oslo: add hero and main images for the collection and each sub-dataset

#66
oslo/A_cardiac/README.md CHANGED
@@ -18,6 +18,10 @@ size_categories:
18
 
19
  # USTB - In-vivo Cardiac (Verasonics P4-2)
20
 
 
 
 
 
21
  ## Dataset Description
22
 
23
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
@@ -52,7 +56,17 @@ Generalized reconstruction and adaptive beamforming of cardiac ultrasound (RFP t
52
 
53
  ## Processing the Dataset
54
 
55
- The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
 
 
 
 
 
 
 
 
 
 
56
 
57
  ## Dataset Format
58
 
 
18
 
19
  # USTB - In-vivo Cardiac (Verasonics P4-2)
20
 
21
+ ![Cine loop of a parasternal long-axis view](assets/hero.gif)
22
+
23
+ *All 50 frames of [`Verasonics_P2-4_parasternal_long_subject_1.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/A_cardiac/Verasonics_P2-4_parasternal_long_subject_1.hdf5), reconstructed from the raw channel data with `reconstruct.py`.*
24
+
25
  ## Dataset Description
26
 
27
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
 
56
 
57
  ## Processing the Dataset
58
 
59
+ The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
60
+
61
+ `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:
62
+
63
+ ```bash
64
+ zea process \
65
+ --dataset hf://nvidia/OpenH-RF/oslo/A_cardiac/Verasonics_P2-4_parasternal_long_subject_1.hdf5 \
66
+ --config hf://nvidia/OpenH-RF/oslo/A_cardiac/pipeline.yaml
67
+ ```
68
+
69
+ This `pipeline.yaml` holds the pipeline, display window and sector limits of that acquisition. Alternatively, all acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
70
 
71
  ## Dataset Format
72
 
oslo/A_cardiac/assets/hero.gif ADDED

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oslo/A_cardiac/assets/main.png ADDED

Git LFS Details

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oslo/A_cardiac/pipeline.yaml ADDED
@@ -0,0 +1,34 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # zea pipeline for A_cardiac/Verasonics_P2-4_parasternal_long_subject_1.hdf5, the example acquisition of this sub-dataset.
2
+ # The shared ../pipeline_sector.yaml plus the per-acquisition settings that
3
+ # ../reconstruct.py takes from ../parameters.yaml (display window in metres,
4
+ # dynamic range, polar_limits), so `zea process` renders it standalone.
5
+
6
+ parameters:
7
+ f_number: 0
8
+ grid_type: polar
9
+ grid_size_x: 400
10
+ grid_size_z: 600
11
+ dynamic_range: [-60, 0]
12
+ selected_transmits: all
13
+ focal_region_length: 0.002
14
+ pfield_kwargs:
15
+ interpolation: bilinear
16
+ percentile: 70
17
+ alpha: 15
18
+ zlims: [0.001, 0.11]
19
+ polar_limits: [-0.6552720665931702, 0.6552720665931702]
20
+ pipeline:
21
+ operations:
22
+ - name: keras.ops.cast
23
+ params:
24
+ dtype: float32
25
+ - name: apply_window
26
+ - name: demodulate
27
+ - name: beamform
28
+ params:
29
+ beamformer: delay_and_sum
30
+ enable_pfield: true
31
+ - name: envelope_detect
32
+ - name: normalize
33
+ - name: log_compress
34
+ - name: scan_convert
oslo/B_carotid/README.md CHANGED
@@ -19,6 +19,10 @@ size_categories:
19
 
20
  # USTB - In-vivo Carotid (Verasonics L7-4)
21
 
 
 
 
 
22
  ## Dataset Description
23
 
24
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
@@ -53,7 +57,17 @@ Generalized reconstruction and adaptive beamforming of vascular ultrasound (RFP
53
 
54
  ## Processing the Dataset
55
 
56
- The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
 
 
 
 
 
 
 
 
 
