| --- |
| Name: "OpenH-RF UBC Module A Corrected Synthetic-Channel S-WAVE Phantom Dataset" |
| license: cc-by-4.0 |
| task_categories: |
| - image-to-image |
| tags: |
| - openh-rf |
| - zea |
| - ultrasound |
| - rf |
| - elastography |
| - phantom |
| - synthetic-data |
| - 3d |
| language: |
| - en |
| size_categories: |
| - 1K<n<10K |
| --- |
| |
| # Module A |
|
|
| ## 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 Contributors |
|
|
| University of British Columbia. Primary contact: Zongze Li |
| (`zongze@student.ubc.ca`). Proposed contributors retained from the original |
| Module A data card: Septimiu E. Salcudean, Robert Rohling, Qi Zeng, Tajwar Abrar |
| Aleef, Hamid Moradi, Mohammad Honarvar, Wanwen Chen, Zijian Wu, Yuxin Chen, Yu |
| Chung Lee, Zongze Li, Patrick Boyan Chen, and Michael Frew. |
|
|
| ## 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 |
|
|
| The dataset package is licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/). |
|
|
| ## 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. |
|
|
| ## Dataset Format |
|
|
| 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. |
|
|
| ```text |
| 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: |
|
|
| ```text |
| 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. The phantom model is CIRS model 039 Shear Wave |
| Liver Fibrosis Phantom. Institutional data-release approval was confirmed in |
| the original contributor data card. |
|
|
