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ubc: restructure the data cards to the common layout

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  1. ubc/module_A/README.md +64 -105
  2. ubc/module_C/README.md +68 -152
ubc/module_A/README.md CHANGED
@@ -1,5 +1,6 @@
1
  ---
2
- Name: "OpenH-RF UBC Module A Corrected Synthetic-Channel S-WAVE Phantom Dataset"
 
3
  license: cc-by-4.0
4
  task_categories:
5
  - image-to-image
@@ -18,101 +19,86 @@ size_categories:
18
  - 1K<n<10K
19
  ---
20
 
21
- # Module A
22
 
23
- ## Dataset Description
24
 
25
- This submission contains eight 3-D Shear-Wave Absolute Vibro-Elastography
26
- (S-WAVE) acquisitions of CIRS model 039 Shear Wave Liver Fibrosis Phantom
27
- samples. The source scanner export contains beamformed 64-line RF rather than
28
- measured pre-beamforming channel capture. Accordingly, every submitted zea
29
- `raw_data` frame (stored at `/tracks/track_0/data/raw_data`) is explicitly
30
- labeled **in-silico/synthetic**: a dense
31
- point-scatterer field is estimated from one corrected source line-RF frame and
32
- forward-simulated through a documented 64-transmit, 128-receive-element model.
33
 
34
- The files are physically delay-consistent and reconstruct with zea-native
35
- scanline delay-and-sum. They are not recovered or measured scanner channel
36
- data, and they must not be represented as such.
37
 
38
- ![Example reconstruction](./assets/module_A.png)
 
 
39
 
40
- ## Dataset Contributors
41
 
42
- - **Organization:** The University of British Columbia (UBC), Department of
43
- Electrical and Computer Engineering and School of Biomedical Engineering.
44
- - **Dataset-preparation contact:** Zongze Li, zongze@student.ubc.ca.
45
- - **Contributors:** Zongze Li, Yu Chung Lee, Qi Zeng, Wanwen Chen, Zijian Wu,
46
- Yuxin Chen, Patrick Boyan Chen, Michael Frew, Tajwar Abrar Aleef, Hamid Moradi, Mohammad Honarvar, Septimiu E. Salcudean, Robert Rohling.
 
 
 
 
 
 
 
 
 
47
 
48
  ## Dataset Creation Date
49
 
50
- 09/01/2026 for this corrected zea-beamformable synthetic-channel package. The source
51
- phantom acquisitions predate this packaging.
52
 
53
  ## License / Terms of Use
54
 
55
- The dataset package is licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).
56
 
57
  ## Intended Usage
58
 
59
- The package supports raw-to-B-mode reconstruction tests, ultrasound
60
- beamforming research, synthetic-channel modeling, per-plane RF analysis, and
61
- 3-D placement using the retained motor-plane geometry. The original proposal
62
- described derived S-WAVE elasticity estimates or maps; those products are not
63
- available in this release due to missing data. `/custom/labels/factory_elasticity_kpa` is the CIRS
64
- factory-rated nominal stiffness, not a derived S-WAVE estimate.
65
 
66
  ## Dataset Characterization
67
 
68
- - Data Collection Method: physical phantom source acquisition followed by a
69
- deterministic in-silico channel simulation.
70
  - Labeling Method: CIRS factory-rated nominal phantom elasticity.
71
  - Acquisition System: Ultrasonix/Sonix with 4DEC9-5/10 end-firing 3-D probe.
72
  - Submitted Data Tier: phantom / simulation.
73
- - Simulation Framework: custom deterministic NumPy/SciPy forward simulator;
74
- files and reconstruction were validated with zea 0.1.4.
75
 
76
  Acquisition and simulation details:
77
 
78
  - Source system: Ultrasonix/Sonix with 4DEC9-5/10 end-firing 3-D probe.
79
- - Source content: 20 motor planes × 25 retained temporal RF frames × 64
80
- beamformed scan lines × 5,196 axial samples per case.
81
- - Corrected RF ordering: the 108 stored 16-line events per plane contain two
82
- complete setup images at events 0-3 and 4-7, followed by four sector-major
83
- groups of 25 temporal frames. Temporal frame `k` is assembled from raw events
84
- `[8+k, 33+k, 58+k, 83+k]`.
85
- - Temporal frames: all corrected source frames 0-24 are retained; none are
86
- deleted or wrapped.
87
- - Cases / nominal stiffnesses: 1.83, 2.8, 6.2, 6.39, 7.79, 11.63, 17.47,
88
- and 21.23 kPa.
89
  - Source line-RF sampling frequency: 40 MHz.
90
- - Source temporal sampling: 250 Hz (4 ms between retained RF frames within a
91
- plane); 20 motor planes span approximately 27.78° from first to last centre.
92
  - Simulated channel sampling frequency: 20 MHz.
93
  - Transmit/demodulation center frequency: 4 MHz.
94
  - Sound speed used by simulation and reconstruction: 1,540 m/s.
95
- - Probe geometry: 128 elements on a 10.0-mm-radius convex arc with 0.17-mm
96
- pitch and 6.5-mm elevation height.
97
- - Sector: 64 focused lines spanning 124.68°; the manufacturer-listed 149°
98
- value is the extended-sector capability, not the normal sector used here.
99
  - Transmit focus: 30 mm; modeled transmit aperture: F/1.5.
100
- - Simulated inter-transmit interval: 250 microseconds; the final interval in
101
- each one-frame file is zero because no later transmit is stored in that file.
102
- - Scatterers: 256 per source line (16,384 per output frame), with deterministic
103
- frame-specific sub-line and sub-sample jitter.
104
- - Channel trace: 3,546 samples (177.3 microseconds), including a final exact-zero
105
- tail of 400 samples (20 microseconds).
106
- - Quantization: `int16`, scaled to an absolute peak of 26,000; no sample reaches
107
- int16 full scale.
 
