colorado-boulder: sync data card and tracked-SSA figures with GitHub

colorado-boulder/README.md

@@ -1,5 +1,5 @@
 ---
-pretty_name: "OpenH-RF — Tracked Swept Synthetic Aperture 3D Phantom Dataset"
+pretty_name: "OpenH-RF — Tracked Swept Synthetic Aperture Ultrasound Datasets"
 license: cc-by-4.0
 task_categories:
   - generalized-reconstruction
@@ -14,15 +14,29 @@ size_categories:
   - n<1K
 ---
 
-# Tracked Swept Synthetic Aperture 3D Phantom Ultrasound Dataset
+# Tracked Swept Synthetic Aperture Ultrasound Datasets
+
+*Freehand, optically tracked swept synthetic aperture (SSA) raw-channel ultrasound from phantoms and in-vivo quadriceps, for the OpenH-RF initiative.*
+
+| 2D ATS 539 phantom | 3D phantom | In-vivo quadriceps |
+|:---:|:---:|:---:|
+| ![Tracked SSA sweep through the 2D ATS 539 phantom](assets/ssa-sweep-phantom2d.gif) | ![Tracked SSA sweep through the 3D phantom](assets/ssa-sweep-phantom3d.gif) | ![Tracked SSA sweep along in-vivo quadriceps muscle](assets/ssa-sweep-invivo.gif) |
+| `Sub-dataset-1` | `Sub-dataset-2` | `Sub-dataset-3` |
+
+Motion-compensated tracked SSA reconstructions, one per sub-dataset. Each frame
+beamforms the raw RF channel data with its own tracked probe pose; a 40 mm window of
+frames is then coherently summed to synthesise a larger effective aperture, and the
+window slides along the freehand sweep. Produced by `reconstruct.py`.
 
 ## 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.
+This dataset contains tracked swept synthetic aperture (SSA) ultrasound acquisitions from three targets: a 2D ATS 539 multipurpose imaging phantom, a 3D ultrasound imaging phantom, and in-vivo quadriceps muscle from healthy volunteer participants.
 
-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.
+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.
 
-This dataset contains phantom data only. It does not contain human subject data, animal data, or protected health information (PHI).
+The purpose of this dataset is to provide reproducible examples for generalized ultrasound reconstruction, with a particular focus on motion-compensated tracked SSA reconstruction using the zea/OpenH-RF data format.
+
+The phantom acquisitions do not contain human subject data, animal data, or protected health information (PHI). The in-vivo acquisitions were collected from healthy volunteer participants and de-identified prior to release.
 
 ## Dataset Contributor(s)
 
@@ -35,39 +49,59 @@ This dataset contains phantom data only. It does not contain human subject data,
 
 ## Dataset Creation Date
 
-06/24/2025
+Data were collected between 08/23/2024 and 06/30/2026.
 
 ## 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.
+The phantom data consist exclusively of phantom ultrasound acquisitions and are cleared for release under CC BY 4.0. The in-vivo data were collected under institutional approval and have been de-identified prior to release. No protected health information (PHI) is included in the released files.
 
 ## 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.
+This dataset is intended for research on generalized ultrasound reconstruction, with a specific 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 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.
 
-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
+The dataset includes acquisitions from three targets:
 
-### Acquisition Details
+- 2D ATS 539 multipurpose imaging phantom
+- 3D ultrasound imaging phantom
+- In-vivo quadriceps muscle from healthy volunteer participants
 
-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.
+The ATS 539 multipurpose imaging phantom contains:
 
-Diverging waves were generated using a negative virtual source with the 20 central array elements active on transmit.
+- Wire targets
+- Cylindrical lesions
+- Tissue-mimicking speckle regions
 
+These targets may be used to assess spatial resolution, contrast, lesion visibility, and speckle characteristics.
+
+### Data Collection Method
+
+Each acquisition consisted of a freehand sweep in the lateral direciton of the transducer.
+All 64 array elements were used during receive. Diverging waves were generated using a negative virtual source while activating the 20 central array elements during transmit.
+For in-vivo targets the transducer was manually swept along the longitudinal direction of the quadriceps while transmitting diverging waves at 400 Hz.
 The transducer was optically tracked using an NDI Polaris Vega® XT optical tracking system manufactured by Northern Digital Inc., Ontario, Canada.
 
