weillcornell/README.md

metadata

license: cc-by-4.0
pretty_name: OpenH-RF QUS Phantom Dataset
task_categories:
  - image-to-image
  - feature-extraction
tags:
  - ultrasound
  - rf
  - openh-rf
  - quantitative-ultrasound
  - phantom
  - raw-channel-data
language:
  - en
size_categories:
  - n<1K

OpenH-RF QUS Phantom Dataset

Pre-beamformed RF channel data from three homogeneous tissue-mimicking phantoms. Each zea HDF5 acquisition is self-contained and includes raw RF, model-derived theoretical backscatter coefficient (BSC), direct per-frame Nakagami maps, and 20-frame pooled Nakagami references.

OpenH-RF Release Inventory

Current OpenH-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.

Contributors

Shangke Liu, Tipu Sultan, Cameron Hoerig, and Jonathan Mamou; Biomedical Ultrasound Research Laboratory (BURL), Weill Cornell Medicine.

Contact: Shangke Liu, shl4035@med.cornell.edu

Dataset Summary

• Verasonics Vantage 256 and GE9LD linear array
• 192 elements, 0.23 mm pitch, 5.2083 MHz center frequency
• One normal-incidence plane wave per frame
• 20.8333 MHz RF sampling; 1540 m/s sound-speed metadata
• 3 phantoms x 2 operators x 20 probe placements x 20 frames
• 120 acquisitions and 2400 frames
• Phantom-only data; no human or animal subjects, clinical metadata, or PHI
• No predefined train/validation/test split

Keep all frames from one acquisition in the same split.

Files

data/<scan_id>.hdf5                         self-contained zea acquisitions
reconstruct.py                              B-mode and QUS example
pipeline.yaml                               zea reconstruction pipeline
LICENSE                                     CC BY 4.0 license
ac1_15m_SK_pipeline.png                     reference zea reconstruction

Scan IDs use ac<number>_<phantom>_<operator>, for example ac1_15m_SK. Phantom IDs are 15m, 18m, and 60m; operator IDs are SK and TP; acquisition numbers run from 1 to 20.

HDF5 Contents

Each file follows zea 0.1.6 and contains one track. Raw RF is stored as int16 ADC counts without demodulation, decimation, or resampling.

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

The five QUS products are zea Map fields with values, Cartesian coordinates in [x,y,z] order and metres, description, unit, min, and max. The BSC field also contains 157 labels of the form 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.

Metadata uses metadata.subject.type="phantom" and a phantom ID. Anatomical annotations and anatomical-view annotations are intentionally omitted. Plane-wave acquisition is recorded in the file description, and the linear array geometry is recorded in the probe fields.

Suggested Tasks

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.

All QUS maps are public reference targets, not hidden competition labels.

Quick Start

For the current release, use an OpenH-RF environment with zea==0.1.6 and a supported Keras backend:

KERAS_BACKEND=jax python reconstruct.py \
  --input data/ac1_15m_SK.hdf5 \
  --output ac1_15m_SK_pipeline.png \
  --frame 0

The script defines the pipeline in code, writes pipeline.yaml, saves the B-mode PNG, then prints the selected frame's RF shape, BSC band and unit, QUS map shapes, and direct per-frame-to-pooled Nakagami errors.

Validation

The original 120 HDF5 files passed zea 0.1.3 File.validate() and File.validate_spec(). Raw RF and embedded maps were checked for shape, dtype, finite values, coordinates, labels, min/max, and the documented frame-broadcast behavior. The original files used zea 0.1.3's default Blosc/Zstd+bitshuffle compression.

The reference uses frame 0 and the common 597 x 300 zea grid at approximately 3-25 mm depth.

Limitations

• 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.
• This release contains Verasonics data only.

License

CC BY 4.0. See LICENSE. Commercial and non-commercial reuse is permitted with attribution. The contributors confirm that these phantom data are cleared for release under CC BY 4.0.