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concordia: restructure the data card to the common layout

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@@ -1,5 +1,6 @@
1
  ---
2
- pretty_name: "OpenH-RF — SynthUS-FSA"
 
3
  license: cc-by-4.0
4
  task_categories:
5
  - image-to-image
@@ -20,50 +21,20 @@ size_categories:
20
 
21
  ![B-mode reconstructions of the five SynthUS-FSA phantom classes](assets/classes.png)
22
 
23
- The five phantom classes, each reconstructed from `data/raw_data`:
24
- `image_0005`, `image_0470`, `image_0640`, `image_1100`, `image_1808`.
25
 
26
- `zea` renders any capture straight from the Hub with the
27
- `pipeline.yaml` in this folder. Try it out with the following command:
28
 
29
- ```bash
30
- zea process \
31
- --dataset hf://nvidia/OpenH-RF/concordia/data/image_0005.hdf5 \
32
- --config hf://nvidia/OpenH-RF/concordia/pipeline.yaml \
33
- --n-frames 1 \
34
- --save-as png
35
- ```
36
 
37
- ## Dataset Description
38
 
39
- SynthUS-FSA is a fully synthetic corpus of pre-beamformed full-synthetic-aperture (FSA)
40
- ultrasound channel-data captures, generated with the Field II simulator to model a
41
- 128-element L11-5v linear array. Each capture fires one transmit event per element
42
- (128 transmits, receive on all 128 elements), so every element-to-element combination
43
- is retained and any receive/transmit beamforming scheme (focused B-mode, multi-angle
44
- plane-wave compounding, diverging-wave, adaptive/compressive schemes) can be
45
- retrospectively synthesized from the same channel data. The dataset is packaged in
46
- [zea](https://zea.readthedocs.io) format — the OpenH-RF reference Python library for
47
- ultrasound file I/O and beamforming — which every `.hdf5` file and `reconstruct.py`
48
- depend on. The dataset targets three
49
- OpenH-RF task categories: (1) generalized reconstruction (FSA channel data paired with
50
- a synthesized full synthetic-aperture B-mode as ground truth), (2) compressed sensing /
51
- adaptive transmit (retrospective sub-selection of the 128 transmit events — derived
52
- from the same captures, no additional files), and (3) segmentation (binary
53
- echogenicity masks on a subset of phantoms). All data is simulated — no clinical,
54
- phantom-hardware, or animal acquisition is involved.
55
-
56
- A similar data-generation approach was used in Sharifzadeh et al. (2024). Users of
57
- this dataset are kindly requested to cite that work:
58
-
59
- > M. Sharifzadeh, S. Goudarzi, A. Tang, H. Benali, and H. Rivaz, "Mitigating
60
- > aberration-induced noise: A deep learning-based aberration-to-aberration approach,"
61
- > *IEEE Transactions on Medical Imaging*, vol. 43, no. 12, pp. 4380–4392, 2024.
62
 
63
  ## Dataset Contributor(s)
64
 
65
- Mostafa Sharifzadeh (mostafa.sharifzadeh@mail.concordia.ca) and Hassan Rivaz
66
- (hassan.rivaz@concordia.ca), IMPACT Lab, Concordia University.
67
 
68
  ## Dataset Creation Date
69
 
@@ -71,127 +42,68 @@ Mostafa Sharifzadeh (mostafa.sharifzadeh@mail.concordia.ca) and Hassan Rivaz
71
 
