tue-cardiac: sync data card and gallery figures with GitHub, replace references/ with assets/

tue-cardiac/LICENSE

@@ -1,395 +0,0 @@
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tue-cardiac/README.md

@@ -1,5 +1,6 @@
 ---
-pretty_name: "OpenH-RF — TU/e Cardiac RF Multi-Transmit"
+name: tue-cardiac
+pretty_name: "TU/e Cardiac RF Multi-Transmit"
 license: cc-by-4.0
 task_categories:
   - other
@@ -23,40 +24,36 @@ size_categories:
 
 # TU/e Cardiac PLAX Multi-Transmit RF
 
+<table width="100%">
+  <tr>
+    <td width="25%"><img src="assets/subject2_focused_harm_nb80.gif" alt="" width="100%"></td>
+    <td width="25%"><img src="assets/subject4_wide_harm_nb80.gif" alt="" width="100%"></td>
+    <td width="25%"><img src="assets/subject6_focused_harm_nb80.gif" alt="" width="100%"></td>
+    <td width="25%"><img src="assets/subject9_wide_harm_nb80.gif" alt="" width="100%"></td>
+  </tr>
+</table>
 
+*Parasternal long-axis cine loops of four volunteers, pulse-inversion harmonic tracks: focused ([`subject-002`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/tue-cardiac/data/subject-002.hdf5)), wide ([`subject-004`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/tue-cardiac/data/subject-004.hdf5)), focused ([`subject-006`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/tue-cardiac/data/subject-006.hdf5)) and wide ([`subject-009`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/tue-cardiac/data/subject-009.hdf5)).*
 
 ## Dataset Description
 
-This dataset contains pre-beamformed radio-frequency (RF) channel data from
-in-vivo human cardiac ultrasound acquisitions of 12 distinct adult healthy
-volunteers, aged 26–33 years. The operator attempted a parasternal long-axis (PLAX)
-view for every participant. Each participant file contains eight separately acquired 100-frame
-tracks (3s,33Hz) that vary the transmit encoding: focused fundamental, focused
-pulse-inversion harmonic, wide fundamental, wide pulse-inversion harmonic,
-plane wave, diverging wave, Hadamard-coded aperture, and random binary-coded
-aperture.
+This dataset contains pre-beamformed radio-frequency (RF) channel data from in-vivo human cardiac ultrasound acquisitions of 12 distinct adult healthy volunteers, aged 26–33 years. The operator attempted a parasternal long-axis (PLAX) view for every participant. Each participant file contains eight separately acquired 100-frame tracks (3s,33Hz) that vary the transmit encoding: focused fundamental, focused pulse-inversion harmonic, wide fundamental, wide pulse-inversion harmonic, plane wave, diverging wave, Hadamard-coded aperture, and random binary-coded aperture.
 
-The data were acquired on a Verasonics Vantage 256 research platform with a
-Philips S5-1 phased-array probe. The contribution is intended to support generalized
-reconstruction, transmit-encoding research, REFoCUS recovery, compressed
-sensing, and comparisons of fundamental and second-harmonic imaging.
+The data were acquired on a Verasonics Vantage 256 research platform with a Philips S5-1 phased-array probe. The contribution is intended to support generalized reconstruction, transmit-encoding research, REFoCUS recovery, compressed sensing, and comparisons of fundamental and second-harmonic imaging.
 
 ## Dataset Contributor(s)
 
-- **Authors:** Simon Penninga and Ruud van Sloun
-- **Contributor and contact:** Simon Penninga (`s.w.penninga@tue.nl`)
-- **Organization:** Biomedical Diagnostics Lab, Eindhoven University of
-  Technology (TU/e), the Netherlands
+- Simon Penninga <s.w.penninga@tue.nl> (author; contact)
+- Ruud van Sloun (author)
+- Biomedical Diagnostics Lab, Eindhoven University of Technology (TU/e), the Netherlands
 
 ## Dataset Creation Date
 
-The recordings were acquired in 2026. The dataset was packaged on 2026-09-02.
+The recordings were acquired in 2026.
 
 ## License / Terms of Use
 
-The dataset license is [Creative Commons Attribution 4.0 International
-(CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/). The full license
-text is provided in [`LICENSE`](LICENSE).
+[Creative Commons Attribution 4.0 International (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/legalcode.en). Retain attribution and identify modifications when reusing the data.
 
 ## Intended Usage
 
@@ -71,48 +68,16 @@ Intended research uses include:
 
 The dataset must not be used as a clinically validated diagnostic product.
 
