wpi/README.md

metadata

name: wpi
pretty_name: eSAF Rotational 3D US Raw Channel Data (Medical FUSION Lab, WPI)
license: cc-by-4.0
task_categories:
  - image-to-image
tags:
  - ultrasound
  - rf
  - open-h-rf
  - 3d
  - beamforming
  - elevational-saf
language:
  - en
size_categories:
  - n<1K

Rotational 3D Ultrasound Raw Channel Data for Elevational SAF

Top view down the rotation axis of a point target at 20 mm depth, 6 mm off-axis, data/tall_elev_H12__point_z020_r6.hdf5. Magenta is the naive per-angle reconstruction, filling in as the array (white line) sweeps 180° about the rotation axis (small circle); cyan is the paired eSAF label shipped in the file; white is where both agree. eSAF collapses the rotational smear arc back onto the target (arc-FWHM 1.26 → 0.39 mm).

Dataset Description

Rotational 3D ultrasound acquisitions of point, pair and off-axis targets, captured with an elevation-focused 1D linear array rotated 180° about its axial axis (1° steps). Each acquisition stores the raw per-element channel RF of a single normal plane-wave transmit at every rotation angle, i.e. the data before in-plane beamforming, which enables flexible offline beamforming and elevational Synthetic Aperture Focusing (eSAF). Every file also carries the eSAF-reconstructed 3D volume as a paired label.

The release is mostly simulated (Field II): a grid of 10 probe types × 19 targets spanning depths where the elevational beam thickness (the artifact eSAF corrects) varies. It is complemented by 5 measured phantom rotational scans with the physical Japan Probe 68-element array (same geometry as the simulation) at 10–45 mm depth. No human or animal subjects.

Dataset Contributor(s)

• Ryo Murakami (contact)
• Medical FUSION Laboratory, Worcester Polytechnic Institute

Dataset Creation Date

06/15/2026

License / Terms of Use

Creative Commons Attribution 4.0 International (CC BY 4.0). Retain attribution and identify modifications when reusing the data.

Intended Usage

Advanced beamforming and elevational resolution recovery for rotational 3D US (eSAF), elevation-PSF / aperture-growth studies, and a reproducible raw-channel-data benchmark for rotational synthetic-aperture reconstruction.

Dataset Characterization

• Data Collection Method: synthetic and phantom.
  • Simulated (190): Field II (MATLAB, xdc_focused_array + calc_scat_multi), scatterers rotated about the axial axis with the transducer fixed. 10 probe types vary lateral aperture (n_el 32/68/128, pitch 0.1/0.2/0.3 mm), elevation height H (4/8/12 mm) and elevation focus R (25/45/90 mm or unfocused), encoded in the probe name (tall_elev_H12 = H 12 mm; baseline_R45_H8 = R 45 mm, H 8 mm) and in probe/*.
  • Measured (5): rotational scans of the Japan Probe 68-element array on a wire/point phantom with a Galil-controlled 180° rotation, acquired as 7-angle CPWC, time-tag-synced to the motor angles and reduced to the centre (0°) plane wave per angle to match the simulation schema.
• Labeling Method: synthetic ground truth. Target positions are exact, and each file's description attribute records probe and target, e.g. probe=tall_elev_H12 target=point_z020_r6 r0=6.0mm z=20.0mm. The paired eSAF volume (custom/saf_bmode) is the label.
• Acquisition system: Japan Probe JP_Linear_68 (baseline): 68 elements, pitch 0.2 mm, element width 0.15 mm, element height 8 mm, elevational lens focus 45 mm; center frequency 10 MHz; sampling 40 MHz; sound speed 1490 m/s; one normal plane-wave transmit per rotation angle; 180° rotation in 1° steps. Parameters match the paper simulation.

Processing the Dataset

The acquisitions can be processed with the reconstruct.py script as provided in the Open-H-RF GitHub repository, together with the pipeline.yaml definition in this folder and the zea library. The script streams the data from the Hugging Face Hub, beamforms the rotation frame closest to ±90° (where an off-axis target lies in-plane) and plots it beside the per-frame rotation angle from metadata/probe_pose. Set ZEA_FILE and FRAME at the top of the script to pick another acquisition or frame. The default, frame 90 (~−90°) of data/experiment__acq_exp_30mm.hdf5, gives:

The rotational eSAF itself (in-plane DAS → recon_3d → safrot_backproj) is the published MATLAB implementation; its output is shipped in every file as custom/saf_bmode:

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

Dataset Format

zea v0.1.6

One zea HDF5 file per acquisition, single track. The raw channel RF and scan parameters are in the standard data/scan groups (tracks/track_0); the probe rotation per frame is the metadata/probe_pose trajectory (euler_xyz, radians, rotation in the z component, zero translation; sampling_frequency = 1.0 Hz is nominal, one pose per frame).

The paired eSAF label is the zea custom field custom/saf_bmode: values is (1, z, x, y) float32 in dB (0 dB = volume max, empty pixels −inf) over a ±2 mm depth window about the target, and coordinates holds the per-pixel [x, y, z] in metres. It lives in custom rather than the data group because it is a single frame, while raw_data has ~180. The per-case arc-FWHM before/after is in the description of custom/saf_bmode/values.

Pre-processing: none for the simulations beyond the forward model; for the measured scans, frame-to-angle synchronisation, per-angle dwell averaging and centre-plane-wave selection. Both remain raw per-element RF (not demodulated or decimated).

Dataset Quantification

Current Open-H-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 axis is listed above under Data Collection Method; each file's own description attribute gives its exact probe/target/r0/depth. (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 beamforms a single rotation frame with the pipeline.yaml chain (Cast → Demodulate → Beamform(delay_and_sum) → EnvelopeDetect → Normalize → LogCompress) and plots the stored rotation trajectory beside it, as a check on the acquisition parameters and the frame-to-angle mapping.

The eSAF labels were checked per case with the arc-FWHM of the rotational smear before and after eSAF, shown here annotated for the case in the hero image:

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).

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 or IRB constraints.

Raw Source Data

The raw pre-conversion outputs are archived under the same CC BY 4.0 license at https://huggingface.co/datasets/RyoMurakami/OpenH-RF-eSAF-raw: the raw Verasonics per-line channel-RF captures (with 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.

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.