| --- |
| 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 |
|
|
| ```text |
| 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: |
|
|
| ```bash |
| 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. |
|
|