72
  ## License / Terms of Use
73
 
74
- CC BY 4.0.
75
-
76
- - **Simulated channel data, phantom parameters, and reconstruction/segmentation
77
- labels** are generated by the contributors (Field II simulation outputs) and
78
- released under CC BY 4.0.
79
- - **Segmentation mask shapes** (anechoic/hypoechoic/hyperechoic classes, 750
80
- captures) are sourced from [Open Images V7](https://storage.googleapis.com/openimages/web/factsfigures_v7.html)'s
81
- animal-class segmentation annotations (Google LLC). Only the binary mask is used — never the underlying source photograph. Open Images V7
82
- licenses its annotations, including segmentation masks, under CC BY 4.0; the
83
- source photographs themselves carry a separate CC BY 2.0 license but are not
84
- used anywhere in this dataset.
85
- - **Diverse-echogenicity amplitude-weight maps** (1,000 captures) are photographs
86
- from Wikimedia Commons, restricted to the `CC-BY-4.0` category and verified
87
- per-image against each file's `CC BY 4.0` license field before acceptance.
88
- `wikimedia_commons_metadata.csv`, at the dataset root, credits each one: a row
89
- per capture, keyed by `DatasetFile` for `image_0751.hdf5` through
90
- `image_1750.hdf5`, giving the source URL, Commons file page, author, title and
91
- license. No photograph appears in the dataset in its original form. Each was
92
- converted to grayscale, resampled to the 400 × 450 weight-map grid,
93
- histogram-equalized and rescaled to `[0, 1]`. Values above 0.9 were then set to
94
- 1 and values below 0.1 to 0, producing the weight map stored as
95
- `data/diverse_source_image`. This conversion is implemented in
96
- `wikimedia_commons_postprocess.py`.
97
- - **Point-target phantoms** (250 captures) use no external asset — purely
98
- synthetic point scatterers.
99
-
100
- All channel data was generated with Field II (Jensen/DTU), distributed for free academic use. Field II's terms do not
101
- restrict redistribution or licensing of simulation *output* data. Per Field II's terms, any use of this dataset should cite:
102
- J.A. Jensen, "Field: A Program for Simulating Ultrasound Systems," *Med. Biol.
103
- Eng. Comp.*, 1996; and J.A. Jensen and N.B. Svendsen, "Calculation of Pressure
104
- Fields from Arbitrarily Shaped, Apodized, and Excited Ultrasound Transducers,"
105
- *IEEE Trans. Ultrason., Ferroelec., Freq. Contr.*, 1992.
106
 
107
  ## Intended Usage
108
 
109
- - **Generalized reconstruction** — learning a direct mapping from raw FSA channel
110
- data to a B-mode image, and/or from FSA to arbitrary retrospective beamforming
111
- targets (focused, multi-angle compounded, diverging-wave, adaptive).
112
- - **Compressed sensing / adaptive transmit** — sparse-aperture and adaptive transmit
113
- design research using retrospective sub-selection of the 128 FSA transmit events.
114
- - **Segmentation** — pixel-aligned echogenicity-region segmentation (anechoic /
115
- hypoechoic / hyperechoic) from raw channel data.
116
- - **Scatterer-level analysis** — `data/scatterers` exposes the exact Field II
117
- point-scatterer cloud (position + amplitude) used to simulate each capture,
118
- for tasks that want ground truth finer than a pixel grid (e.g. quantitative
119
- ultrasound, scatterer-density estimation).
120
 
121
  ## Dataset Characterization
122
 
123
- - **Data Collection Method:** synthetic (Field II full-synthetic-aperture
124
- simulation).
125
  - **Labeling Method:** synthetic ground truth.
126
- - Segmentation masks (anechoic/hypoechoic/hyperechoic) are Open Images V7
127
- animal-class segmentation annotations, used for shape only.
128
- - Diverse-echogenicity amplitude weighting uses a Wikimedia Commons photograph
129
- as a continuous grayscale weight map, preserved as `data/diverse_source_image`
130
- so an end user can see what pattern the capture was generated from.
131
- - The reconstruction-target B-mode (`data/image`) is synthesized from the same
132
- FSA capture (see *Data Validation* below), not an independent acquisition.
133
- - **Acquisition system (simulated):** 128-element linear array (model: L11-5v),
134
- center frequency 5.208 MHz, element width 0.27 mm, kerf 0.03 mm, pitch 0.3 mm,
135
- element height 5 mm, elevation focus (Rfocus) 20 mm. Simulated at 104.16 MHz (a
136
- high rate required for Field II's numerical precision), then decimated ×5 to a
137
- delivered sampling rate of 20.832 MHz. Sound speed 1540 m/s.
138
- Receive dynamic-focus reconstruction uses F-number 1.75 (baked into
139
- `reconstruct.py`'s `F_NUMBER` constant — zea's own default is 1.0, so this must be
140
- supplied explicitly rather than relying on the file alone to reproduce the
141
- reference images).
142
- - **Transmit pulse:** Hann-windowed 2.5-cycle tone burst at the 5.208 MHz center
143
- frequency, sampled at the native 104.16 MHz simulation rate. −6dB fractional
144
- bandwidth ≈ 76.5% (stored as `probe/probe_bandwidth_percent`).
145
- - **Coordinate convention:** x = lateral, y = elevation (always 0 for this 2D
146
- acquisition), z = axial/depth — the standard zea convention, applied throughout
147
- `probe_geometry`, `transmit_origins`, and every map's `coordinates` field.
148
- - **Frame timing:** each file is a single static frame (`n_frames=1`) with no
149
- simulated motion or pulse-repetition-frequency concept, so `scan/time_to_next_transmit`
150
- is intentionally omitted rather than populated with a fabricated value. Likewise, no
151
- time-gain-compensation was applied to this synthetic data, so `scan/tgc_gain_curve`
152
- is omitted.
 
