twente-microbubblesim: sync card, pipelines and figures with GitHub (GH#37)

twente-microbubblesim/README.md

@@ -20,7 +20,11 @@ size_categories:
 
 ## Dataset Description
 
-This synthetic 3-D ultrasound dataset contains nonlinear radiofrequency (RF) responses from microbubble contrast agents for cardiovascular-flow imaging. It was generated to study the effect of ultrasound transmit-waveform shape on RF signals and deep-learning methods for microbubble super-resolution. It contains simulated data, not clinical, phantom, or in-vivo animal data.
+This synthetic 3-D ultrasound dataset contains nonlinear radiofrequency (RF) responses from microbubble contrast agents for cardiovascular-flow imaging. It was generated to study the effect of ultrasound transmit-waveform shape on RF signals and deep-learning methods for microbubble super-resolution. It contains exclusively simulated data.
+
+![alt text](./assets/pulses_waveform.png)
+The 12 different driving-pulse waveforms used in this simulated dataset.
+
 
 ## Dataset Contributor(s)
 
@@ -58,7 +62,16 @@ Every pulse track has its own verified pipeline file, `pipeline/pipeline_track_<
 
 `demodulate → downsample (factor 1) → delay-and-sum beamform → envelope detect → normalize → log compress`
 
-Set `PATH` to one `.hdf5` acquisition, `PULSE` to the pulse label (for example `REF`, `DPT` or `L1.7`) and `CONFIG_PATH` to the matching track's pipeline. The script applies that track's beamforming peak-time reference (`custom/track_i_t_peak`) and, with `SHOW_BUBBLES`, overlays the ground-truth bubble positions.
+Each pipeline's `parameters:` block carries that pulse's beamforming peak-time reference `t_peak` (copied from `custom/track_i_t_peak`, identical in every file), the lateral field of view and the dynamic range. `zea` renders the B-mode straight from the Hub with one of these files; pass the matching track index with `--track`. Try it out with the following command:
+
+```bash
+zea process \
+  --dataset hf://nvidia/OpenH-RF/twente-microbubblesim/data/Monodispers/RFDATA00002.hdf5 \
+  --config hf://nvidia/OpenH-RF/twente-microbubblesim/pipeline/pipeline_track_6_REF.yaml \
+  --track 6
+```
+
+In `reconstruct.py`, set `ZEA_FILE` to one `.hdf5` acquisition and `PULSE` to the pulse label (for example `REF`, `DPT` or `L1.7`); the script picks the matching track and pipeline and overlays the ground-truth bubble positions on the B-mode.
 
 ## Dataset Format
 
@@ -135,11 +148,11 @@ All 500 HDF5 files were checked for the expected zea container structure, 12 ord
 
 <table>
   <tr>
-    <td align="center"><strong>Monodispers — REF S23.7</strong><br>
-      <img src="REF_monodisperse.png" alt="Monodispers REF S23.7 image" width="280">
+    <td align="center"><strong>Monodispers — REF</strong><br>
+      <img src="./assets/REF_monodisperse.png" alt="Monodispers REF S23.7 image" width="280">
     </td>
-    <td align="center"><strong>SonoVue — REF S23.7</strong><br>
-      <img src="REF_sonovue.png" alt="SonoVue REF S23.7 image" width="280">
+    <td align="center"><strong>Monodispers — S3.4</strong><br>
+      <img src="./assets/S3.4_monodisperse.png" alt="SonoVue REF S23.7 image" width="280">
     </td>
   </tr>
 </table>
@@ -147,11 +160,9 @@ All 500 HDF5 files were checked for the expected zea container structure, 12 ord
 ## Known Issues
 
 - The transmit setup is an unfocused plane wave by design: steering angle is zero, no finite focus distance is used (`infinite focus`), transmit delays are zero, and apodization is unity for every transmit element. These are intentional simulation settings rather than missing calibration fields.
-- RF amplitude and several custom-element units remain source-defined and should be confirmed against the simulator documentation.
 - The HDF5 files store only the official nominal bandwidth endpoints (1.0–4.0 MHz). The measured transfer-function −6 dB bounds (approximately 1.52–3.70 MHz) and corresponding 83.4% fractional bandwidth are documented in this README but are not stored as HDF5 data fields.
 - The simulator is a private, unpublished derivative of the cited simulator; no public software package or Git commit is required to use the released RF data. The internal dataset-generation release label is recorded in the HDF5 metadata and should be used when referring to this generation run.
 - No train/validation/test split is provided.
-- `reconstruct.py` imports `utils.py`; keep both files together.
 
 ## Ethical Considerations
 
@@ -161,4 +172,15 @@ The dataset is synthetic, so participant consent, de-identification, and IRB app
 
 When using the dataset, cite:
 
-R. Zorgdrager et al., “Waveform-Specific Performance of Deep Learning-Based Super-Resolution for Ultrasound Contrast Imaging,” *IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control*, 2025. [doi:10.1109/TUFFC.2025.3537298](https://doi.org/10.1109/TUFFC.2025.3537298)
+```bibtex
+@ARTICLE{10858770,
+  author={Zorgdrager, Rienk and Blanken, Nathan and Wolterink, Jelmer M. and Versluis, Michel and Lajoinie, Guillaume},
+  journal={IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control}, 
+  title={Waveform-Specific Performance of Deep Learning-Based Super-Resolution for Ultrasound Contrast Imaging}, 
+  year={2025},
+  volume={72},
+  number={4},
+  pages={427-439},
+  keywords={Imaging;Ultrasonic imaging;Transducers;Chirp;RF signals;Superresolution;Signal to noise ratio;Signal resolution;Frequency control;Acoustics;Chirp;deep learning;flow imaging;microbubbles;super-resolution;ultrasound contrast imaging},
+  doi={10.1109/TUFFC.2025.3537298}}
+```

twente-microbubblesim/pipeline/pipeline_track_0_DPT.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [5.688e-06] # DPT beamforming timing reference in s (custom track_0_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_10_SDC.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [3.356e-06] # SDC beamforming timing reference in s (custom track_10_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_11_SUC.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [3.328e-06] # SUC beamforming timing reference in s (custom track_11_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_1_L1.7.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [3.54e-06] # L1.7 beamforming timing reference in s (custom track_1_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_2_L2.5.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [1.952e-06] # L2.5 beamforming timing reference in s (custom track_2_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_3_L3.4.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [3.776e-06] # L3.4 beamforming timing reference in s (custom track_3_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_4_LDC.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [8.348e-06] # LDC beamforming timing reference in s (custom track_4_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_5_LUC.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [7.76e-06] # LUC beamforming timing reference in s (custom track_5_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_6_REF.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [1.472e-06] # REF beamforming timing reference in s (custom track_6_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_7_S1.7.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [1.804e-06] # S1.7 beamforming timing reference in s (custom track_7_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_8_S2.5.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [1.952e-06] # S2.5 beamforming timing reference in s (custom track_8_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate

twente-microbubblesim/pipeline/pipeline_track_9_S3.4.yaml

@@ -1,3 +1,8 @@
+parameters:
+  t_peak: [2.016e-06] # S3.4 beamforming timing reference in s (custom track_9_t_peak)
+  xlims: [-0.014, 0.014] # 28 mm
+  dynamic_range: [-30, 0]
+
 pipeline:
   operations:
     - name: demodulate