oslo: add hero and main images for the collection and each sub-dataset
#66
by tristan-deep - opened
- oslo/A_cardiac/README.md +15 -1
- oslo/A_cardiac/assets/hero.gif +3 -0
- oslo/A_cardiac/assets/main.png +3 -0
- oslo/A_cardiac/pipeline.yaml +34 -0
- oslo/B_carotid/README.md +15 -1
- oslo/B_carotid/assets/hero.png +3 -0
- oslo/B_carotid/assets/main.png +3 -0
- oslo/B_carotid/pipeline.yaml +41 -0
- oslo/C_verasonics_phantom/README.md +15 -1
- oslo/C_verasonics_phantom/assets/hero.png +3 -0
- oslo/C_verasonics_phantom/assets/main.png +3 -0
- oslo/C_verasonics_phantom/pipeline.yaml +34 -0
- oslo/D_alpinion_phantom/README.md +15 -1
- oslo/D_alpinion_phantom/assets/hero.png +3 -0
- oslo/D_alpinion_phantom/assets/main.png +3 -0
- oslo/D_alpinion_phantom/pipeline.yaml +29 -0
- oslo/E_simulation/README.md +15 -1
- oslo/E_simulation/assets/hero.png +3 -0
- oslo/E_simulation/assets/main.png +3 -0
- oslo/E_simulation/pipeline.yaml +28 -0
- oslo/F_motion/README.md +15 -1
- oslo/F_motion/assets/hero.gif +3 -0
- oslo/F_motion/assets/main.png +3 -0
- oslo/F_motion/pipeline.yaml +29 -0
- oslo/README.md +3 -3
- oslo/assets/hero.png +3 -0
- oslo/assets/main.png +3 -0
oslo/A_cardiac/README.md
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# USTB - In-vivo Cardiac (Verasonics P4-2)
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## Dataset Description
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Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
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## Processing the Dataset
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-
The
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## Dataset Format
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# USTB - In-vivo Cardiac (Verasonics P4-2)
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*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`.*
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## Dataset Description
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Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
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## Processing the Dataset
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The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
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`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:
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```bash
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zea process \
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--dataset hf://nvidia/OpenH-RF/oslo/A_cardiac/Verasonics_P2-4_parasternal_long_subject_1.hdf5 \
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--config hf://nvidia/OpenH-RF/oslo/A_cardiac/pipeline.yaml
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```
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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)).
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## Dataset Format
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oslo/A_cardiac/assets/hero.gif
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Git LFS Details
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oslo/A_cardiac/assets/main.png
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Git LFS Details
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oslo/A_cardiac/pipeline.yaml
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# zea pipeline for A_cardiac/Verasonics_P2-4_parasternal_long_subject_1.hdf5, the example acquisition of this sub-dataset.
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# The shared ../pipeline_sector.yaml plus the per-acquisition settings that
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# ../reconstruct.py takes from ../parameters.yaml (display window in metres,
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# dynamic range, polar_limits), so `zea process` renders it standalone.
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parameters:
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f_number: 0
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grid_type: polar
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grid_size_x: 400
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grid_size_z: 600
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dynamic_range: [-60, 0]
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selected_transmits: all
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focal_region_length: 0.002
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pfield_kwargs:
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interpolation: bilinear
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percentile: 70
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alpha: 15
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zlims: [0.001, 0.11]
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polar_limits: [-0.6552720665931702, 0.6552720665931702]
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pipeline:
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operations:
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- name: keras.ops.cast
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params:
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dtype: float32
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- name: apply_window
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- name: demodulate
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- name: beamform
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params:
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beamformer: delay_and_sum
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enable_pfield: true
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- name: envelope_detect
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- name: normalize
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- name: log_compress
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- name: scan_convert
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oslo/B_carotid/README.md
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# USTB - In-vivo Carotid (Verasonics L7-4)
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## Dataset Description
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Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
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## Processing the Dataset
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-
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## Dataset Format
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# USTB - In-vivo Carotid (Verasonics L7-4)
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*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`.*
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## Dataset Description
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Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
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## Processing the Dataset
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The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
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`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:
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```bash
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zea process \
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--dataset hf://nvidia/OpenH-RF/oslo/B_carotid/L7_FI_carotid_cross_1.hdf5 \
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--config hf://nvidia/OpenH-RF/oslo/B_carotid/pipeline.yaml
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```
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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)).
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## Dataset Format
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oslo/B_carotid/assets/hero.png
ADDED
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Git LFS Details
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oslo/B_carotid/assets/main.png
ADDED
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Git LFS Details
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oslo/B_carotid/pipeline.yaml
ADDED
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# zea pipeline for B_carotid/L7_FI_carotid_cross_1.hdf5, the example acquisition of this sub-dataset.
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# The shared ../pipeline_scanline.yaml plus the per-acquisition settings that
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# ../reconstruct.py takes from ../parameters.yaml (display window in metres,
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# dynamic range), so `zea process` renders it standalone.
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# zea process writes the pixel array as-is, so the grid is sized for square
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# pixels (scanline: resized after log compression).
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parameters:
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f_number: 1.75
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dynamic_range: [-60, 0]
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enable_scanline: true
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grid_type: cartesian