 
108
 
109
  ## Dataset Format
110
 
111
- There are 8 × 20 × 25 = **4,000** one-frame HDF5 files. One file per source
112
- frame keeps full zea schema validation and reconstruction memory-bounded.
113
- For motion analysis, group files by case and motor plane, then order `f00`
114
- through `f24`; `/custom/source_provenance/source_timing` retains the source
115
- clock index, within-plane temporal offset, and relative plane timestamp.
116
 
117
  ```text
118
  module_A/
@@ -129,8 +115,7 @@ module_A/
129
 
130
  Each HDF5 file contains the following per-sample features:
131
 
132
- Numeric arrays use zea 0.1.4's native frame-chunked Blosc/Zstd plus bitshuffle
133
- compression; reading these arrays requires `hdf5plugin`, which is imported by zea.
134
 
135
  | Name | Shape | Dtype | Units | Description |
136
  |---|---:|---|---|---|
@@ -144,8 +129,7 @@ compression; reading these arrays requires `hdf5plugin`, which is imported by ze
144
  | `/custom/simulation/scatterer_positions` | `(16384, 3)` | `float32` | m | Point-scatterer positions used for channel simulation. |
145
  | `/custom/source_provenance/*` | mixed | mixed | documented per field | Source indices, plane transform, timing, and excitation settings. |
146
 
147
- Synthetic provenance is written at the HDF5 root and on the raw-data dataset:
148
- `synthetic=true`, `in_silico=true`, and `data_origin=in-silico/synthetic`.
149
 
150
  ## Dataset Quantification
151
 
@@ -156,21 +140,15 @@ Synthetic provenance is written at the HDF5 root and on the raw-data dataset:
156
  - Train / validation / test split: not predefined.
157
  - Per-sample raw tensor: `1 × 64 × 3546 × 128 × 1`, `int16`.
158
  - Per-sample source line-RF tensor: `64 × 5196`, `int16`.
159
- - Exact HDF5 payload size: **108,889,767,936 bytes** (108.890 GB; 101.412
160
- GiB).
161
 
162
  ## Subject Metadata
163
 
164
- The source consists of eight phantom acquisitions only, one for each listed
165
- factory-rated stiffness. There are no human or animal subjects and no subject
166
- demographics. The phantom model is CIRS model 039 Shear Wave Liver Fibrosis
167
- Phantom.
168
 
169
  ## Data Validation
170
 
171
- The contributor reports validation with Python 3.12.3 and zea 0.1.4.
172
- The contributor's reconstruction reads only the zea `raw_data` field and
173
- acquisition parameters, not the stored image or preserved source line RF:
174
 
175
  ```text
176
  Cast to float32
@@ -184,41 +162,22 @@ Cast to float32
184
  -> PNG
185
  ```
186
 
187
- In scanline mode the output has 64 angular lines—one per stored focused
188
- transmit. zea constructs the one-line-per-transmit grid and the one-hot aligned
189
- transmit mask internally; no custom `flat_pfield` or transmit-weight code is
190
- used.
191
 
192
- `pipeline.yaml` records the reconstruction configuration.
193
- `zlims: [0.0001, 0.100023]` are line depths from
194
- each transmit origin on the curved element surface.
195
 
196
- The contributor reports structural checks across all files, plus full zea
197
- schema validation and raw-only reconstruction on three distributed samples
198
- from each case (24 samples). For those samples, the preserved source line RF
199
- was also compared with the original E-scan events.
200
 
201
- This HF release includes the HDF5 files, this card, and the pipeline
202
- configuration. Review outputs, standalone reconstruction scripts, and
203
- validation sidecars are not included.
204
 
205
  ## Known Issues
206
 
207
- - The measured source is beamformed line RF. The submitted 128-channel data are
208
- deterministic forward simulations conditioned on that source.
209
- - The simulation preserves source-derived spatial and temporal contrast but
210
- cannot recover proprietary scanner receive processing or true measured
211
- element-level noise/coupling.
212
- - The stored image is a reference only and is deliberately excluded from the
213
- reconstruction path.
214
- - Mechanical excitation frequencies (40, 50, and 60 Hz) are simultaneous.
215
- Configured phases are retained in source setting units; absolute
216
- actuator-to-ultrasound phase synchronization is not claimed.
217
- - A scanner TGC curve, probe bandwidth, and exact transmit waveform were not
218
- available. Reconstruction therefore applies no TGC and uses the documented
219
- simulation pulse.
220
 
221
  ## Ethical Considerations
222
 
223
- The data are phantom acquisitions only. There are no human subjects, no PHI,
224
- and no patient demographics.
 
1
  ---
2
+ name: ubc-module-a
