ubc/module_A/README.md

metadata

name: ubc-module-a
pretty_name: UBC Module A Corrected Synthetic-Channel S-WAVE Phantom Dataset
license: cc-by-4.0
task_categories:
  - image-to-image
tags:
  - open-h-rf
  - zea
  - ultrasound
  - rf
  - elastography
  - phantom
  - synthetic-data
  - 3d
language:
  - en
size_categories:
  - 1K<n<10K

UBC Module A — Synthetic-Channel S-WAVE Liver Fibrosis Phantom

Scan-converted scanline B-mode of a CIRS 039 liver fibrosis phantom, reconstructed from the synthetic channel data in acquisitions/.

Dataset Description

This submission contains eight 3-D Shear-Wave Absolute Vibro-Elastography (S-WAVE) acquisitions of CIRS model 039 Shear Wave Liver Fibrosis Phantom samples. The source scanner export contains beamformed 64-line RF rather than measured pre-beamforming channel capture. Accordingly, every submitted zea raw_data frame (stored at /tracks/track_0/data/raw_data) is explicitly labeled in-silico/synthetic: a dense point-scatterer field is estimated from one corrected source line-RF frame and forward-simulated through a documented 64-transmit, 128-receive-element model.

The files are physically delay-consistent and reconstruct with zea-native scanline delay-and-sum. They are not recovered or measured scanner channel data, and they must not be represented as such.

Dataset Contributor(s)

• Zongze Li zongze@student.ubc.ca (dataset-preparation contact)
• Yu Chung Lee
• Qi Zeng
• Wanwen Chen
• Zijian Wu
• Yuxin Chen
• Patrick Boyan Chen
• Michael Frew
• Tajwar Abrar Aleef
• Hamid Moradi
• Mohammad Honarvar
• Septimiu E. Salcudean
• Robert Rohling
• The University of British Columbia (UBC), Department of Electrical and Computer Engineering and School of Biomedical Engineering

Dataset Creation Date

09/01/2026 for this corrected zea-beamformable synthetic-channel package. The source phantom acquisitions predate this packaging.

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

The package supports raw-to-B-mode reconstruction tests, ultrasound beamforming research, synthetic-channel modeling, per-plane RF analysis, and 3-D placement using the retained motor-plane geometry. The original proposal described derived S-WAVE elasticity estimates or maps; those products are not available in this release due to missing data. /custom/labels/factory_elasticity_kpa is the CIRS factory-rated nominal stiffness, not a derived S-WAVE estimate.

Dataset Characterization

• Data Collection Method: physical phantom source acquisition followed by a deterministic in-silico channel simulation.
• Labeling Method: CIRS factory-rated nominal phantom elasticity.
• Acquisition System: Ultrasonix/Sonix with 4DEC9-5/10 end-firing 3-D probe.
• Submitted Data Tier: phantom / simulation.
• Simulation Framework: custom deterministic NumPy/SciPy forward simulator; files and reconstruction were validated with zea 0.1.4.

Acquisition and simulation details:

• Source system: Ultrasonix/Sonix with 4DEC9-5/10 end-firing 3-D probe.
• Source content: 20 motor planes × 25 retained temporal RF frames × 64 beamformed scan lines × 5,196 axial samples per case.
• Corrected RF ordering: the 108 stored 16-line events per plane contain two complete setup images at events 0-3 and 4-7, followed by four sector-major groups of 25 temporal frames. Temporal frame k is assembled from raw events [8+k, 33+k, 58+k, 83+k].
• Temporal frames: all corrected source frames 0-24 are retained; none are deleted or wrapped.
• Cases / nominal stiffnesses: 1.83, 2.8, 6.2, 6.39, 7.79, 11.63, 17.47, and 21.23 kPa.
• Source line-RF sampling frequency: 40 MHz.
• Source temporal sampling: 250 Hz (4 ms between retained RF frames within a plane); 20 motor planes span approximately 27.78° from first to last centre.
• Simulated channel sampling frequency: 20 MHz.
• Transmit/demodulation center frequency: 4 MHz.
• Sound speed used by simulation and reconstruction: 1,540 m/s.
• Probe geometry: 128 elements on a 10.0-mm-radius convex arc with 0.17-mm pitch and 6.5-mm elevation height.
• Sector: 64 focused lines spanning 124.68°; the manufacturer-listed 149° value is the extended-sector capability, not the normal sector used here.
• Transmit focus: 30 mm; modeled transmit aperture: F/1.5.
• Simulated inter-transmit interval: 250 microseconds; the final interval in each one-frame file is zero because no later transmit is stored in that file.
• Scatterers: 256 per source line (16,384 per output frame), with deterministic frame-specific sub-line and sub-sample jitter.
• Channel trace: 3,546 samples (177.3 microseconds), including a final exact-zero tail of 400 samples (20 microseconds).
• Quantization: int16, scaled to an absolute peak of 26,000; no sample reaches int16 full scale.