 
57
 
58
  ## Dataset Format
59
 
 
19
 
20
  # USTB - In-vivo Carotid (Verasonics L7-4)
21
 
22
+ ![Focused B-mode of a carotid cross-section](assets/hero.png)
23
+
24
+ *First frame of [`L7_FI_carotid_cross_1.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/B_carotid/L7_FI_carotid_cross_1.hdf5), reconstructed from the raw channel data with `reconstruct.py`.*
25
+
26
  ## Dataset Description
27
 
28
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
 
57
 
58
  ## Processing the Dataset
59
 
60
+ The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
61
+
62
+ `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:
63
+
64
+ ```bash
65
+ zea process \
66
+ --dataset hf://nvidia/OpenH-RF/oslo/B_carotid/L7_FI_carotid_cross_1.hdf5 \
67
+ --config hf://nvidia/OpenH-RF/oslo/B_carotid/pipeline.yaml
68
+ ```
69
+
70
+ This `pipeline.yaml` holds the pipeline and display window of that acquisition. Alternatively, all acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
71
 
72
  ## Dataset Format
73
 
oslo/B_carotid/assets/hero.png ADDED

Git LFS Details

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oslo/B_carotid/assets/main.png ADDED

Git LFS Details

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oslo/B_carotid/pipeline.yaml ADDED
@@ -0,0 +1,41 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # zea pipeline for B_carotid/L7_FI_carotid_cross_1.hdf5, the example acquisition of this sub-dataset.
2
+ # The shared ../pipeline_scanline.yaml plus the per-acquisition settings that
3
+ # ../reconstruct.py takes from ../parameters.yaml (display window in metres,
4
+ # dynamic range), so `zea process` renders it standalone.
5
+ # zea process writes the pixel array as-is, so the grid is sized for square
6
+ # pixels (scanline: resized after log compression).
7
+
8
+ parameters:
9
+ f_number: 1.75
10
+ dynamic_range: [-60, 0]
11
+ enable_scanline: true
12
+ grid_type: cartesian
13
+ selected_transmits: all
14
+ grid_size_z: 700
15
+ zlims: [0.001, 0.06]
16
+ xlims: [-0.019, 0.019]
17
+ pipeline:
18
+ operations:
19
+ - name: keras.ops.cast
20
+ params:
21
+ dtype: float32
22
+ - name: apply_window
23
+ - name: demodulate
24
+ - name: beamform
25
+ params:
26
+ beamformer: delay_and_sum
27
+ enable_aligned_apodization: true
28
+ enable_pfield: false
29
+ - name: envelope_detect
30
+ - name: normalize
31
+ - name: log_compress
32
+ - name: keras.ops.expand_dims
33
+ params:
34
+ axis: -1
35
+ - name: keras.ops.image.resize
36
+ params:
37
+ size: [700, 449]
38
+ interpolation: bilinear
39
+ - name: keras.ops.squeeze
40
+ params:
41
+ axis: -1
oslo/C_verasonics_phantom/README.md CHANGED
@@ -18,6 +18,10 @@ size_categories:
18
 
19
  # USTB - Phantom (Verasonics L7-4 / P4)
20
 
 
 
 
 
21
  ## Dataset Description
22
 
23
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
@@ -52,7 +56,17 @@ Generalized reconstruction, image-quality assessment (resolution, contrast, dyna
52
 
53
  ## Processing the Dataset
54
 
55
- The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
 
 
 
 
 
 
 
 
 
 
56
 
57
  ## Dataset Format
58
 
 
18
 
19
  # USTB - Phantom (Verasonics L7-4 / P4)
20
 
21
+ ![Phased-array sector B-mode of a cyst phantom](assets/hero.png)
22
+
23
+ *First frame of [`FI_P4_cysts_center.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/C_verasonics_phantom/FI_P4_cysts_center.hdf5), reconstructed from the raw channel data with `reconstruct.py`.*
24
+
25
  ## Dataset Description
26
 