3
+ pretty_name: "UBC Module A Corrected Synthetic-Channel S-WAVE Phantom Dataset"
4
  license: cc-by-4.0
5
  task_categories:
6
  - image-to-image
 
19
  - 1K<n<10K
20
  ---
21
 
22
+ # UBC Module A — Synthetic-Channel S-WAVE Liver Fibrosis Phantom
23
 
24
+ ![Example reconstruction](./assets/module_A.png)
25
 
26
+ *Scan-converted scanline B-mode of a CIRS 039 liver fibrosis phantom, reconstructed from the synthetic channel data in [`acquisitions/`](https://huggingface.co/datasets/nvidia/OpenH-RF/tree/main/ubc/module_A/acquisitions).*
 
 
 
 
 
 
 
27
 
28
+ ## Dataset Description
 
 
29
 
30
+ 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.
31
+
32
+ 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.
33
 
34
+ ## Dataset Contributor(s)
35
 
36
+ - Zongze Li <zongze@student.ubc.ca> (dataset-preparation contact)
37
+ - Yu Chung Lee
38
+ - Qi Zeng
39
+ - Wanwen Chen
40
+ - Zijian Wu
41
+ - Yuxin Chen
42
+ - Patrick Boyan Chen
43
+ - Michael Frew
44
+ - Tajwar Abrar Aleef
45
+ - Hamid Moradi
46
+ - Mohammad Honarvar
47
+ - Septimiu E. Salcudean
48
+ - Robert Rohling
49
+ - The University of British Columbia (UBC), Department of Electrical and Computer Engineering and School of Biomedical Engineering
50
 
51
  ## Dataset Creation Date
52
 
53
+ 09/01/2026 for this corrected zea-beamformable synthetic-channel package. The source phantom acquisitions predate this packaging.
 
54
 
55
  ## License / Terms of Use
56
 
57
+ [Creative Commons Attribution 4.0 International (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/legalcode.en). Retain attribution and identify modifications when reusing the data.
58
 
59
  ## Intended Usage
60
 
61
+ 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.
 
 
 
 
 
62
 
63
  ## Dataset Characterization
64
 
65
+ - Data Collection Method: physical phantom source acquisition followed by a deterministic in-silico channel simulation.
 
66
  - Labeling Method: CIRS factory-rated nominal phantom elasticity.
67
  - Acquisition System: Ultrasonix/Sonix with 4DEC9-5/10 end-firing 3-D probe.
68
  - Submitted Data Tier: phantom / simulation.
69
+ - Simulation Framework: custom deterministic NumPy/SciPy forward simulator; files and reconstruction were validated with zea 0.1.4.
 
70
 
71
  Acquisition and simulation details:
72
 
73
  - Source system: Ultrasonix/Sonix with 4DEC9-5/10 end-firing 3-D probe.
74
+ - Source content: 20 motor planes × 25 retained temporal RF frames × 64 beamformed scan lines × 5,196 axial samples per case.
75
+ - 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]`.
76
+ - Temporal frames: all corrected source frames 0-24 are retained; none are deleted or wrapped.
77
+ - Cases / nominal stiffnesses: 1.83, 2.8, 6.2, 6.39, 7.79, 11.63, 17.47, and 21.23 kPa.
 
 
 
 
 
 
78
  - Source line-RF sampling frequency: 40 MHz.
79
+ - 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.
 
80
  - Simulated channel sampling frequency: 20 MHz.
81
  - Transmit/demodulation center frequency: 4 MHz.
82
  - Sound speed used by simulation and reconstruction: 1,540 m/s.
83
+ - Probe geometry: 128 elements on a 10.0-mm-radius convex arc with 0.17-mm pitch and 6.5-mm elevation height.
84
+ - Sector: 64 focused lines spanning 124.68°; the manufacturer-listed 149° value is the extended-sector capability, not the normal sector used here.
 
 
85
  - Transmit focus: 30 mm; modeled transmit aperture: F/1.5.
86
+ - 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.
87
+ - Scatterers: 256 per source line (16,384 per output frame), with deterministic frame-specific sub-line and sub-sample jitter.
88
+ - Channel trace: 3,546 samples (177.3 microseconds), including a final exact-zero tail of 400 samples (20 microseconds).
89
+ - Quantization: `int16`, scaled to an absolute peak of 26,000; no sample reaches int16 full scale.
90
+
91
+ ## Processing the Dataset
92
+
93
+ The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/ubc/module_A/reconstruct.py) as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub.
94
+
95
+ `reconstruct.py` reconstructs one frame (default `case_1.83/ubc_swave_cirs_1.83_p10_f13.hdf5`); [`reconstruct_multiframe.py`](https://github.com/open-h/OpenH-RF/blob/main/datasets/ubc/module_A/reconstruct_multiframe.py) reconstructs the temporal sequence at one motor plane (`CASE_ID`, `PLANE`, `N_FRAMES`) into an animated GIF.
96
 
97
  ## Dataset Format
98
 
99
+ [zea v0.1.4](https://github.com/tue-bmd/zea)
100
+
101
+ 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.
 
 
102
 
103
  ```text
104
  module_A/
 