Processing the Dataset

The acquisitions can be processed with the pipeline.yaml definition in this folder and the zea library.

zea streams the data from the Hugging Face Hub and processes it according to the pipeline. You can try it out with the following command:

zea process \
  --dataset hf://nvidia/Open-H-RF/ubc/module_A/acquisitions/case_1.83/ubc_swave_cirs_1.83_p10_f13.hdf5 \
  --config hf://nvidia/Open-H-RF/ubc/module_A/pipeline.yaml

Alternatively, you can use the reconstruct.py script as provided in the Open-H-RF GitHub repository.

reconstruct.py reconstructs one frame (default case_1.83/ubc_swave_cirs_1.83_p10_f13.hdf5); reconstruct_multiframe.py reconstructs the temporal sequence at one motor plane (CASE_ID, PLANE, N_FRAMES) into an animated GIF.

Dataset Format

zea v0.1.4

There are 8 × 20 × 25 = 4,000 one-frame HDF5 files. One file per source frame keeps full zea schema validation and reconstruction memory-bounded. For motion analysis, group files by case and motor plane, then order f00 through f24; /custom/source_provenance/source_timing retains the source clock index, within-plane temporal offset, and relative plane timestamp.

module_A/
  acquisitions/
    case_1.83/
      ubc_swave_cirs_1.83_p00_f00.hdf5
      ...
    case_2.8/
      ...
    ...
  README.md
  pipeline.yaml

Each HDF5 file contains the following per-sample features:

Numeric arrays use zea 0.1.4's native frame-chunked Blosc/Zstd plus bitshuffle compression; reading these arrays requires hdf5plugin, which is imported by zea.

Name	Shape	Dtype	Units	Description
/tracks/track_0/data/raw_data	(1, 64, 3546, 128, 1)	int16	scaled ADC-like counts	Synthetic RF ordered frame, transmit, axial sample, receive element, RF component.
/probe/probe_geometry	(128, 3)	float32	m	Curved-array element positions.
/tracks/track_0/scan/polar_angles	(64,)	float32	rad	Focused transmit angles.
/tracks/track_0/scan/t0_delays	(64, 128)	float32	s	Per-transmit element delays.
/tracks/track_0/data/image/values	(1, 256, 64, 1)	uint8	display intensity	Native line-RF reference display; not used as a reconstruction input.
/custom/source_provenance/source_native_line_rf	(64, 5196)	int16	source ADC counts	Preserved source beamformed line RF for this selection.
/custom/source_provenance/source_event_indices	(4,)	int32	zero-based event index	Original 16-line E-scan event selected for sectors 0-3.
/custom/simulation/scatterer_positions	(16384, 3)	float32	m	Point-scatterer positions used for channel simulation.
/custom/source_provenance/*	mixed	mixed	documented per field	Source indices, plane transform, timing, and excitation settings.

Synthetic provenance is written at the HDF5 root and on the raw-data dataset: synthetic=true, in_silico=true, and data_origin=in-silico/synthetic.

Dataset Quantification

• Number of source acquisitions: 8.
• Number of motor planes per acquisition: 20.
• Number of retained temporal RF frames per plane: 25.
• Number of submitted HDF5 samples: 4,000.
• Train / validation / test split: not predefined.
• Per-sample raw tensor: 1 × 64 × 3546 × 128 × 1, int16.
• Per-sample source line-RF tensor: 64 × 5196, int16.
• Exact HDF5 payload size: 108,889,767,936 bytes (108.890 GB; 101.412 GiB).

Subject Metadata

The source consists of eight phantom acquisitions only, one for each listed factory-rated stiffness. There are no human or animal subjects and no subject demographics. The phantom model is CIRS model 039 Shear Wave Liver Fibrosis Phantom.

Data Validation

The contributor reports validation with Python 3.12.3 and zea 0.1.4. The contributor's reconstruction reads only the zea raw_data field and acquisition parameters, not the stored image or preserved source line RF:

Cast to float32
  -> RF demodulation
  -> zea delay_and_sum with enable_scanline=true
     and enable_aligned_apodization=true
  -> Envelope detection
  -> 99.5th-percentile normalization
  -> -50..0 dB log compression
  -> sector scan conversion
  -> PNG

In scanline mode the output has 64 angular lines—one per stored focused transmit. zea constructs the one-line-per-transmit grid and the one-hot aligned transmit mask internally; no custom flat_pfield or transmit-weight code is used.

pipeline.yaml records the reconstruction configuration. zlims: [0.0001, 0.100023] are line depths from each transmit origin on the curved element surface.

The contributor reports structural checks across all files, plus full zea schema validation and raw-only reconstruction on three distributed samples from each case (24 samples). For those samples, the preserved source line RF was also compared with the original E-scan events.

This HF release includes the HDF5 files, this card, and the pipeline configuration. Review outputs, standalone reconstruction scripts, and validation sidecars are not included.

Known Issues

• The measured source is beamformed line RF. The submitted 128-channel data are deterministic forward simulations conditioned on that source.
• The simulation preserves source-derived spatial and temporal contrast but cannot recover proprietary scanner receive processing or true measured element-level noise/coupling.
• The stored image is a reference only and is deliberately excluded from the reconstruction path.
• Mechanical excitation frequencies (40, 50, and 60 Hz) are simultaneous. Configured phases are retained in source setting units; absolute actuator-to-ultrasound phase synchronization is not claimed.
• A scanner TGC curve, probe bandwidth, and exact transmit waveform were not available. Reconstruction therefore applies no TGC and uses the documented simulation pulse.

Ethical Considerations

The data are phantom acquisitions only. There are no human subjects, no PHI, and no patient demographics.