 
 
 
 
 
 
153
 
154
  ## Dataset Format
155
 
156
- The dataset is 2,000 individual zea HDF5 files (one acquisition per file) under
157
- `data/` (zea format; `zea_version` 0.1.6). Reference figures are in
158
- `examples/`; `reconstruct.py`, `pipeline.yaml`, and this card sit
159
- at the repository root. Per file:
160
-
161
- - `data/raw_data` — full FSA channel data, `int16`, quantized from the native
162
- simulated (float32) values by per-file peak-scaling into the int16 range
163
- (~5e-5 relative quantization step — well below any physically meaningful signal
164
- feature, equivalent to how real ultrasound hardware ADCs store raw channel data).
165
- - `data/image` — the reference B-mode: a synthetic transmit aperture (STA)
166
- reconstruction that delay-and-sums all 128 single-element FSA transmits with
167
- zea's default DAS pipeline over the intended imaging FOV (see *Subject
168
- Metadata*). This is exactly what `reconstruct.py` reproduces from `data/raw_data`.
169
- - `data/segmentation` — boolean mask with labels `["background", <class>]`,
170
- present only for anechoic/hypoechoic/hyperechoic phantoms (750 captures) —
171
- the Open Images V7 mask directly. Not produced for diverse or point-target
172
- phantoms (no defined region to segment in either case).
173
- - `data/echogenicity_multiplier` — present alongside `data/segmentation`
174
- (same 750 captures): the scalar amplitude multiplier Field II applied to
175
- every scatterer inside that region, e.g. "hypoechoic at 0.23×," not just
176
- "hypoechoic." A single number per file, so it's stored without a
177
- `coordinates` grid (optional per zea's `Map` spec — this isn't spatial).
178
- - `data/diverse_source_image` — present only for diverse-class phantoms
179
- (1,000 captures): the grayscale natural-image echogenicity weight map
180
- (continuous `[0, 1]` values) each capture's scatterer amplitudes were
181
- generated from. Not a mask — just the reference image, so an end user can
182
- see what pattern produced the capture.
183
- - `data/scatterers` — the exact Field II point-scatterer cloud used to
184
- simulate the capture (every capture, all classes): `values` = per-scatterer
185
- amplitude (a.u.), `coordinates` = per-scatterer `(x, y, z)` position in
186
- metres. ~275,000 scatterers per capture, stored via zea's custom-data
187
- extension mechanism as a `(1, n_scatterers, 1)` / `(n_scatterers, 1, 3)`
188
- pair rather than a regular pixel grid (a point cloud has no grid to speak
189
- of). This is the ground truth Field II actually simulated from — finer than
190
- any pixel-grid label derived from it.
191
-
192
- Pre-processing applied before packaging: anti-alias FIR decimation (factor 5,
193
- 104.16 MHz → 20.832 MHz) and int16 quantization, both described above. zea's
194
- The original submission used lossless `lzf` HDF5 compression; re-saving may change storage compression without changing the RF representation.
195
 
196
  ## Dataset Quantification
197
 
@@ -207,16 +119,12 @@ This dataset comprises 2,000 FSA captures across five echogenicity classes:
207
  | Diverse (natural-image-derived) | 1,000 | 0751–1750 | No | `data/diverse_source_image` |
208
  | Point-target | 250 | 1751–2000 | No | — |
209
 
210
- `data/scatterers` (the raw point-scatterer cloud) is present for all 2,000
211
- captures regardless of class.
212
 
213
- Each capture's class label is stored in its file metadata
214
- (`metadata/annotations/label`).
215
 
216
  - **Stored HDF5 size:** 82.39 GB total; 41.20 MB per file on average. RF remains int16 and post-decimation.
217
- - **Train / validation / test split:** none predefined — the corpus is released
218
- as a single set for users to partition as their task requires (class membership
219
- and index ranges are given above).
220
  - **Per-sample feature table:**
221
 