115
 
116
  Each HDF5 file contains the following per-sample features:
117
 
118
+ 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.
 
119
 
120
  | Name | Shape | Dtype | Units | Description |
121
  |---|---:|---|---|---|
 
129
  | `/custom/simulation/scatterer_positions` | `(16384, 3)` | `float32` | m | Point-scatterer positions used for channel simulation. |
130
  | `/custom/source_provenance/*` | mixed | mixed | documented per field | Source indices, plane transform, timing, and excitation settings. |
131
 
132
+ 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`.
 
133
 
134
  ## Dataset Quantification
135
 
 
140
  - Train / validation / test split: not predefined.
141
  - Per-sample raw tensor: `1 × 64 × 3546 × 128 × 1`, `int16`.
142
  - Per-sample source line-RF tensor: `64 × 5196`, `int16`.
143
+ - Exact HDF5 payload size: **108,889,767,936 bytes** (108.890 GB; 101.412 GiB).
 
144
 
145
  ## Subject Metadata
146
 
147
+ 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.
 
 
 
148
 
149
  ## Data Validation
150
 
151
+ 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:
 
 
152
 
153
  ```text
154
  Cast to float32
 
162
  -> PNG
163
  ```
164
 
165
+ 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.
 
 
 
166
 
167
+ `pipeline.yaml` records the reconstruction configuration. `zlims: [0.0001, 0.100023]` are line depths from each transmit origin on the curved element surface.
 
 
168
 
169
+ 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.
 
 
 
170
 
171
+ This HF release includes the HDF5 files, this card, and the pipeline configuration. Review outputs, standalone reconstruction scripts, and validation sidecars are not included.
 
 
172
 
173
  ## Known Issues
174
 
175
+ - The measured source is beamformed line RF. The submitted 128-channel data are deterministic forward simulations conditioned on that source.
176
+ - The simulation preserves source-derived spatial and temporal contrast but cannot recover proprietary scanner receive processing or true measured element-level noise/coupling.
177
+ - The stored image is a reference only and is deliberately excluded from the reconstruction path.
178
+ - 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.
179
+ - A scanner TGC curve, probe bandwidth, and exact transmit waveform were not available. Reconstruction therefore applies no TGC and uses the documented simulation pulse.
 
 
 
 
 
 
 
 
180
 
181
  ## Ethical Considerations
182
 
183
+ The data are phantom acquisitions only. There are no human subjects, no PHI, and no patient demographics.
 
ubc/module_C/README.md CHANGED
@@ -1,5 +1,6 @@
1
  ---
2
- pretty_name: "OpenH-RF — UBC Module C Fetal Phantom"
 
3
  license: cc-by-4.0
4
  task_categories:
5
  - image-to-image
@@ -21,30 +22,34 @@ size_categories:
21
  - "1K<n<10K"
22
  ---
23
 
24
- # UBC Module C
25
 
26
- ## Dataset Description
27
 
28
- This dataset contains **3,845 two-dimensional ultrasound frames from two
29
- sessions** with the Kyoto Kagaku Fetus Ultrasound Examination Phantom
30
- “SPACE FAN-ST.” Each frame contains **synthetic RF channel data**, preserved
31
- beamformed IQ, a source-derived B-mode reference, and relative-time links to
32
- NDI tracking, BK scanner viewport video, and Intel RealSense video.
33
 
34
- The RF channels were simulated from already beamformed and compounded BK3500
35
- IQ using a custom scatterer model and assumed transmit/receive geometry. They
36
- are not measured pre-beamforming channels. Modalities have temporal
37
- synchronization only; no validated spatial registration is supplied.
38
 
39
- ![Example reconstruction](./assets/module_C.png)
40
 
41
- ## Dataset Contributors
42
 
43
- - **Organization:** The University of British Columbia (UBC), Department of
44
- Electrical and Computer Engineering and School of Biomedical Engineering.
45
- - **Dataset-preparation contact:** Zongze Li, zongze@student.ubc.ca.
46
- - **Contributors:** Zongze Li, Yu Chung Lee, Qi Zeng, Wanwen Chen, Zijian Wu,
47
- Yuxin Chen, Patrick Boyan Chen, Michael Frew, Tajwar Abrar Aleef, Hamid Moradi, Mohammad Honarvar, Septimiu E. Salcudean, Robert Rohling.
 
 
 
 
 
 
 
 
 
 
 
48
 
49
  ## Dataset Creation Date
50
 
@@ -53,39 +58,18 @@ synchronization only; no validated spatial registration is supplied.
53
 
54
  ## License / Terms of Use
55
 
56
- The dataset is licensed under **Creative Commons Attribution 4.0 International
57
- (CC BY 4.0)** (https://creativecommons.org/licenses/by/4.0/). The HDF5 `metadata/credit` field carries
58
- the following attribution with the contributor names and contact listed above:
59
-
60
- > University of British Columbia OpenH-RF contributors (2026). *UBC Module C:
61
- > Synthetic Channel Proxy and Multimodal Fetal Phantom Ultrasound*. OpenH-RF.
62
- > CC BY 4.0.
63
 
64
  ## Intended Usage
65
 
66
- Research uses include synthetic RF-to-B-mode reconstruction, denoising,
67
- super-resolution, fetal-phantom scan-plane assessment, and temporally aligned
68
- multimodal learning. The dataset is for research and technical evaluation,
69
- not clinical diagnosis. Source-derived reference images are not independent
70
- physical ground truth for the simulated channels.
71
 
72
  ## Dataset Characterization
73
 
74
- - **Collection:** Phantom ultrasound and simultaneous room-camera and tracking
75
- recordings, followed by deterministic synthetic-channel generation.
76
- - **Acquisition system:** BK3500 ultrasound; NDI Tool-2 tracked-marker poses;
77
- NDI Tool-1 reference-tool poses; Intel RealSense RGB, left/right infrared,
78
- and encoded depth video.
79
- - **Labels:** Source indices, synchronization validity flags, and simulation
80
- provenance. No manual fetal-structure segmentations or verified phantom
81
- configuration labels are supplied.
82
- - **Simulation framework:** Custom NumPy/SciPy scatterer forward model using
83
- four-point fractional delays, pulse filtering, frame-specific noise, and
84
- `int16` quantization. Session 1 preserves its original amplitudes and shared random draws,
85
- with scatterer depths evaluated on each frame's source IQ axial grid. Session 2 uses fixed
86
- deterministic positions and reflectivity draws for the session, with
87
- frame amplitudes derived from its IQ envelope.
88
- No two-channel proxy data are included as equivalent RF measurements.
89
 
90
  ### Ultrasound and synthetic-channel parameters
91
 
@@ -107,17 +91,19 @@ physical ground truth for the simulated channels.
107
  | Zero-amplitude tail | 20 µs / 300 samples | Stored raw-data attributes |
108
  | Target maximum magnitude | 26,000 counts | Below `int16` full scale |
109
 
110
- The element geometry and dimensions are simulation assumptions, not measured
111
- probe specifications. The relationship between the recorded 98-mm focus and
112
- the proprietary scanner transmit law is unknown.
 