27
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
 
56
 
57
  ## Processing the Dataset
58
 
59
+ The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
60
+
61
+ `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:
62
+
63
+ ```bash
64
+ zea process \
65
+ --dataset hf://nvidia/OpenH-RF/oslo/C_verasonics_phantom/FI_P4_cysts_center.hdf5 \
66
+ --config hf://nvidia/OpenH-RF/oslo/C_verasonics_phantom/pipeline.yaml
67
+ ```
68
+
69
+ This `pipeline.yaml` holds the pipeline, display window and sector limits of that acquisition. Alternatively, all acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
70
 
71
  ## Dataset Format
72
 
oslo/C_verasonics_phantom/assets/hero.png ADDED

Git LFS Details

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  • Pointer size: 131 Bytes
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oslo/C_verasonics_phantom/assets/main.png ADDED

Git LFS Details

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oslo/C_verasonics_phantom/pipeline.yaml ADDED
@@ -0,0 +1,34 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # zea pipeline for C_verasonics_phantom/FI_P4_cysts_center.hdf5, the example acquisition of this sub-dataset.
2
+ # The shared ../pipeline_sector.yaml plus the per-acquisition settings that
3
+ # ../reconstruct.py takes from ../parameters.yaml (display window in metres,
4
+ # dynamic range, polar_limits), so `zea process` renders it standalone.
5
+
6
+ parameters:
7
+ f_number: 0
8
+ grid_type: polar
9
+ grid_size_x: 400
10
+ grid_size_z: 600
11
+ dynamic_range: [-60, 0]
12
+ selected_transmits: all
13
+ focal_region_length: 0.002
14
+ pfield_kwargs:
15
+ interpolation: bilinear
16
+ percentile: 70
17
+ alpha: 15
18
+ zlims: [0.001, 0.115]
19
+ polar_limits: [-0.7853981852531433, 0.7853981852531433]
20
+ pipeline:
21
+ operations:
22
+ - name: keras.ops.cast
23
+ params:
24
+ dtype: float32
25
+ - name: apply_window
26
+ - name: demodulate
27
+ - name: beamform
28
+ params:
29
+ beamformer: delay_and_sum
30
+ enable_pfield: true
31
+ - name: envelope_detect
32
+ - name: normalize
33
+ - name: log_compress
34
+ - name: scan_convert
oslo/D_alpinion_phantom/README.md CHANGED
@@ -18,6 +18,10 @@ size_categories:
18
 
19
  # USTB - Phantom (Alpinion L3-8)
20
 
 
 
 
 
21
  ## Dataset Description
22
 
23
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
@@ -52,7 +56,17 @@ Generalized reconstruction and image-quality assessment on a second hardware pla
52
 
53
  ## Processing the Dataset
54
 
55
- The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
 
 
 
 
 
 
 
 
 
 
56
 
57
  ## Dataset Format
58
 
 
18
 
19
  # USTB - Phantom (Alpinion L3-8)
20
 
21
+ ![Plane-wave compounded B-mode of hypoechoic cysts](assets/hero.png)
22
+
23
+ *First frame of [`Alpinion_L3-8_CPWC_hypoechoic.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/D_alpinion_phantom/Alpinion_L3-8_CPWC_hypoechoic.hdf5), reconstructed from the raw channel data with `reconstruct.py`.*
24
+
25
  ## Dataset Description
26
 
27
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
 
56
 
57
  ## Processing the Dataset
58
 
59
+ The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
60
+
61
+ `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:
62
+
63
+ ```bash
64
+ zea process \
65
+ --dataset hf://nvidia/OpenH-RF/oslo/D_alpinion_phantom/Alpinion_L3-8_CPWC_hypoechoic.hdf5 \
66
+ --config hf://nvidia/OpenH-RF/oslo/D_alpinion_phantom/pipeline.yaml
67
+ ```
68
+
69
+ This `pipeline.yaml` holds the pipeline and display window of that acquisition. Alternatively, all acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
70
 