222
  | Field | Shape | Dtype | Units | Description |
@@ -238,72 +146,24 @@ Each capture's class label is stored in its file metadata
238
 
239
  ## Subject Metadata
240
 
241
- Not applicable — no human or animal subjects. Each "subject" is a simulated
242
- phantom of ≈275,000 scatterers. The reconstructed image FOV is 45 mm (lateral) ×
243
- 40 mm (axial), starting 10 mm from the transducer face. The scatterer field is
244
- deliberately larger than this FOV (≈49.5 mm wide, extending to 54 mm deep) so
245
- that beamforming at the FOV edges is fully supported by surrounding scatterers
246
- and free of edge-truncation artifacts; only the reconstruction grid is cropped
247
- to the FOV, while `data/raw_data` and `data/scatterers` retain the full extent.
248
- Per-class amplitude weighting inside the mask/weight-map region:
249
 
250
  - **Anechoic:** scatterer amplitude zeroed.
251
- - **Hypoechoic:** amplitude × U[0.07, 0.50]; the exact per-capture draw is
252
- preserved in `data/echogenicity_multiplier`.
253
- - **Hyperechoic:** amplitude × U[2, 8]; same per-capture preservation via
254
- `data/echogenicity_multiplier`.
255
- - **Diverse:** continuous grayscale weight map from a Wikimedia Commons
256
- photograph (histogram-equalized, normalized to [0, 1], clipped at the
257
- extremes) — preserved as `data/diverse_source_image`.
258
  - **Point-target:** 10–20 point targets per phantom (count ~ U[10, 20], rounded to an integer), each target's amplitude an independent U[15, 35] draw. The targets consist of adjacent groups of high-amplitude scatterers within `data/scatterers`.
259
 
260
- All classes except point-target additionally include 2–5 extra bright point
261
- scatterers (amplitude 18–22) scattered at valid random positions, for realism.
262
 
263
  ## Data Validation
264
 
265
- **Setup:** `reconstruct.py` requires `zea>=0.1.1`, `matplotlib`,
266
- and `KERAS_BACKEND=jax` (or `torch`/`tensorflow`) set before import. This submission
267
- was built and verified against the [OpenH-RF repo](https://github.com/open-h/OpenH-RF)'s environment (`uv sync` inside a clone of that repo installs `zea` and every other
268
- dependency this script needs — see that repo's README for the exact commands).
269
-
270
- `reconstruct.py` (+ `pipeline.yaml`, zea's default DAS pipeline: Cast → ApplyWindow →
271
- Demodulate → Beamform → EnvelopeDetect → Normalize → LogCompress; each stage is
272
- explained in `reconstruct.py`'s own module docstring) reconstructs a synthetic
273
- transmit aperture (STA) B-mode from `data/raw_data` using all 128 transmits, over
274
- the same field of view as the stored `data/image` reference. It renders that
275
- reconstruction on physical mm axes next to the capture's class-specific label
276
- — segmentation foreground for anechoic/hypoechoic/hyperechoic,
277
- `data/diverse_source_image` for diverse, none for point-target — and the
278
- `data/scatterers` cloud coloured by |amplitude|, all on shared equal-aspect mm
279
- axes, confirming the label, reconstruction, and scatterer field are spatially
280
- registered. [`assets/reference_capture.png`](assets/reference_capture.png) is one such figure.
281
 
282
  ## Known Issues
283
 
284
- - **`data/image` is a log-compressed dB B-mode, not raw beamformed RF** —
285
- This is a minor packaging note, not a coverage
286
- gap, precisely because the data is FSA: `data/raw_data` retains every
287
- element-to-element transmit/receive combination (128 single-element transmit
288
- firings × 128-element receive aperture on the L11-5v), which is a more
289
- general representation than any one fixed beamformed product could be: by
290
- delay-and-sum with the appropriate per-element transmit delays and apodization
291
- (linear superposition over the 128 single-element firings), it is a sufficient
292
- basis to retrospectively synthesize other transmit/receive schemes — multi-angle
293
- plane-wave compounding at arbitrary steering angles, diverging-wave imaging from
294
- an arbitrary virtual source behind the array, conventional focused/multi-line
295
- transmit — with no re-acquisition. `reconstruct.py` as shipped only implements
296
- one of these (the full 128-transmit STA beamforming used to produce
297
- `data/image`, via zea's default DAS pipeline, `pipeline.yaml`); it does not take
298
- a scheme argument. Reconstructing a different scheme means modifying
299
- `reconstruct.py` accordingly — supplying the corresponding transmit
300
- delays/apodization to zea's `Beamform` op.
301
 
