Add weillcornell README + pipeline(s) from accepted_submissions

weillcornell/README.md

@@ -0,0 +1,154 @@
+---
+license: cc-by-4.0
+pretty_name: OpenH-RF QUS Phantom Dataset
+task_categories:
+  - image-to-image
+  - feature-extraction
+tags:
+  - ultrasound
+  - rf
+  - openh-rf
+  - quantitative-ultrasound
+  - phantom
+  - raw-channel-data
+language:
+  - en
+size_categories:
+  - n<1K
+---
+
+# OpenH-RF QUS Phantom Dataset
+
+Pre-beamformed RF channel data from three homogeneous tissue-mimicking
+phantoms. Each zea HDF5 acquisition is self-contained and includes raw RF,
+model-derived theoretical backscatter coefficient (BSC), direct per-frame
+Nakagami maps, and 20-frame pooled Nakagami references.
+
+## Contributors
+
+Shangke Liu, Tipu Sultan, Cameron Hoerig, and Jonathan Mamou;
+Biomedical Ultrasound Research Laboratory (BURL), Weill Cornell Medicine.
+
+Contact: Shangke Liu, shl4035@med.cornell.edu
+
+## Dataset Summary
+
+- Verasonics Vantage 256 and GE9LD linear array
+- 192 elements, 0.23 mm pitch, 5.2083 MHz center frequency
+- One normal-incidence plane wave per frame
+- 20.8333 MHz RF sampling; 1540 m/s sound-speed metadata
+- 3 phantoms x 2 operators x 20 probe placements x 20 frames
+- 120 acquisitions and 2400 frames
+- Phantom-only data; no human or animal subjects, clinical metadata, or PHI
+- No predefined train/validation/test split
+
+Keep all frames from one acquisition in the same split.
+
+## Files
+
+```text
+data/<scan_id>.hdf5                         self-contained zea acquisitions
+reconstruct.py                              B-mode and QUS example
+pipeline.yaml                               zea reconstruction pipeline
+LICENSE                                     CC BY 4.0 license
+ac1_15m_SK_pipeline.png                     reference zea reconstruction
+```
+
+Scan IDs use `ac<number>_<phantom>_<operator>`, for example
+`ac1_15m_SK`. Phantom IDs are `15m`, `18m`, and `60m`; operator IDs are
+`SK` and `TP`; acquisition numbers run from 1 to 20.
+
+## HDF5 Contents
+
+Each file follows zea 0.1.3 and contains one track. Raw RF is stored as `int16`
+ADC counts without demodulation, decimation, or resampling.
+
+| Field under `tracks/track_0/data/` | Shape | dtype | Unit | Meaning |
+|---|---|---|---|---|
+| `raw_data` | `(20,1,n_ax,192,1)` | `int16` | ADC counts | Raw RF input |
+| `theoretical_bsc/values` | `(20,z,x,157)` | `float32` | `m^-1 sr^-1` | Model-derived BSC target |
+| `nakagami_m_per_frame/values` | `(20,z,x)` | `float32` | `1` | Direct single-frame shape estimate |
+| `nakagami_omega_per_frame/values` | `(20,z,x)` | `float32` | `a.u.^2` | Direct single-frame spread estimate |
+| `nakagami_m_pooled/values` | `(20,z,x)` | `float32` | `1` | 20-frame pooled shape reference |
+| `nakagami_omega_pooled/values` | `(20,z,x)` | `float32` | `a.u.^2` | 20-frame pooled spread reference |
+
+The five QUS products are zea Map fields with `values`, Cartesian
+`coordinates` in `[x,y,z]` order and metres, `description`, `unit`, `min`, and
+`max`. The BSC field also contains 157 `labels` of the form
+`frequency_hz=<value>`, spanning 3.3162435-6.4900716 MHz.
+
+Map grids are `(z,x)=(26,35)` for `15m` and `18m`, and `(53,35)` for `60m`.
+The analysis windows are approximately 2.96 mm axial by 4.37 mm lateral with
+75% overlap. Nakagami maps use normal-incidence delay-and-sum beamforming,
+Hann receive apodization, and intensity-domain maximum-likelihood fitting,
+with `omega = E[A^2]`.
+
+The theoretical BSC is a homogeneous phantom material property: each phantom
