Add colorado-boulder README + pipeline(s) from accepted_submissions

colorado-boulder/README.md

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+---
+pretty_name: "OpenH-RF — Tracked Swept Synthetic Aperture 3D Phantom Dataset"
+license: cc-by-4.0
+task_categories:
+  - generalized-reconstruction
+tags:
+  - ultrasound
+  - rf
+  - openh-rf
+  - 3d
+language:
+  - en
+size_categories:
+  - n<1K
+---
+
+# Tracked Swept Synthetic Aperture 3D Phantom Ultrasound Dataset
+
+## Dataset Description
+
+This dataset contains tracked swept synthetic aperture (SSA) ultrasound acquisitions of a 3D ultrasound imaging phantom. The data were acquired using a Verasonics Vantage research ultrasound system with a P4-2 phased array transducer.
+
+The dataset includes raw RF channel data, acquisition parameters, probe geometry, transmit information, and frame-wise tracked probe pose metadata. Its purpose is to provide a reproducible example of motion-compensated SSA reconstruction from raw channel data using the zea/OpenH-RF data format.
+
+This dataset contains phantom data only. It does not contain human subject data, animal data, or protected health information (PHI).
+
+## Dataset Contributor(s)
+
+**Contributing organization:** University of Colorado Boulder, Bottenus Lab
+
+**Contributors:**
+
+- Anet Sanchez
+- Nick Bottenus
+
+## Dataset Creation Date
+
+06/24/2025
+
+## License / Terms of Use
+
+This dataset is released under the Creative Commons Attribution 4.0 International License (CC BY 4.0).
+
+The contributed data consist exclusively of phantom ultrasound acquisitions and are cleared for release under CC BY 4.0. Patient consent, clinical data-use agreements, and PHI de-identification are not applicable because the dataset does not contain human subject data.
+
+## Intended Usage
+
+This dataset is intended for research on generalized ultrasound reconstruction, with a particular focus on tracked swept synthetic aperture imaging, motion-compensated beamforming, coherent compounding, and ultrasound image-quality evaluation.
+
+For SSA reconstruction, each raw RF frame is beamformed using its corresponding tracked transducer pose. The resulting beamformed IQ frames are placed on a common reconstruction grid and coherently summed to synthesize a larger effective aperture. Because the reconstruction relies on coherent compounding, summation is performed before envelope detection, normalization, and log compression.
+
+## Dataset Characterization
+
+- **Data Collection Method:** Phantom ultrasound acquisition
+- **Labeling Method:** N/A; no manual labels or segmentation masks are provided
+- **Acquisition System:** Verasonics Vantage research ultrasound scanner with a Verasonics P4-2 phased array transducer
+
+### Acquisition Details
+
+The transducer was manually swept over the phantom field of view while diverging-wave transmissions were acquired at 400 Hz. All 64 array elements were used on receive.
+
+Diverging waves were generated using a negative virtual source with the 20 central array elements active on transmit.
+
+The transducer was optically tracked using an NDI Polaris Vega® XT optical tracking system manufactured by Northern Digital Inc., Ontario, Canada.
+
+### Probe and Geometry
+
+The acquisition used a Verasonics P4-2 phased array transducer with 64 elements. The center frequency stored in the acquisition and used for reconstruction is 2.5 MHz.
+
+The probe geometry, transmit origins, transmit delays, transmit apodization, and other acquisition parameters are stored in the zea/OpenH-RF file. Frame-wise probe translations and rotations are stored using the native `metadata/probe_pose` structure.
+
+## Dataset Format
+
+The dataset is distributed in the zea/OpenH-RF HDF5 format.
+
+Each file includes:
+
+- Raw RF channel data
+- Sampling and center frequencies
+- Transmit delays and apodization
+- Transmit origins
+- Probe geometry
+- Sound-speed information
+- Frame-wise tracked probe translations
+- Frame-wise tracked probe rotations
+
+The stored RF channel data have not been beamformed, envelope detected, normalized, or log compressed. The accompanying reconstruction pipeline performs these processing steps.
+
+## Dataset Quantification
+
+- **Number of phantom objects:** 1
+- **Number of acquisitions:** 10
+- **Number of RF frames per acquisition:** 1200
+- **Number of transmit events per frame:** 1
+- **Number of receive elements:** 64
+- **Number of active transmit elements:** 20
+
+### Per-File Feature Summary
+
+| Feature | Shape | Data type | Units | Description |
+|---|---:|---|---|---|
+| Raw RF data | `n_frames × n_tx × n_ax × n_elements × n_channels` | `float32` | acquisition units | Raw RF channel measurements |
+| Probe translation | `n_frames × 3` | `float32` | m | Frame-wise tracked probe position |
+| Probe rotation | `n_frames × 4` | `float32` | unit quaternion | Frame-wise tracked probe orientation in `xyzw` order |
+| Probe geometry | `64 × 3` | `float32` | m | Array-element coordinates |
+| Transmit origins | `n_tx × 3` | `float32` | m | Diverging-wave virtual-source coordinates |
+| Transmit delays | `n_tx × 64` | `float32` | s | Per-element transmit delays |
+| Transmit apodization | `n_tx × 64` | `float32` | unitless | Per-element transmit activation and weighting |
+
+## Subject Metadata
+
+This dataset contains one 3D ultrasound imaging phantom.
+
+- **Subject type:** 3D phantom
+- **Anatomical region:** Not applicable
+- **Human participants:** None
+- **Animal subjects:** None
+- **Protected health information:** None
+- **Scanner:** Verasonics Vantage
+- **Probe:** Verasonics P4-2 phased array
+
+## Data Validation
+
+The submission includes a `zea.Pipeline` that reconstructs a representative tracked SSA B-mode image from the raw RF channel data.
+
+The pipeline performs:
+
+1. Frame-wise demodulation
+2. Application of the tracked probe pose
+3. Delay-and-sum beamforming onto a common reconstruction grid
+4. Coherent summation of the beamformed IQ frames
+5. Envelope detection
+6. Normalization
+7. Log compression
+
+The reconstruction is defined in `pipeline.yaml` and executed using `reconstruct.py`. A representative reconstructed B-mode image is included with the dataset.
+
+## Known Issues
+
+- Optical tracking measurements may contain small position and orientation uncertainties.
+- Reconstruction quality depends on tracking calibration accuracy and coherent alignment between frames.
+
+
+## Ethical Considerations
+
+This dataset contains phantom ultrasound data only. It does not contain human participants, animal subjects, personal identifiers, clinical records, or protected health information.
+
+Human-subject consent and institutional review board approval are therefore not applicable.
+

colorado-boulder/pipeline.yaml

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+pipeline:
+    operations:
+    -   name: map
+        operations:
+        -   name: keras.ops.squeeze
+            params:
+                axis: 0
+                jit_compile: false
+        -   name: keras.ops.cast
+            params:
+                dtype: float32
+                jit_compile: false
+        -   name: demodulate
+            params:
+                jit_compile: false
+        -   name: apply_probe_pose
+            params:
+                jit_compile: false
+        -   name: beamform
+            params:
+                jit_options: null
+                num_patches: 200
+                with_batch_dim: false
+        -   name: keras.ops.expand_dims
+            params:
+                axis: 0
+                jit_compile: false
+        params:
+            argnames:
+            - data
+            - probe_translation
+            - probe_rotation
+            batch_size: 1
+            with_batch_dim: false
+    -   name: keras.ops.sum
+        params:
+            axis: 0
+    - envelope_detect
+    -   name: normalize
+        params:
+            output_range:
+            - 0.0
+            - 1.0
+    - log_compress
+    with_batch_dim: false