71
  ## Dataset Format
72
 
oslo/D_alpinion_phantom/assets/hero.png ADDED

Git LFS Details

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oslo/D_alpinion_phantom/assets/main.png ADDED

Git LFS Details

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  • Pointer size: 131 Bytes
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oslo/D_alpinion_phantom/pipeline.yaml ADDED
@@ -0,0 +1,29 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # zea pipeline for D_alpinion_phantom/Alpinion_L3-8_CPWC_hypoechoic.hdf5, the example acquisition of this sub-dataset.
2
+ # The shared ../pipeline.yaml plus the per-acquisition settings that
3
+ # ../reconstruct.py takes from ../parameters.yaml (display window in metres,
4
+ # dynamic range), so `zea process` renders it standalone.
5
+ # zea process writes the pixel array as-is, so the grid is sized for square
6
+ # pixels.
7
+
8
+ parameters:
9
+ f_number: 1.75
10
+ grid_size_x: 507
11
+ grid_size_z: 600
12
+ dynamic_range: [-60, 0]
13
+ selected_transmits: all
14
+ zlims: [0.005, 0.05]
15
+ xlims: [-0.019, 0.019]
16
+ pipeline:
17
+ operations:
18
+ - name: keras.ops.cast
19
+ params:
20
+ dtype: float32
21
+ - name: apply_window
22
+ - name: demodulate
23
+ - name: beamform
24
+ params:
25
+ beamformer: delay_and_sum
26
+ enable_pfield: false
27
+ - name: envelope_detect
28
+ - name: normalize
29
+ - name: log_compress
oslo/E_simulation/README.md CHANGED
@@ -19,6 +19,10 @@ size_categories:
19
 
20
  # USTB - Simulation (Field II)
21
 
 
 
 
 
22
  ## Dataset Description
23
 
24
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
@@ -53,7 +57,17 @@ Generalized reconstruction, beamformer development and validation with known gro
53
 
54
  ## Processing the Dataset
55
 
56
- The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
 
 
 
 
 
 
 
 
 
 
57
 
58
  ## Dataset Format
59
 
 
19
 
20
  # USTB - Simulation (Field II)
21
 
22
+ ![B-mode of the PICMUS numerical phantom](assets/hero.png)
23
+
24
+ *First frame of [`PICMUS_numerical_calib_v2.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/E_simulation/PICMUS_numerical_calib_v2.hdf5), reconstructed from the raw channel data with `reconstruct.py`.*
25
+
26
  ## Dataset Description
27
 
28
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
 
57
 
58
  ## Processing the Dataset
59
 
60
+ The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
61
+
62
+ `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:
63
+
64
+ ```bash
65
+ zea process \
66
+ --dataset hf://nvidia/OpenH-RF/oslo/E_simulation/PICMUS_numerical_calib_v2.hdf5 \
67
+ --config hf://nvidia/OpenH-RF/oslo/E_simulation/pipeline.yaml
68
+ ```
69
+
70
+ This `pipeline.yaml` holds the pipeline and display window of that acquisition. Alternatively, all acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)).
71
 
72
  ## Dataset Format
73
 
oslo/E_simulation/assets/hero.png ADDED

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oslo/E_simulation/assets/main.png ADDED

