weillcornell/README.md

metadata

name: weillcornell
license: cc-by-4.0
pretty_name: Weill Cornell QUS Phantom Dataset
task_categories:
  - image-to-image
  - feature-extraction
tags:
  - ultrasound
  - rf
  - open-h-rf
  - quantitative-ultrasound
  - phantom
  - raw-channel-data
language:
  - en
size_categories:
  - n<1K

Weill Cornell QUS Phantom Dataset

B-mode (frame 0) and 20-frame pooled Nakagami maps from data/ac10_15m_SK.hdf5. The BSC curves are material-model references for the three phantoms; pooled Nakagami maps are statistical references.

Dataset Description

Pre-beamformed RF channel data from three homogeneous tissue-mimicking phantoms, acquired for quantitative ultrasound (QUS). Next to the raw RF, each acquisition carries the phantom's model-derived theoretical backscatter coefficient (BSC), direct per-frame Nakagami maps, and 20-frame pooled Nakagami references, so single-frame QUS estimators can be trained and evaluated against targets stored in the same file.

Dataset Contributor(s)

• Shangke Liu shl4035@med.cornell.edu (contact)
• Tipu Sultan
• Cameron Hoerig
• Jonathan Mamou
• Biomedical Ultrasound Research Laboratory (BURL), Weill Cornell Medicine

Dataset Creation Date

Not specified by the contributors.

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

1. Reconstruct B-mode from one frame of raw RF.
2. Predict the phantom's theoretical BSC curve from one RF frame. This is a material-model target, not a local experimentally estimated BSC curve.
3. Predict pooled Nakagami m or omega from one RF frame. Use the supplied direct per-frame map as the single-frame baseline.

For Nakagami predictions, report MAE/RMSE and map correlation against the pooled reference. For BSC predictions, report the frequency range and unit and state whether evaluation uses linear BSC or a specified dB conversion.

Dataset Characterization

• Data collection method: phantom — three homogeneous tissue-mimicking phantoms (15m, 18m, 60m), each scanned by two operators (SK, TP) at 20 probe placements
• Labeling method: derived — BSC from the phantom material model; Nakagami maps estimated from the RF
• Acquisition system: Verasonics Vantage 256, GE9LD linear array, 192 elements, 0.23 mm pitch, 5.2083 MHz center frequency, 20.8333 MHz RF sampling
• Transmit sequence: one normal-incidence plane wave per frame; 1540 m/s sound speed

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/weillcornell/data/ac10_15m_SK.hdf5 \
  --config hf://nvidia/Open-H-RF/weillcornell/pipeline.yaml

Alternatively, you can use the reconstruct.py script as provided in the Open-H-RF GitHub repository. Besides the B-mode, it prints the selected frame's BSC band and unit, the QUS map shapes, and the error of the direct per-frame Nakagami maps against the pooled references.

Dataset Format

zea v0.1.6

Each file contains one track. Raw RF is stored as int16 ADC counts without demodulation, decimation, or resampling. The five QUS targets are zea Map fields next to raw_data, with Cartesian coordinates in metres. The BSC field has 157 frequency labels (frequency_hz=<value>) spanning 3.3162435-6.4900716 MHz.

Map grids are (z,x)=(26,35) for 15m and 18m, and (53,35) for 60m. The analysis windows are approximately 2.96 mm axial by 4.37 mm lateral with 75% overlap. Nakagami maps use normal-incidence delay-and-sum beamforming, Hann receive apodization, and intensity-domain maximum-likelihood fitting, with omega = E[A^2].

The theoretical BSC is a homogeneous phantom material property: each phantom has one curve, broadcast over space and all 20 frames. The pooled Nakagami maps are also repeated along the frame axis so every single-frame input has the same 20-frame reference. The pooled estimate includes the selected input frame.

Dataset Quantification

Current Open-H-RF release: 120 HDF5 files; 1.00 GB (1,002,700,800 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 / frames: 120 acquisitions (3 phantoms x 2 operators x 20 probe placements, one HDF5 file each), 20 frames per acquisition — 2,400 frames total
• File naming: data/ac<n>_<phantom>_<operator>.hdf5, with n from 1 to 20, e.g. ac10_15m_SK.hdf5
• Splits: no predefined train/validation/test split. Keep all frames from one acquisition in the same split.

Field under tracks/track_0/data/	Shape	dtype	Unit	Meaning
raw_data	(20,1,n_ax,192,1)	int16	ADC counts	Raw RF input
theoretical_bsc/values	(20,z,x,157)	float32	m^-1 sr^-1	Model-derived BSC target
nakagami_m_per_frame/values	(20,z,x)	float32	1	Direct single-frame shape estimate
nakagami_omega_per_frame/values	(20,z,x)	float32	a.u.^2	Direct single-frame spread estimate
nakagami_m_pooled/values	(20,z,x)	float32	1	20-frame pooled shape reference
nakagami_omega_pooled/values	(20,z,x)	float32	a.u.^2	20-frame pooled spread reference

Subject Metadata

No human or animal subjects. metadata/subject/type is phantom and metadata/subject/id names the phantom (phantom_15m, phantom_18m, phantom_60m).

Data Validation

A zea.Pipeline (cast → demodulate → DAS beamforming → envelope detection → normalization → log compression) is defined in pipeline.yaml, on a common 301 x 600 grid (isotropic ~0.073 mm pixels) for every acquisition. Its output for frame 0 of ac10_15m_SK is shown at the top of this card. Raw RF and the embedded maps were checked for shape, dtype, finite values, coordinates, labels, min/max, and the frame-broadcast behavior described above.

Known Issues

• Acquisition timestamps, PRF, explicit TGC curves, and emitted waveforms are unavailable; do not use these frames for calibrated temporal or flow analysis.
• Repeated frames are strongly correlated.
• BSC targets are model-derived references, not independent experimental BSC measurements; there are three unique phantom curves.
• Pooled Nakagami maps are lower-variance statistical references, not independent physical ground truth.
• Nakagami omega depends on gain, attenuation, beam sensitivity, and RF amplitude scale; it is not system-independent.

Ethical Considerations

Phantom-only data; no human or animal subjects, clinical metadata, or PHI. The contributors confirm that these phantom data are cleared for release under CC BY 4.0.