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selected_transmits: all
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grid_size_z: 700
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zlims: [0.001, 0.06]
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xlims: [-0.019, 0.019]
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pipeline:
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operations:
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- name: keras.ops.cast
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params:
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dtype: float32
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- name: apply_window
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- name: demodulate
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- name: beamform
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params:
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beamformer: delay_and_sum
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enable_aligned_apodization: true
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enable_pfield: false
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- name: envelope_detect
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- name: normalize
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- name: log_compress
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- name: keras.ops.expand_dims
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params:
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axis: -1
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- name: keras.ops.image.resize
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params:
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size: [700, 449]
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interpolation: bilinear
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- name: keras.ops.squeeze
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params:
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axis: -1
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oslo/C_verasonics_phantom/README.md
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# USTB - Phantom (Verasonics L7-4 / P4)
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## Dataset Description
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Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
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## Processing the Dataset
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-
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## Dataset Format
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# USTB - Phantom (Verasonics L7-4 / P4)
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*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`.*
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## Dataset Description
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Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
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## Processing the Dataset
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The example acquisition can be processed with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea).
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`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:
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```bash
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zea process \
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--dataset hf://nvidia/OpenH-RF/oslo/C_verasonics_phantom/FI_P4_cysts_center.hdf5 \
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--config hf://nvidia/OpenH-RF/oslo/C_verasonics_phantom/pipeline.yaml
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```
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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)).
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## Dataset Format
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oslo/C_verasonics_phantom/assets/hero.png
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Git LFS Details
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oslo/C_verasonics_phantom/assets/main.png
ADDED
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Git LFS Details
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oslo/C_verasonics_phantom/pipeline.yaml
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# zea pipeline for C_verasonics_phantom/FI_P4_cysts_center.hdf5, the example acquisition of this sub-dataset.
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# The shared ../pipeline_sector.yaml plus the per-acquisition settings that
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# ../reconstruct.py takes from ../parameters.yaml (display window in metres,
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# dynamic range, polar_limits), so `zea process` renders it standalone.
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parameters:
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f_number: 0
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grid_type: polar
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grid_size_x: 400
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grid_size_z: 600
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dynamic_range: [-60, 0]
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selected_transmits: all
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focal_region_length: 0.002
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pfield_kwargs:
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interpolation: bilinear
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percentile: 70
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alpha: 15
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zlims: [0.001, 0.115]
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polar_limits: [-0.7853981852531433, 0.7853981852531433]
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pipeline:
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operations:
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- name: keras.ops.cast
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params:
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dtype: float32
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- name: apply_window
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- name: demodulate
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- name: beamform
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params:
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beamformer: delay_and_sum
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enable_pfield: true
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- name: envelope_detect
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- name: normalize
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- name: log_compress
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- name: scan_convert
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oslo/D_alpinion_phantom/README.md
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# USTB - Phantom (Alpinion L3-8)
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## Dataset Description
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Part of the **UltraSound ToolBox (USTB) Channel Capture Collection** (see the [collection card](../README.md)).
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## Processing the Dataset
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-
The
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## Dataset Format
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# USTB - Phantom (Alpinion L3-8)
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| 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
|
oslo/D_alpinion_phantom/assets/main.png
ADDED
|
Git LFS Details
|
oslo/D_alpinion_phantom/pipeline.yaml
ADDED
|
@@ -0,0 +1,29 @@
|
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|
| 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
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
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|
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|
|
|
|
| 57 |
|
| 58 |
## Dataset Format
|
| 59 |
|
|
|
|
| 19 |
|
| 20 |
# USTB - Simulation (Field II)
|
| 21 |
|
| 22 |
+

|
| 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
|
Git LFS Details
|
oslo/E_simulation/assets/main.png
ADDED
|
Git LFS Details
|
oslo/E_simulation/pipeline.yaml
ADDED
|
@@ -0,0 +1,28 @@
|
|
|
|
|
|
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|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 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
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 57 |
|
| 58 |
## Dataset Format
|
| 59 |
|
|
|
|
| 19 |
|
| 20 |
# USTB - Motion Estimation (SWE / ARFI, Verasonics L7-4)
|
| 21 |
|
| 22 |
+

|
| 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
|
Git LFS Details
|
oslo/F_motion/assets/main.png
ADDED
|
Git LFS Details
|
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 |
-
, 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 |
+

|
| 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 |
|
oslo/assets/hero.png
ADDED
|
Git LFS Details
|
oslo/assets/main.png
ADDED
|
Git LFS Details
|