302
  ## Ethical Considerations
303
 
304
- Entirely synthetic data. No human or animal subjects are involved, and no IRB/ethics
305
- approval is required or applicable. The "animal-class" Open Images V7 segmentation
306
- annotations and Wikimedia Commons photographs referenced elsewhere in this card
307
- contribute only geometric silhouette shapes and grayscale texture patterns,
308
- respectively — no live animal or human subject, tissue, or imagery of either is
309
- used anywhere in this dataset.
 
1
  ---
2
+ name: concordia
3
+ pretty_name: "SynthUS-FSA"
4
  license: cc-by-4.0
5
  task_categories:
6
  - image-to-image
 
21
 
22
  ![B-mode reconstructions of the five SynthUS-FSA phantom classes](assets/classes.png)
23
 
24
+ *The five phantom classes (anechoic, hypoechoic, hyperechoic, diverse, point-target), each reconstructed from `data/raw_data`: [`image_0005`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/concordia/data/image_0005.hdf5), [`image_0470`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/concordia/data/image_0470.hdf5), [`image_0640`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/concordia/data/image_0640.hdf5), [`image_1100`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/concordia/data/image_1100.hdf5), [`image_1808`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/concordia/data/image_1808.hdf5).*
 
25
 
26
+ ## Dataset Description
 
27
 
28
+ SynthUS-FSA is a fully synthetic corpus of pre-beamformed full-synthetic-aperture (FSA) ultrasound channel-data captures, generated with the Field II simulator to model a 128-element L11-5v linear array. Each capture fires one transmit event per element (128 transmits, receive on all 128 elements), so every element-to-element combination is retained and any receive/transmit beamforming scheme (focused B-mode, multi-angle plane-wave compounding, diverging-wave, adaptive/compressive schemes) can be retrospectively synthesized from the same channel data. The dataset is packaged in [zea](https://zea.readthedocs.io) format — the OpenH-RF reference Python library for ultrasound file I/O and beamforming — which every `.hdf5` file and `reconstruct.py` depend on. The dataset targets three OpenH-RF task categories: (1) generalized reconstruction (FSA channel data paired with a synthesized full synthetic-aperture B-mode as ground truth), (2) compressed sensing / adaptive transmit (retrospective sub-selection of the 128 transmit events — derived from the same captures, no additional files), and (3) segmentation (binary echogenicity masks on a subset of phantoms). All data is simulated — no clinical, phantom-hardware, or animal acquisition is involved.
 
 
 
 
 
 
29
 
30
+ A similar data-generation approach was used in Sharifzadeh et al. (2024). Users of this dataset are kindly requested to cite that work:
31
 
32
+ > M. Sharifzadeh, S. Goudarzi, A. Tang, H. Benali, and H. Rivaz, "Mitigating aberration-induced noise: A deep learning-based aberration-to-aberration approach," *IEEE Transactions on Medical Imaging*, vol. 43, no. 12, pp. 4380–4392, 2024.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
33
 
34
  ## Dataset Contributor(s)
35
 
36
+ - Mostafa Sharifzadeh <mostafa.sharifzadeh@mail.concordia.ca> (IMPACT Lab, Concordia University)
37
+ - Hassan Rivaz <hassan.rivaz@concordia.ca> (IMPACT Lab, Concordia University)
38
 
39
  ## Dataset Creation Date
40
 
 
42
 
43
  ## License / Terms of Use
44
 
45
+ [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.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
46
 
47
  ## Intended Usage
48
 
49
+ - **Generalized reconstruction** — learning a direct mapping from raw FSA channel data to a B-mode image, and/or from FSA to arbitrary retrospective beamforming targets (focused, multi-angle compounded, diverging-wave, adaptive).
50
+ - **Compressed sensing / adaptive transmit** — sparse-aperture and adaptive transmit design research using retrospective sub-selection of the 128 FSA transmit events.
51
+ - **Segmentation** — pixel-aligned echogenicity-region segmentation (anechoic / hypoechoic / hyperechoic) from raw channel data.
52
+ - **Scatterer-level analysis** — `data/scatterers` exposes the exact Field II point-scatterer cloud (position + amplitude) used to simulate each capture, for tasks that want ground truth finer than a pixel grid (e.g. quantitative ultrasound, scatterer-density estimation).
 