+has one curve, broadcast over space and all 20 frames. The pooled Nakagami maps
+are also repeated along the frame axis so every single-frame input has the same
+20-frame reference. The pooled estimate includes the selected input frame.
+
+Metadata uses `metadata.subject.type="phantom"` and a phantom ID. Anatomical
+annotations and anatomical-view annotations are intentionally omitted.
+Plane-wave acquisition is recorded in the file description, and the linear
+array geometry is recorded in the probe fields.
+
+## Suggested Tasks
+
+1. Reconstruct B-mode from one frame of raw RF.
+2. Predict the phantom's theoretical BSC curve from one RF frame. This is a
+   material-model target, not a local experimentally estimated BSC curve.
+3. Predict pooled Nakagami `m` or `omega` from one RF frame. Use the supplied
+   direct per-frame map as the single-frame baseline.
+
+For Nakagami predictions, report MAE/RMSE and map correlation against the
+pooled reference. For BSC predictions, report the frequency range and unit and
+state whether evaluation uses linear BSC or a specified dB conversion.
+
+All QUS maps are public reference targets, not hidden competition labels.
+
+## Quick Start
+
+Use an OpenH-RF environment with `zea==0.1.3` and a supported Keras backend:
+
+```bash
+KERAS_BACKEND=jax python reconstruct.py \
+  --input data/ac1_15m_SK.hdf5 \
+  --output ac1_15m_SK_pipeline.png \
+  --frame 0
+```
+
+The script defines the pipeline in code, writes `pipeline.yaml`, saves the
+B-mode PNG, then prints the selected frame's RF shape, BSC band and unit, QUS
+map shapes, and direct per-frame-to-pooled Nakagami errors.
+
+## Validation
+
+All 120 HDF5 files pass zea 0.1.3 `File.validate()` and
+`File.validate_spec()`. Raw RF and embedded maps were checked for shape, dtype,
+finite values, coordinates, labels, min/max, and the documented frame-broadcast
+behavior. Files use zea 0.1.3's default Blosc/Zstd+bitshuffle compression.
+
+![Reference zea reconstruction of ac1_15m_SK frame 0](ac1_15m_SK_pipeline.png)
+
+The reference uses frame 0 and the common 597 x 300 zea grid at approximately
+3-25 mm depth.
+
+## Limitations
+
+- Acquisition timestamps, PRF, explicit TGC curves, and emitted waveforms are
+  unavailable; do not use these frames for calibrated temporal or flow analysis.
+- Repeated frames are strongly correlated.
+- BSC targets are model-derived references, not independent experimental BSC
+  measurements; there are three unique phantom curves.
+- Pooled Nakagami maps are lower-variance statistical references, not
+  independent physical ground truth.
+- Nakagami `omega` depends on gain, attenuation, beam sensitivity, and RF
+  amplitude scale; it is not system-independent.
+- This release contains Verasonics data only.
+
+## License
+
+CC BY 4.0. See `LICENSE`. Commercial and non-commercial reuse is permitted
+with attribution. The contributors confirm that these phantom data are cleared
+for release under CC BY 4.0.

weillcornell/pipeline.yaml

@@ -0,0 +1,26 @@
+pipeline:
+    operations:
+    -   name: keras.ops.cast
+        params:
+            dtype: float32
+    - demodulate
+    - beamform
+    - envelope_detect
+    -   name: normalize
+        params:
+            output_range:
+            - 0.0
+            - 1.0
+    - log_compress
+parameters:
+    grid_size_x: 300
+    grid_size_z: 597
+    xlims:
+    - -0.021965
+    - 0.021965
+    zlims:
+    - 0.0029568189236411115
+    - 0.02498497892364108
+    dynamic_range:
+    - -60
+    - 0