Git LFS Details

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oslo/E_simulation/pipeline.yaml ADDED
@@ -0,0 +1,28 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # zea pipeline for E_simulation/PICMUS_numerical_calib_v2.hdf5, the example acquisition of this sub-dataset.
2
+ # The shared ../pipeline_iq.yaml plus the per-acquisition settings that
3
+ # ../reconstruct.py takes from ../parameters.yaml (display window in metres,
4
+ # dynamic range), so `zea process` renders it standalone.
5
+ # zea process writes the pixel array as-is, so the grid is sized for square
6
+ # pixels.
7
+
8
+ parameters:
9
+ f_number: 1.75
10
+ grid_size_x: 507
11
+ grid_size_z: 600
12
+ dynamic_range: [-60, 0]
13
+ selected_transmits: all
14
+ zlims: [0.005, 0.05]
15
+ xlims: [-0.019, 0.019]
16
+ pipeline:
17
+ operations:
18
+ - name: keras.ops.cast
19
+ params:
20
+ dtype: float32
21
+ - name: apply_window
22
+ - name: beamform
23
+ params:
24
+ beamformer: delay_and_sum
25
+ enable_pfield: false
26
+ - name: envelope_detect
27
+ - name: normalize
28
+ - name: log_compress
oslo/F_motion/README.md CHANGED
@@ -19,6 +19,10 @@ size_categories:
19
 
20
  # USTB - Motion Estimation (SWE / ARFI, Verasonics L7-4)
21
 
 
 
 
 
22
  ## Dataset Description
23
 
24
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
@@ -53,7 +57,17 @@ Motion estimation (RFP task 6.4): shear-wave velocity estimation, ARFI displacem
53
 
54
  ## Processing the Dataset
55
 
56
- The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)). These plane-wave tracking acquisitions use the non-focused `compound` pipeline, and the reference reconstruction shows a single tracking frame.
 
 
 
 
 
 
 
 
 
 
57
 
58
  ## Dataset Format
59
 
 
19
 
20
  # USTB - Motion Estimation (SWE / ARFI, Verasonics L7-4)
21
 
22
+ ![Shear waves travelling outward after an acoustic push](assets/hero.gif)
23
+
24
+ *First push-track sequence (frames 1-49) of [`SWE_L7_type_III.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/F_motion/SWE_L7_type_III.hdf5): B-mode (left) and axial displacement between consecutive frames (right), a lag-one autocorrelation (Kasai) estimate on the IQ beamformed with `pipeline.yaml`. The displacement estimate is not part of the reference pipeline.*
25
+
26
  ## Dataset Description
27
 
28
  Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
 
57
 
58
  ## Processing the Dataset
59
 
60
+ The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
61
+
62
+ `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:
63
+
64
+ ```bash
65
+ zea process \
66
+ --dataset hf://nvidia/OpenH-RF/oslo/F_motion/SWE_L7_type_III.hdf5 \
67
+ --config hf://nvidia/OpenH-RF/oslo/F_motion/pipeline.yaml
68
+ ```
69
+
70
+ This `pipeline.yaml` holds the pipeline and display window of that acquisition. Alternatively, all acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py) at the root of this collection, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` definitions at the collection root and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub; `parameters.yaml` picks the pipeline, display window and dynamic range per acquisition (see the [collection card](../README.md#processing-the-dataset)). These plane-wave tracking acquisitions use the non-focused `compound` pipeline, and the reference reconstruction shows a single tracking frame.
71
 
72
  ## Dataset Format
73
 
oslo/F_motion/assets/hero.gif ADDED

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oslo/F_motion/pipeline.yaml ADDED
@@ -0,0 +1,29 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # zea pipeline for F_motion/SWE_L7_type_III.hdf5, the example acquisition of this sub-dataset.
2
+ # The shared ../pipeline.yaml plus the per-acquisition settings that
3
+ # ../reconstruct.py takes from ../parameters.yaml (display window in metres,
4
+ # dynamic range), so `zea process` renders it standalone.
5
+ # zea process writes the pixel array as-is, so the grid is sized for square
6
+ # pixels.
7
+
8
+ parameters:
9
+ f_number: 1.75
10
+ grid_size_x: 585
11
+ grid_size_z: 600
12
+ dynamic_range: [-60, 0]
13
+ selected_transmits: all
14
+ zlims: [0.001, 0.04]
15
+ xlims: [-0.019, 0.019]
16
+ pipeline:
17
+ operations:
18
+ - name: keras.ops.cast
19
+ params:
20
+ dtype: float32
21
+ - name: apply_window
22
+ - name: demodulate
23
+ - name: beamform
24
+ params:
25
+ beamformer: delay_and_sum
26
+ enable_pfield: false
27
+ - name: envelope_detect
28
+ - name: normalize
29
+ - name: log_compress
oslo/README.md CHANGED
@@ -18,9 +18,9 @@ size_categories:
18
 