 
 
 
 
 
 
53
 
54
  ## Dataset Characterization
55
 
56
+ - **Data Collection Method:** synthetic (Field II full-synthetic-aperture simulation).
 
57
  - **Labeling Method:** synthetic ground truth.
58
+ - Segmentation masks (anechoic/hypoechoic/hyperechoic) are Open Images V7 animal-class segmentation annotations, used for shape only.
59
+ - Diverse-echogenicity amplitude weighting uses a Wikimedia Commons photograph as a continuous grayscale weight map, preserved as `data/diverse_source_image` so an end user can see what pattern the capture was generated from.
60
+ - The reconstruction-target B-mode (`data/image`) is synthesized from the same FSA capture (see *Data Validation* below), not an independent acquisition.
61
+ - **Acquisition system (simulated):** 128-element linear array (model: L11-5v), center frequency 5.208 MHz, element width 0.27 mm, kerf 0.03 mm, pitch 0.3 mm, element height 5 mm, elevation focus (Rfocus) 20 mm. Simulated at 104.16 MHz (a high rate required for Field II's numerical precision), then decimated ×5 to a delivered sampling rate of 20.832 MHz. Sound speed 1540 m/s. Receive dynamic-focus reconstruction uses F-number 1.75 (baked into `reconstruct.py`'s `F_NUMBER` constant — zea's own default is 1.0, so this must be supplied explicitly rather than relying on the file alone to reproduce the reference images).
62
+ - **Transmit pulse:** Hann-windowed 2.5-cycle tone burst at the 5.208 MHz center frequency, sampled at the native 104.16 MHz simulation rate. −6dB fractional bandwidth ≈ 76.5% (stored as `probe/probe_bandwidth_percent`).
63
+ - **Coordinate convention:** x = lateral, y = elevation (always 0 for this 2D acquisition), z = axial/depth — the standard zea convention, applied throughout `probe_geometry`, `transmit_origins`, and every map's `coordinates` field.
64
+ - **Frame timing:** each file is a single static frame (`n_frames=1`) with no simulated motion or pulse-repetition-frequency concept, so `scan/time_to_next_transmit` is intentionally omitted rather than populated with a fabricated value. Likewise, no time-gain-compensation was applied to this synthetic data, so `scan/tgc_gain_curve` is omitted.
65
+
66
+ ## Source Attribution
67
+
68
+ The dataset as a whole is released under CC BY 4.0. Its components come from the following sources:
69
+
70
+ - **Simulated channel data, phantom parameters, and reconstruction/segmentation labels** are generated by the contributors (Field II simulation outputs) and released under CC BY 4.0.
71
+ - **Segmentation mask shapes** (anechoic/hypoechoic/hyperechoic classes, 750 captures) are sourced from [Open Images V7](https://storage.googleapis.com/openimages/web/factsfigures_v7.html)'s animal-class segmentation annotations (Google LLC). Only the binary mask is used — never the underlying source photograph. Open Images V7 licenses its annotations, including segmentation masks, under CC BY 4.0; the source photographs themselves carry a separate CC BY 2.0 license but are not used anywhere in this dataset.
72
+ - **Diverse-echogenicity amplitude-weight maps** (1,000 captures) are photographs from Wikimedia Commons, restricted to the `CC-BY-4.0` category and verified per-image against each file's `CC BY 4.0` license field before acceptance. `wikimedia_commons_metadata.csv`, at the dataset root, credits each one: a row per capture, keyed by `DatasetFile` for `image_0751.hdf5` through `image_1750.hdf5`, giving the source URL, Commons file page, author, title and license. No photograph appears in the dataset in its original form. Each was converted to grayscale, resampled to the 400 × 450 weight-map grid, histogram-equalized and rescaled to `[0, 1]`. Values above 0.9 were then set to 1 and values below 0.1 to 0, producing the weight map stored as `data/diverse_source_image`. This conversion is implemented in `wikimedia_commons_postprocess.py`.
73
+ - **Point-target phantoms** (250 captures) use no external asset — purely synthetic point scatterers.
74
+
75
+ All channel data was generated with Field II (Jensen/DTU), distributed for free academic use. Field II's terms do not restrict redistribution or licensing of simulation *output* data. Per Field II's terms, any use of this dataset should cite: J.A. Jensen, "Field: A Program for Simulating Ultrasound Systems," *Med. Biol. Eng. Comp.*, 1996; and J.A. Jensen and N.B. Svendsen, "Calculation of Pressure Fields from Arbitrarily Shaped, Apodized, and Excited Ultrasound Transducers," *IEEE Trans. Ultrason., Ferroelec., Freq. Contr.*, 1992.
76
+
77
+ ## Processing the Dataset
78
+
79
+ The acquisitions can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
80
+
81
+ `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:
82
+
83
+ ```bash
84
+ zea process \
85
+ --dataset hf://nvidia/OpenH-RF/concordia/data/image_0005.hdf5 \
86
+ --config hf://nvidia/OpenH-RF/concordia/pipeline.yaml \
87
+ --n-frames 1 \
88
+ --save-as png
89
+ ```
90
+
91
+ Alternatively, you can use the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/concordia/reconstruct.py) as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF).
92
 