 
113
 
 
114
 
115
  ## Dataset Format
116
 
117
- Each zea HDF5 file contains one frame and is written with **zea 0.1.5**.
118
- The writer-version field describes serialization,
119
- not processing speed. Source IQ and its display reference are under
120
- `/custom/source_provenance`.
121
 
122
  ### Package layout
123
 
@@ -129,33 +115,13 @@ not processing speed. Source IQ and its display reference are under
129
  | `external_camera/session_XX/` | RealSense MP4 video |
130
  | [`pipeline.yaml`](pipeline.yaml) | Shared reconstruction configuration for both sessions |
131
 
132
- `session_XX` denotes `session_01` or `session_02`. All public identifiers are
133
- neutral session labels. HDF5 `source_file` values identify private source
134
- container aliases, not downloadable package files; the source IQ is embedded
135
- in each sample. This HF release includes HDF5 files, this card, the pipeline
136
- configuration, and the source BK viewport and RealSense MP4 videos.
137
- Composite review videos, standalone scripts, timing/tracking tables,
138
- calibration sidecars, and validation reports are not included. References
139
- inside unchanged HDF5 metadata may identify sidecars from the source package
140
- that are not available in this release.
141
 
142
  ### Timestamp conventions
143
 
144
- **All acquisition timestamps are session-relative. Absolute wall-clock times
145
- are intentionally withheld for de-identification.** IQ, BK viewport, NDI
146
- reference-tool, and RealSense host times are relative to the first **source** IQ
147
- frame of their own session, even when that frame is excluded from the release. RealSense device time is relative to its first camera frame.
148
- Negative host-relative camera times can precede the first IQ frame.
149
- Each one-frame zea probe-pose timestamp is locally zero, with session-relative
150
- IQ time stored separately in `/custom/synchronization`.
151
-
152
- Use alignment indices and validity flags, not video frame rate alone, to link
153
- modalities. The HDF5 Tool-2 previous/next/recorded-last indices address the
154
- **status-zero subset** of the source tracking records. Tool-1 reference
155
- indices address the full source reference-tool records. These standalone
156
- tables are not included in this HF release. MP4 playback time is an encoded
157
- presentation timeline, not an acquisition clock; use the per-frame
158
- synchronization metadata retained in HDF5.
159
 
160
  ## Dataset Quantification
161
 
@@ -170,20 +136,11 @@ synchronization metadata retained in HDF5.
170
  | Frames per RealSense stream | 1,591 | 3,677 | 5,268 |
171
  | Valid BK / NDI Tool-2 / NDI Tool-1 / RealSense links | 1,339 each | 2,506 each | 3,845 each |
172
 
173
- **Frame selection:** Every retained ultrasound frame has a valid BK video link,
174
- RealSense video link, interpolated NDI Tool-2 pose, and NDI Tool-1 reference
175
- link. Each BK frame and each RealSense frame is associated with **at most one**
176
- retained ultrasound frame. Selection maximizes the number of chronological
177
- matches, then minimizes the sum of absolute BK/RealSense timing offsets; source
178
- frame order breaks remaining ties. Original frame indices, relative times, and
179
- noise seeds are preserved. HDF5 files contain only retained ultrasound frames;
180
- videos retain their full temporal context.
181
 
182
  **HDF5 storage:** session_01: 205,236,518,547 bytes (191.14 GiB); session_02: 388,206,776,234 bytes (361.55 GiB). Total: **593,443,294,781 bytes (552.69 GiB)**. Files use lossless compression.
183
 
184
- **Splits:** None supplied. Neighboring frames and the two sessions share a
185
- phantom and acquisition setting. Split by session for temporal separation;
186
- this does not establish generalization to different phantoms or patients.
187
 
188
  ### Per-sample feature table
189
 
@@ -212,48 +169,24 @@ this does not establish generalization to different phantoms or patients.
212
  | `/custom/synchronization/*` | scalar or small vector | mixed | s, ms, rad, m, index, or unitless | Relative-time frame links, validity flags, NDI poses, source-frame fields, and deterministic simulation seeds |
213
  | `/custom/session_calibration/image_t_tracker` | `(4, 4)` | `float64` | translation in mm; linear-block units unconfirmed | Source-supplied transform; direction and spatial registration unconfirmed |
214
 
215
- `N_IQ` is 1,824, 1,840, or 1,888, as recorded per frame in
216
- `/custom/synchronization/source_valid_axial_samples`. The synthetic RF tensor
217
- has a fixed 3,153 axial samples regardless of source IQ length.
218
 
219
- Scalar zea fields additionally store the 15-MHz sampling frequency, 3.75-MHz
220
- center and demodulation frequencies, and 1,540-m/s sound speed. Dataset-level
221
- attributes provide descriptions and units for individual fields.
222
 
223
 
224
  ### Camera representation and calibration
225
 
226
- RGB and left/right IR are privacy crops, independently reviewed for each
227
- session: `x=320, y=200, width=720, height=520` from 1280 × 720 source frames.
228
- All source frames and their order are retained at 30 encoded fps. Crop-adjusted
229
- principal points satisfy `cx_crop = cx_source − 320` and
230
- `cy_crop = cy_source − 200`; focal lengths, distortion coefficients, and
231
- inter-camera extrinsics are unchanged. Depth remains an uncropped encoded
232
- preview. Standalone calibration and crop-check sidecars are not included in
233
- this HF release.
234
 
