geometry` | (68, 3) | float32 | m | element positions (lateral x, 0, 0) | |
| | `scan/sampling_frequency` | scalar | float32 | Hz | 4.0e7 | |
| | `scan/center_frequency` | scalar | float32 | Hz | 1.0e7 | |
| | `scan/sound_speed` | scalar | float32 | m/s | 1490 | |
| | `scan/initial_times` | (1,) | float32 | s | t0 (first-sample time) | |
| | `scan/t0_delays` | (1, 68) | float32 | s | transmit delays (0; normal plane wave) | |
| | `scan/polar_angles` | (1,) | float32 | rad | transmit steering (0) | |
| | `custom/scan/rotation_angles_deg` | (180,) | float32 | deg | probe rotation angle per frame (zea custom element) | |
| | `custom/labels/saf_bmode_volume` | (n_el, n_el, n_z) | float32 | a.u. | **paired label**: elevational-SAF reconstructed 3D B-mode volume `B_SAF(x,y,z)` (normalized envelope) | |
| | `custom/labels/saf_x_mm` / `saf_y_mm` | (n_el,) | float32 | mm | lateral / elevation axes of `saf_bmode_volume` | |
| | `custom/labels/saf_z_mm` | (n_z,) | float32 | mm | depth axis of `saf_bmode_volume` (target ± ~2 mm) | |
|
|
| ## Subject Metadata |
| N/A (synthetic phantom; no subjects/PHI). |
|
|
| ## 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° (the frame where an off-axis target lies in-plane) 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** |
| (`custom/scan/rotation_angles_deg`) so downstream users know how to interpret the |
| frame axis — the special data this dataset adds, per reviewer feedback: |
| ``` |
| python ../reconstruct.py --input data/<probe>__<target>.hdf5 --output out.png |
| ``` |
| The rotational **eSAF** across frames — the contribution of this dataset — is implemented in |
| `../matlab/saf` (`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`), and the resulting paired `custom/labels/saf_bmode_volume` |
| is stored in 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_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`) 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`). |
|
|
| ## 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. |
|
|