93
  ## Dataset Format
94
 
95
+ [zea v0.1.6](https://github.com/tue-bmd/zea)
96
+
97
+ The dataset is 2,000 individual zea HDF5 files (one acquisition per file) under `data/` (zea format; `zea_version` 0.1.6). Reference figures are in `examples/`; `reconstruct.py`, `pipeline.yaml`, and this card sit at the repository root. Per file:
98
+
99
+ - `data/raw_data` — full FSA channel data, `int16`, quantized from the native simulated (float32) values by per-file peak-scaling into the int16 range (~5e-5 relative quantization step — well below any physically meaningful signal feature, equivalent to how real ultrasound hardware ADCs store raw channel data).
100
+ - `data/image` — the reference B-mode: a synthetic transmit aperture (STA) reconstruction that delay-and-sums all 128 single-element FSA transmits with zea's default DAS pipeline over the intended imaging FOV (see *Subject Metadata*). This is exactly what `reconstruct.py` reproduces from `data/raw_data`.
101
+ - `data/segmentation` — boolean mask with labels `["background", <class>]`, present only for anechoic/hypoechoic/hyperechoic phantoms (750 captures) — the Open Images V7 mask directly. Not produced for diverse or point-target phantoms (no defined region to segment in either case).
102
+ - `data/echogenicity_multiplier` — present alongside `data/segmentation` (same 750 captures): the scalar amplitude multiplier Field II applied to every scatterer inside that region, e.g. "hypoechoic at 0.23×," not just "hypoechoic." A single number per file, so it's stored without a `coordinates` grid (optional per zea's `Map` spec — this isn't spatial).
103
+ - `data/diverse_source_image` — present only for diverse-class phantoms (1,000 captures): the grayscale natural-image echogenicity weight map (continuous `[0, 1]` values) each capture's scatterer amplitudes were generated from. Not a mask — just the reference image, so an end user can see what pattern produced the capture.
104
+ - `data/scatterers` — the exact Field II point-scatterer cloud used to simulate the capture (every capture, all classes): `values` = per-scatterer amplitude (a.u.), `coordinates` = per-scatterer `(x, y, z)` position in metres. ~275,000 scatterers per capture, stored via zea's custom-data extension mechanism as a `(1, n_scatterers, 1)` / `(n_scatterers, 1, 3)` pair rather than a regular pixel grid (a point cloud has no grid to speak of). This is the ground truth Field II actually simulated from — finer than any pixel-grid label derived from it.
105
+
106
+ Pre-processing applied before packaging: anti-alias FIR decimation (factor 5, 104.16 MHz → 20.832 MHz) and int16 quantization, both described above. zea's The original submission used lossless `lzf` HDF5 compression; re-saving may change storage compression without changing the RF representation.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
107
 
108
  ## Dataset Quantification
109
 
 
119
  | Diverse (natural-image-derived) | 1,000 | 0751–1750 | No | `data/diverse_source_image` |
120
  | Point-target | 250 | 1751–2000 | No | — |
121
 
122
+ `data/scatterers` (the raw point-scatterer cloud) is present for all 2,000 captures regardless of class.
 
123
 
124
+ Each capture's class label is stored in its file metadata (`metadata/annotations/label`).
 
125
 
126
  - **Stored HDF5 size:** 82.39 GB total; 41.20 MB per file on average. RF remains int16 and post-decimation.
127
+ - **Train / validation / test split:** none predefined — the corpus is released as a single set for users to partition as their task requires (class membership and index ranges are given above).
 