235
  ## Data Validation
236
 
237
  ### Reconstruction
238
 
239
- The contributor reports validation with Python 3.12, zea 0.1.5, and a
240
- CUDA 12.8 / PyTorch configuration. The retained `pipeline.yaml` records the
241
- shared reconstruction configuration; the standalone reconstruction entry
242
- point and its dependency file are not included in this HF release.
243
-
244
- The contributor's reconstruction reads synthetic `raw_data`, zea scan/probe parameters, and
245
- imaging depth. zea's native aligned scanline DAS uses exactly one transmit per
246
- scanline, followed by envelope detection, normalization, log compression, and
247
- the documented display conversion. Source IQ, stored B-mode, and videos are
248
- not reconstruction inputs. Prepared pipelines are reused only for matching
249
- scan/probe parameters and precision/device settings.
250
-
251
- The contributor's mixed-precision qualification compares against float32,
252
- using float32 if scanline RMSE exceeds 0.001 dB or maximum difference exceeds
253
- 0.05 dB. This describes the contributor's validation, not a runnable command
254
- included in this release. The contributor reports reconstruction of 90 frames
255
- across the two sessions, with four endpoints shared with a six-frame precision
256
- comparison. This does not imply that every RF file has been reconstructed.
257
 
258
  ### Software references
259
 
@@ -272,38 +205,21 @@ comparison. This does not imply that every RF file has been reconstructed.
272
 
273
  ## Known Issues
274
 
275
- - **Synthetic provenance:** Already beamformed IQ cannot recover original
276
- element-level receive signals. RF and source-derived B-mode share source
277
- information; similarity is not independent physical validation.
278
- - **Unverified acquisition geometry:** The synthetic geometry is assumed.
279
- Scanner transmit law, receive aperture, RF time-zero, and proprietary
280
- compound/multibeam processing are unavailable.
281
- - **Display approximation:** Scan conversion uses a 31.1-mm display aperture,
282
- ±14.96° scanline range, virtual apex, and 4% black border. This differs from
283
- the 38.4-mm synthetic receive aperture and does not alter DAS delays.
284
- - **Spatial registration:** Probe/tool poses and ultrasound/cameras are
285
- **temporally synchronized only, not spatially registered**. The source-supplied
286
- `image_t_tracker` matrix has an **unconfirmed transform direction**. No
287
- camera-to-NDI or camera-to-ultrasound transform, calibrated probe-tip mapping,
288
- or phantom-anatomical registration is supplied. NDI axis interpretation is
289
- unverified. RealSense inter-camera calibration does not establish those mappings.
290
- - **Camera encoding:** RGB/IR are lossy H.264 crops. Depth is an H.264 display
291
- preview, not lossless metric Z16 depth.
292
- - **Identical infrared views:** Within each session, source IR-left/right are
293
- byte-identical, as are their cropped derivatives. They are not independent
294
- stereo views; supplied stereo extrinsics do not resolve this source limitation.
295
 
296
  ## Ethical Considerations
297
 
298
- Ultrasound content is phantom and simulation data, with no patient records,
299
- demographics, or animal subjects. Patient consent, human-subject IRB approval,
300
- and animal-welfare review are not applicable to that content.
301
-
302
- Room-camera recordings originally captured people. Released RGB/IR crops
303
- retain hands/forearms but exclude faces and the wider room. Uncropped RGB/IR,
304
- audio, original source identifiers, absolute acquisition clocks, and local
305
- filesystem paths are excluded. The camera review fully decoded all ten retained streams, inspected
306
- 48 distributed frames per stream, and reviewed every face-detector hit.
307
- The contributor reports that the reviewed hits were false positives and no
308
- faces were visible in the crops. The underlying review records are not
309
- included in this HF release.
 
1
  ---
2
+ name: ubc-module-c
3
+ pretty_name: "UBC Module C Fetal Phantom"
4
  license: cc-by-4.0
5
  task_categories:
6
  - image-to-image
 
22
  - "1K<n<10K"
23
  ---
24
 
25
+ # UBC Module C — Synthetic-Channel Multimodal Fetal Phantom
26
 
27
+ ![Example reconstruction](./assets/module_C.png)
28
 
29
+ *Scan-converted B-mode of the Kyoto Kagaku SPACE FAN-ST fetal phantom, reconstructed from the synthetic channel data in [`acquisitions/`](https://huggingface.co/datasets/nvidia/OpenH-RF/tree/main/ubc/module_C/acquisitions).*
 
 
 
 
30
 
31
+ ## Dataset Description
 
 
 
32
 
33
+ This dataset contains **3,845 two-dimensional ultrasound frames from two sessions** with the Kyoto Kagaku Fetus Ultrasound Examination Phantom “SPACE FAN-ST.” Each frame contains **synthetic RF channel data**, preserved beamformed IQ, a source-derived B-mode reference, and relative-time links to NDI tracking, BK scanner viewport video, and Intel RealSense video.
34
 
35
+ The RF channels were simulated from already beamformed and compounded BK3500 IQ using a custom scatterer model and assumed transmit/receive geometry. They are not measured pre-beamforming channels. Modalities have temporal synchronization only; no validated spatial registration is supplied.
36
 
37
+ ## Dataset Contributor(s)
38
+
39
+ - Zongze Li <zongze@student.ubc.ca> (dataset-preparation contact)
40
+ - Yu Chung Lee
41
+ - Qi Zeng
42
+ - Wanwen Chen
43
+ - Zijian Wu
44
+ - Yuxin Chen
45
+ - Patrick Boyan Chen
46
+ - Michael Frew
47
+ - Tajwar Abrar Aleef
48
+ - Hamid Moradi
49
+ - Mohammad Honarvar
50
+ - Septimiu E. Salcudean
51
+ - Robert Rohling
52
+ - The University of British Columbia (UBC), Department of Electrical and Computer Engineering and School of Biomedical Engineering
53
 
54
  ## Dataset Creation Date
55
 
 
58
 
59
  ## License / Terms of Use
60
 
61
+ [Creative Commons Attribution 4.0 International (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/legalcode.en). Retain attribution and identify modifications when reusing the data.
 