-## Citation
-
-Suggested citation for the dataset:
-
-> Penninga, S., & van Sloun, R. (2026). *TU/e Cardiac RF Multi-Transmit* [Data set].
-> Biomedical Diagnostics Lab, Eindhoven University of Technology. OpenH-RF.
-
-```bibtex
-@misc{penninga_tue_cardiac_plax_2026,
-  title        = {TU/e Cardiac PLAX Multi-Transmit RF},
-  author       = {Penninga, Simon W. and van Sloun, Ruud J. G.},
-  year         = {2026},
-  publisher    = {Biomedical Diagnostics Lab, Eindhoven University of Technology},
-  howpublished = {OpenH-RF dataset},
-}
-```
-
-
 ## Dataset Characterization
 
-- **Data collection method:** in-vivo human cardiac ultrasound on a research
-  platform.
+- **Data collection method:** in-vivo human cardiac ultrasound on a research platform.
 - **Anatomy and view:** heart; attempted parasternal long-axis (PLAX) view.
-- **Cohort:** 12 adult healthy volunteers, aged 26–33 years, recruited from
-  among researcher colleagues. No known pathologies were reported.
-- **Labeling method:** acquisition-derived track labels plus the shared
-  contributor-supplied cohort label `healthy_volunteer`. This is not a clinical
-  diagnosis. No segmentation, diagnostic, or image-quality labels are supplied.
-- **Acquisition protocol:** the eight modes were acquired sequentially in the
-  fixed order shown below. The probe was kept as steady as possible, but no
-  probe tracking was available. Before each recording, the volunteer was
-  instructed to breathe out.
+- **Cohort:** 12 adult healthy volunteers, aged 26–33 years, recruited from among researcher colleagues. No known pathologies were reported.
+- **Acquisition protocol:** the eight modes were acquired sequentially in the fixed order shown below. The probe was kept as steady as possible. Before each recording, the volunteer was instructed to breathe out.
 - **Operator:** No ultrasound training or prior experience.
-- **System settings:** receive gain and TGC settings were fixed across all
-  participants and tracks.
-- **Acquisition system:** Verasonics Vantage 256 with a Philips S5-1 phased-array
-  probe.
-- **Probe:** phased-array, 80 active elements; recorded geometry has shape `(80, 3)` in
-  metres, nominal probe center frequency 3.125 MHz, and 128% fractional
-  bandwidth.
-- **Receive sampling:** 15.625 MHz; 2,304 axial samples; raw `int16` RF with
-  one real channel.
+- **Acquisition system:** Verasonics Vantage 256 with a Philips S5-1 phased-array probe.
+- **Probe:** phased-array, 80 active elements, nominal probe center frequency 3.125 MHz, and 128% fractional bandwidth.
+- **Receive sampling:** 15.625 MHz; 2,304 axial samples; raw `int16` RF with one real channel. For pulse inversion imaging, the two acquisitions are summed in buffer.
 - **Nominal sound speed:** 1,540 m/s.
 - **Frame rate:** approximately 33 frames/s for each track.
 - **Coordinate convention:** x = lateral, y = elevation, z = axial/depth.
@@ -126,12 +91,19 @@ Suggested citation for the dataset:
 | 05 | `planewave` | Steered plane wave, ±45° | 80 | 3.90625 MHz | Infinite transmit focus |
 | 06 | `diverging` | Diverging wave, ±45° | 80 | 3.90625 MHz | Negative virtual-focus distance varies with steering angle |
 | 07 | `hadamard` | Full-aperture Hadamard code | 80 | 3.90625 MHz | Zero transmit delays and ±1 apodization; REFoCUS decoding required |
-| 08 | `random` | Full-aperture fixed random binary code | 80 | 3.90625 MHz | Zero transmit delays and ±1 apodization; regularized REFoCUS decoding required |
+| 08 | `random` | Full-aperture fixed random binary code | 80 | 3.90625 MHz | Zero transmit delays and ±1 apodization; REFoCUS decoding required |
+
+## Processing the Dataset
+
+The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/tue-cardiac/reconstruct.py) as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipelines/*.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.
+
+Each file holds the eight transmit-encoding tracks. Set `ZEA_FILE`, `TRACK` and `FRAME` at the top of the script, together with the matching pipeline under `pipelines/` as `CONFIG` (`PIPELINE_FOR_TRACK` lists which track uses which; see also [Data Validation](#data-validation)). The image is written to `assets/`.
 