 
128
  - **Per-sample feature table:**
129
 
130
  | Field | Shape | Dtype | Units | Description |
 
146
 
147
  ## Subject Metadata
148
 
149
+ Not applicable — no human or animal subjects. Each "subject" is a simulated phantom of ≈275,000 scatterers. The reconstructed image FOV is 45 mm (lateral) × 40 mm (axial), starting 10 mm from the transducer face. The scatterer field is deliberately larger than this FOV (≈49.5 mm wide, extending to 54 mm deep) so that beamforming at the FOV edges is fully supported by surrounding scatterers and free of edge-truncation artifacts; only the reconstruction grid is cropped to the FOV, while `data/raw_data` and `data/scatterers` retain the full extent. Per-class amplitude weighting inside the mask/weight-map region:
 
 
 
 
 
 
 
150
 
151
  - **Anechoic:** scatterer amplitude zeroed.
152
+ - **Hypoechoic:** amplitude × U[0.07, 0.50]; the exact per-capture draw is preserved in `data/echogenicity_multiplier`.
153
+ - **Hyperechoic:** amplitude × U[2, 8]; same per-capture preservation via `data/echogenicity_multiplier`.
154
+ - **Diverse:** continuous grayscale weight map from a Wikimedia Commons photograph (histogram-equalized, normalized to [0, 1], clipped at the extremes) — preserved as `data/diverse_source_image`.
 
 
 
 
155
  - **Point-target:** 10–20 point targets per phantom (count ~ U[10, 20], rounded to an integer), each target's amplitude an independent U[15, 35] draw. The targets consist of adjacent groups of high-amplitude scatterers within `data/scatterers`.
156
 
157
+ All classes except point-target additionally include 2–5 extra bright point scatterers (amplitude 18–22) scattered at valid random positions, for realism.
 
158
 
159
  ## Data Validation
160
 
161
+ `reconstruct.py` (+ `pipeline.yaml`, zea's default DAS pipeline: Cast → ApplyWindow → Demodulate → Beamform → EnvelopeDetect → Normalize → LogCompress; each stage is explained in `reconstruct.py`'s own module docstring) reconstructs a synthetic transmit aperture (STA) B-mode from `data/raw_data` using all 128 transmits, over the same field of view as the stored `data/image` reference. It renders that reconstruction on physical mm axes next to the capture's class-specific label — segmentation foreground for anechoic/hypoechoic/hyperechoic, `data/diverse_source_image` for diverse, none for point-target — and the `data/scatterers` cloud coloured by |amplitude|, all on shared equal-aspect mm axes, confirming the label, reconstruction, and scatterer field are spatially registered. [`assets/reference_capture.png`](assets/reference_capture.png) is one such figure.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
162
 
163
  ## Known Issues
164
 
165
+ - **`data/image` is a log-compressed dB B-mode, not raw beamformed RF** — This is a minor packaging note, not a coverage gap, precisely because the data is FSA: `data/raw_data` retains every element-to-element transmit/receive combination (128 single-element transmit firings × 128-element receive aperture on the L11-5v), which is a more general representation than any one fixed beamformed product could be: by delay-and-sum with the appropriate per-element transmit delays and apodization (linear superposition over the 128 single-element firings), it is a sufficient basis to retrospectively synthesize other transmit/receive schemes — multi-angle plane-wave compounding at arbitrary steering angles, diverging-wave imaging from an arbitrary virtual source behind the array, conventional focused/multi-line transmit — with no re-acquisition. `reconstruct.py` as shipped only implements one of these (the full 128-transmit STA beamforming used to produce `data/image`, via zea's default DAS pipeline, `pipeline.yaml`); it does not take a scheme argument. Reconstructing a different scheme means modifying `reconstruct.py` accordingly — supplying the corresponding transmit delays/apodization to zea's `Beamform` op.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
166
 
167
  ## Ethical Considerations
168
 
169
+ Entirely synthetic data. No human or animal subjects are involved, and no IRB/ethics approval is required or applicable. The "animal-class" Open Images V7 segmentation annotations and Wikimedia Commons photographs referenced elsewhere in this card contribute only geometric silhouette shapes and grayscale texture patterns, respectively — no live animal or human subject, tissue, or imagery of either is used anywhere in this dataset.