19
  # UltraSound ToolBox (USTB) Channel Capture Collection
20
 
21
- ![Focused sector B-mode of an apical four-chamber view](assets/Verasonics_P2-4_apical_four_chamber_subject_1_zea_bmode.png)
22
 
23
- *Apical four-chamber view reconstructed from the raw channel data, [`A_cardiac/Verasonics_P2-4_apical_four_chamber_subject_1.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/A_cardiac/Verasonics_P2-4_apical_four_chamber_subject_1.hdf5).*
24
 
25
  ## Dataset Description
26
 
@@ -57,7 +57,7 @@ Total: **39 acquisitions**, 8.61 GB of stored HDF5 data.
57
 
58
  ## Processing the Dataset
59
 
60
- Every acquisition is reconstructable from the file alone — all acquisition parameters live in the zea `/scan` and `/probe` groups. The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py), as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` and `parameters.yaml` definitions in this folder and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub: set `PATHS` to the acquisition to reconstruct (default: the apical four-chamber cardiac scan above) and `REFOCUS = True` to also emit the REFoCUS variant. See [Reconstruction Details](#reconstruction-details) for how each acquisition's pipeline is chosen.
61
 
62
  ## Dataset Format
63
 
 
18
 
19
  # UltraSound ToolBox (USTB) Channel Capture Collection
20
 
21
+ ![B-modes from five of the six sub-datasets: in-vivo cardiac, in-vivo carotid, Verasonics and Alpinion phantoms, and simulation](assets/hero.png)
22
 
23
+ *First frames reconstructed from the raw channel data with `reconstruct.py`. Top: [`A_cardiac/Verasonics_P2-4_parasternal_long_subject_1`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/A_cardiac/Verasonics_P2-4_parasternal_long_subject_1.hdf5), [`A_cardiac/Verasonics_P2-4_apical_four_chamber_subject_1`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/A_cardiac/Verasonics_P2-4_apical_four_chamber_subject_1.hdf5), [`C_verasonics_phantom/FI_P4_cysts_center`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/C_verasonics_phantom/FI_P4_cysts_center.hdf5). Bottom: [`B_carotid/L7_FI_carotid_cross_1`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/B_carotid/L7_FI_carotid_cross_1.hdf5), [`C_verasonics_phantom/L7_FI_Verasonics_CIRS`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/C_verasonics_phantom/L7_FI_Verasonics_CIRS.hdf5), [`D_alpinion_phantom/Alpinion_L3-8_CPWC_hypoechoic`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/D_alpinion_phantom/Alpinion_L3-8_CPWC_hypoechoic.hdf5), [`E_simulation/PICMUS_numerical_calib_v2`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/oslo/E_simulation/PICMUS_numerical_calib_v2.hdf5). Panels are scaled to a common height per row, not to a common physical scale.*
24
 
25
  ## Dataset Description
26
 
 
57
 
58
  ## Processing the Dataset
59
 
60
+ Every acquisition is reconstructable from the file alone — all acquisition parameters live in the zea `/scan` and `/probe` groups. The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/oslo/reconstruct.py), as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline*.yaml` and `parameters.yaml` definitions in this folder and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub: set `PATHS` to the acquisition to reconstruct (default: the apical four-chamber cardiac scan above) and `REFOCUS = True` to also emit the REFoCUS variant. See [Reconstruction Details](#reconstruction-details) for how each acquisition's pipeline is chosen. Each sub-dataset folder also holds a `pipeline.yaml` for its example acquisition, so it can be rendered with a single `zea process` command (see the sub-dataset cards).
61
 
62
  ## Dataset Format
63
 
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