--- 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//.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 (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/__.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 : 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.