 
 
 
 
 
62
 
63
  ## Intended Usage
64
 
65
+ Research uses include synthetic RF-to-B-mode reconstruction, denoising, super-resolution, fetal-phantom scan-plane assessment, and temporally aligned multimodal learning. The dataset is for research and technical evaluation, not clinical diagnosis. Source-derived reference images are not independent physical ground truth for the simulated channels.
 
 
 
 
66
 
67
  ## Dataset Characterization
68
 
69
+ - **Collection:** Phantom ultrasound and simultaneous room-camera and tracking recordings, followed by deterministic synthetic-channel generation.
70
+ - **Acquisition system:** BK3500 ultrasound; NDI Tool-2 tracked-marker poses; NDI Tool-1 reference-tool poses; Intel RealSense RGB, left/right infrared, and encoded depth video.
71
+ - **Labels:** Source indices, synchronization validity flags, and simulation provenance. No manual fetal-structure segmentations or verified phantom configuration labels are supplied.
72
+ - **Simulation framework:** Custom NumPy/SciPy scatterer forward model using four-point fractional delays, pulse filtering, frame-specific noise, and `int16` quantization. Session 1 preserves its original amplitudes and shared random draws, with scatterer depths evaluated on each frame's source IQ axial grid. Session 2 uses fixed deterministic positions and reflectivity draws for the session, with frame amplitudes derived from its IQ envelope. No two-channel proxy data are included as equivalent RF measurements.
 
 
 
 
 
 
 
 
 
 
 
73
 
74
  ### Ultrasound and synthetic-channel parameters
75
 
 
91
  | Zero-amplitude tail | 20 µs / 300 samples | Stored raw-data attributes |
92
  | Target maximum magnitude | 26,000 counts | Below `int16` full scale |
93
 
94
+ The element geometry and dimensions are simulation assumptions, not measured probe specifications. The relationship between the recorded 98-mm focus and the proprietary scanner transmit law is unknown.
95
+
96
+ ## Processing the Dataset
97
+
98
+ The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/ubc/module_C/reconstruct.py) as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub.
99
 
100
+ Set `ZEA_FILE` and `FRAME` at the top of the script to pick a frame (default `session_01/session_01_f1306.hdf5`).
101
 
102
  ## Dataset Format
103
 
104
+ [zea v0.1.5](https://github.com/tue-bmd/zea)
105
+
106
+ Each zea HDF5 file contains one frame and is written with **zea 0.1.5**. The writer-version field describes serialization, not processing speed. Source IQ and its display reference are under `/custom/source_provenance`.
 
107
 
108
  ### Package layout
109
 
 
115
  | `external_camera/session_XX/` | RealSense MP4 video |
116
  | [`pipeline.yaml`](pipeline.yaml) | Shared reconstruction configuration for both sessions |
117
 
118
+ `session_XX` denotes `session_01` or `session_02`. All public identifiers are neutral session labels. HDF5 `source_file` values identify private source container aliases, not downloadable package files; the source IQ is embedded in each sample. This HF release includes HDF5 files, this card, the pipeline configuration, and the source BK viewport and RealSense MP4 videos. Composite review videos, standalone scripts, timing/tracking tables, calibration sidecars, and validation reports are not included. References inside unchanged HDF5 metadata may identify sidecars from the source package that are not available in this release.
 
 
 
 
 
 
 
 
119
 
120
  ### Timestamp conventions
121
 
122
+ **All acquisition timestamps are session-relative. Absolute wall-clock times are intentionally withheld for de-identification.** IQ, BK viewport, NDI reference-tool, and RealSense host times are relative to the first **source** IQ frame of their own session, even when that frame is excluded from the release. RealSense device time is relative to its first camera frame. Negative host-relative camera times can precede the first IQ frame. Each one-frame zea probe-pose timestamp is locally zero, with session-relative IQ time stored separately in `/custom/synchronization`.
123
+
124
+ Use alignment indices and validity flags, not video frame rate alone, to link modalities. The HDF5 Tool-2 previous/next/recorded-last indices address the **status-zero subset** of the source tracking records. Tool-1 reference indices address the full source reference-tool records. These standalone tables are not included in this HF release. MP4 playback time is an encoded presentation timeline, not an acquisition clock; use the per-frame synchronization metadata retained in HDF5.
 
 
 
 
 
 
 
 
 
 
 
 
125
 
126
  ## Dataset Quantification
127
 
 
136
  | Frames per RealSense stream | 1,591 | 3,677 | 5,268 |
137
  | Valid BK / NDI Tool-2 / NDI Tool-1 / RealSense links | 1,339 each | 2,506 each | 3,845 each |
138
 
139
+ **Frame selection:** Every retained ultrasound frame has a valid BK video link, RealSense video link, interpolated NDI Tool-2 pose, and NDI Tool-1 reference link. Each BK frame and each RealSense frame is associated with **at most one** retained ultrasound frame. Selection maximizes the number of chronological matches, then minimizes the sum of absolute BK/RealSense timing offsets; source frame order breaks remaining ties. Original frame indices, relative times, and noise seeds are preserved. HDF5 files contain only retained ultrasound frames; videos retain their full temporal context.
 