-### Probe and Geometry
+### Labeling Method
+
+None (N/A).
+
+### Acquisition System
 
-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.
+- Verasonics Vantage research ultrasound scanner
+- Verasonics P4-2 phased array transducer
+- 64 elements
+- Reconstruction center frequency: 2.5 MHz
+- Sampling frequency: 10 MHz
+- Optical tracking: NDI Polaris Vega XT
+
+---
 
-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
 
@@ -84,20 +118,21 @@ Each file includes:
 - 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.
+The stored RF channel data have not been beamformed, demodulated, envelope detected, normalized, or log compressed. These processing steps are performed by the accompanying reconstruction pipeline.
 
 ## Dataset Quantification
 
 **Current OpenH-RF release:** 62 HDF5 files; 16.04 GB (16,037,117,952 bytes) stored; root `zea_version` **0.1.6**. Sizes include all HDF5 contents and use decimal units (MB = 10^6 bytes, GB = 10^9 bytes, TB = 10^12 bytes), not decoded-array memory or original-source download sizes.
 
-- **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
+- Number of phantom objects: 2
+- Number of volunteer participants: 7
+- Number of acquisitions: 62
+- Number of RF frames per acquisition: 1200–1600
+- Number of transmit events per frame: 1
+- Number of receive elements: 64
+- Number of active transmit elements: 20
 
-### Per-File Feature Summary
+### Per-acquisition contents
 
 | Feature | Shape | Data type | Units | Description |
 |---|---:|---|---|---|
@@ -133,42 +168,62 @@ migration is still pending. Replacement files are uploaded only after
 per-file validation; readers supporting both revisions should check the
 canonical locations first, then the legacy locations.
 
+This dataset contains acquisitions from two ultrasound imaging phantoms and healthy volunteer participants.
 
-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
+- Subject types: 2D imaging phantom, 3D phantom, and in-vivo human ultrasound data
+- 2D phantom model: ATS 539
+- 2D phantom target types: wires, cylindrical lesions, and tissue-mimicking speckle
+- In-vivo anatomical region: quadriceps muscle
+- Human participants: healthy volunteer participants for the in-vivo dataset
+- 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 submission includes a `zea.Pipeline` that reconstructs representative tracked SSA B-mode images 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
+4. Coherent SSA compounding
 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.
+The reconstruction is defined in `pipeline.yaml` and executed using `reconstruct.py`:
+
+```bash
+python reconstruct.py
+```
+
+The script streams an acquisition straight from the Hub, selects tracked frames at
+roughly 1 mm lateral spacing, and writes the reconstruction to `ssa_bmode.png`. Point
+`DATA_FILE` at any acquisition in the corpus to reconstruct it.
+[`assets/main_bmode.png`](./assets/main_bmode.png) was produced this way, compounding
+the full sweep into one image; the loops at the top of this card slide a shorter
+aperture window along the sweep instead.
+
+`reconstruct.py` defines the custom `apply_probe_pose` operation that `pipeline.yaml`
+refers to, which applies the frame-wise `metadata/probe_pose` to the probe geometry
+and transmit origins before beamforming.
 
 ## Known Issues
 
 - Optical tracking measurements may contain small position and orientation uncertainties.
 - Reconstruction quality depends on tracking calibration accuracy and coherent alignment between frames.
-
+- The in-vivo dataset is intended for research use and has not been optimized for clinical workflows.
 
 ## 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.
+The phantom acquisitions contain phantom ultrasound data only. They do not contain human participants, animal subjects, personal identifiers, clinical records, or protected health information.
+
+Human-subject consent and institutional review board approval are not applicable to the phantom acquisitions.
+
+The in-vivo data were acquired from volunteer participants with informed consent under IRB-approved protocol #24-0176.
 
-Human-subject consent and institutional review board approval are therefore not applicable.
+All released in-vivo data have been de-identified. No protected health information or participant-identifying metadata are included.