 
 
 
 
 
 
140
 
141
  **HDF5 storage:** session_01: 205,236,518,547 bytes (191.14 GiB); session_02: 388,206,776,234 bytes (361.55 GiB). Total: **593,443,294,781 bytes (552.69 GiB)**. Files use lossless compression.
142
 
143
+ **Splits:** None supplied. Neighboring frames and the two sessions share a phantom and acquisition setting. Split by session for temporal separation; this does not establish generalization to different phantoms or patients.
 
 
144
 
145
  ### Per-sample feature table
146
 
 
169
  | `/custom/synchronization/*` | scalar or small vector | mixed | s, ms, rad, m, index, or unitless | Relative-time frame links, validity flags, NDI poses, source-frame fields, and deterministic simulation seeds |
170
  | `/custom/session_calibration/image_t_tracker` | `(4, 4)` | `float64` | translation in mm; linear-block units unconfirmed | Source-supplied transform; direction and spatial registration unconfirmed |
171
 
172
+ `N_IQ` is 1,824, 1,840, or 1,888, as recorded per frame in `/custom/synchronization/source_valid_axial_samples`. The synthetic RF tensor has a fixed 3,153 axial samples regardless of source IQ length.
 
 
173
 
174
+ Scalar zea fields additionally store the 15-MHz sampling frequency, 3.75-MHz center and demodulation frequencies, and 1,540-m/s sound speed. Dataset-level attributes provide descriptions and units for individual fields.
 
 
175
 
176
 
177
  ### Camera representation and calibration
178
 
179
+ RGB and left/right IR are privacy crops, independently reviewed for each session: `x=320, y=200, width=720, height=520` from 1280 × 720 source frames. All source frames and their order are retained at 30 encoded fps. Crop-adjusted principal points satisfy `cx_crop = cx_source − 320` and `cy_crop = cy_source − 200`; focal lengths, distortion coefficients, and inter-camera extrinsics are unchanged. Depth remains an uncropped encoded preview. Standalone calibration and crop-check sidecars are not included in this HF release.
 
 
 
 
 
 
 
180
 
181
  ## Data Validation
182
 
183
  ### Reconstruction
184
 
185
+ The contributor reports validation with Python 3.12, zea 0.1.5, and a CUDA 12.8 / PyTorch configuration. The retained `pipeline.yaml` records the shared reconstruction configuration; the standalone reconstruction entry point and its dependency file are not included in this HF release.
186
+
187
+ The contributor's reconstruction reads synthetic `raw_data`, zea scan/probe parameters, and imaging depth. zea's native aligned scanline DAS uses exactly one transmit per scanline, followed by envelope detection, normalization, log compression, and the documented display conversion. Source IQ, stored B-mode, and videos are not reconstruction inputs. Prepared pipelines are reused only for matching scan/probe parameters and precision/device settings.
188
+
189
+ The contributor's mixed-precision qualification compares against float32, using float32 if scanline RMSE exceeds 0.001 dB or maximum difference exceeds 0.05 dB. This describes the contributor's validation, not a runnable command included in this release. The contributor reports reconstruction of 90 frames across the two sessions, with four endpoints shared with a six-frame precision comparison. This does not imply that every RF file has been reconstructed.
 
 
 
 
 
 
 
 
 
 
 
 
 
190
 
191
  ### Software references
192
 
 
205
 
206
  ## Known Issues
207
 
208
+ - **Synthetic provenance:** Already beamformed IQ cannot recover original element-level receive signals. RF and source-derived B-mode share source information; similarity is not independent physical validation.
209
+ - **Unverified acquisition geometry:** The synthetic geometry is assumed. Scanner transmit law, receive aperture, RF time-zero, and proprietary compound/multibeam processing are unavailable.
210
+ - **Display approximation:** Scan conversion uses a 31.1-mm display aperture, ±14.96° scanline range, virtual apex, and 4% black border. This differs from the 38.4-mm synthetic receive aperture and does not alter DAS delays.
211
+ - **Spatial registration:** Probe/tool poses and ultrasound/cameras are **temporally synchronized only, not spatially registered**. The source-supplied `image_t_tracker` matrix has an **unconfirmed transform direction**. No camera-to-NDI or camera-to-ultrasound transform, calibrated probe-tip mapping, or phantom-anatomical registration is supplied. NDI axis interpretation is unverified. RealSense inter-camera calibration does not establish those mappings.
212
+ - **Camera encoding:** RGB/IR are lossy H.264 crops. Depth is an H.264 display preview, not lossless metric Z16 depth.
213
+ - **Identical infrared views:** Within each session, source IR-left/right are byte-identical, as are their cropped derivatives. They are not independent stereo views; supplied stereo extrinsics do not resolve this source limitation.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
214
 
215
  ## Ethical Considerations
216
 
217
+ Ultrasound content is phantom and simulation data, with no patient records, demographics, or animal subjects. Patient consent, human-subject IRB approval, and animal-welfare review are not applicable to that content.
218
+
219
+ Room-camera recordings originally captured people. Released RGB/IR crops retain hands/forearms but exclude faces and the wider room. Uncropped RGB/IR, audio, original source identifiers, absolute acquisition clocks, and local filesystem paths are excluded. The camera review fully decoded all ten retained streams, inspected 48 distributed frames per stream, and reviewed every face-detector hit. The contributor reports that the reviewed hits were false positives and no faces were visible in the crops. The underlying review records are not included in this HF release.
220
+
221
+ ## Citation
222
+
223
+ The HDF5 `metadata/credit` field carries the following attribution:
224
+
225
+ > University of British Columbia OpenH-RF contributors (2026). *UBC Module C: Synthetic Channel Proxy and Multimodal Fetal Phantom Ultrasound*. OpenH-RF. CC BY 4.0.