 ## Dataset Format
 
-The final dataset contains 12 zea HDF5 files under `data/`, one per
-pseudonymized participant:
+[zea v0.1.4](https://github.com/tue-bmd/zea)
+
+The final dataset contains 12 zea HDF5 files under `data/`, one per pseudonymized participant:
 
 ```text
 data/
@@ -140,22 +112,9 @@ data/
   subject-012.hdf5
 ```
 
-Each file has one shared `/probe` group, one de-identified `/metadata` group,
-and eight entries under `/tracks`. Track labels identify the transmit encoding.
-Raw channel data for each track are stored at:
-
-```text
-/tracks/track_N/data/raw_data
-```
+Each file has one shared `/probe` group, one de-identified `/metadata` group, and eight entries under `/tracks`. Track labels identify the transmit encoding. Raw channel data for each track are stored at:
 
-The source tensor order is preserved as
-`(n_frames, n_tx, n_ax, n_el, n_ch) = (100, 80, 2304, 80, 1)` with dtype
-`int16`. Values are uncalibrated Verasonics receive samples.
-The source Verasonics workspaces are converted with zea. Probe geometry,
-transmit delays, transmit apodizations, waveforms, receive sampling, time-gain
-compensation, sound speed, and relative transmit timing are retained. Exact
-participant acquisition dates/times, source filenames, local paths, and the
-private source-directory-to-pseudonym mapping are not retained.
+The source tensor order is preserved as `(n_frames, n_tx, n_ax, n_el, n_ch) = (100, 80, 2304, 80, 1)` with dtype `int16`. Values are uncalibrated Verasonics receive samples.
 
 ### Core per-file feature table
 
@@ -183,25 +142,62 @@ private source-directory-to-pseudonym mapping are not retained.
 | `/tracks/track_N/scan/waveforms_one_way` | track dependent | float32 | V | One-way transmit waveform model |
 | `/tracks/track_N/scan/waveforms_two_way` | track dependent | float32 | V | Two-way transmit waveform model |
 
-## Dataset Quantification
+## Transmit Types
+
+<table width="100%">
+  <tr>
+    <th>Focused fundamental</th>
+    <th>Focused pulse-inversion harmonic</th>
+    <th>Wide fundamental</th>
+    <th>Wide pulse-inversion harmonic</th>
+  </tr>
+  <tr>
+    <td><img src="assets/subject-002_focused_fund_frame-000.png" alt="Focused fundamental cardiac image"></td>
+    <td><img src="assets/subject-002_focused_harm_frame-000.png" alt="Focused pulse-inversion harmonic cardiac image"></td>
+    <td><img src="assets/subject-002_wide_fund_frame-000.png" alt="Wide fundamental cardiac image"></td>
+    <td><img src="assets/subject-002_wide_harm_frame-000.png" alt="Wide pulse-inversion harmonic cardiac image"></td>
+  </tr>
+  <tr>
+    <th>Plane wave</th>
+    <th>Diverging wave</th>
+    <th>Hadamard-coded aperture</th>
+    <th>Random binary-coded aperture</th>
+  </tr>
+  <tr>
+    <td><img src="assets/subject-002_planewave_frame-000.png" alt="Plane-wave cardiac image"></td>
+    <td><img src="assets/subject-002_diverging_frame-000.png" alt="Diverging-wave cardiac image"></td>
+    <td><img src="assets/subject-002_hadamard_frame-000.png" alt="Hadamard-coded aperture cardiac image"></td>
+    <td><img src="assets/subject-002_random_frame-000.png" alt="Random binary-coded aperture cardiac image"></td>
+  </tr>
+  <tr>
+    <td colspan="4"><small>Output images of <code>reconstruct.py</code> for every transmit type of subject 2.</small></td>
+  </tr>
+</table>
+
+## Citation
+
+Suggested citation for the dataset:
+
+> Penninga, S. W., & van Sloun, R. J. G. (2026). *TU/e Cardiac RF Multi-Transmit* [Data set]. Eindhoven University of Technology, OpenH-RF.
+
+```bibtex
+@misc{penninga_tue_cardiac_plax_2026,
+  title        = {TU/e Cardiac PLAX Multi-Transmit RF},
+  author       = {Penninga, Simon W. and van Sloun, Ruud J. G.},
+  year         = {2026},
+  publisher    = {Biomedical Diagnostics Lab, Eindhoven University of Technology},
+  howpublished = {OpenH-RF dataset},
+}
+```
 
-**Current OpenH-RF release:** 12 HDF5 files; 199.18 GB (199,180,025,844 bytes) stored; root `zea_version` **0.1.4**. 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.
+## Dataset Quantification
 
-- **Participants/files:** 12 distinct people represented by 12 pseudonymous HDF5 files.
+**Current OpenH-RF release:** 12 HDF5 files; 199.18 GB (199,180,025,844 bytes) stored; root `zea_version` **0.1.4**.
+- **Participants/files:** 12 distinct people represented by 12 HDF5 files.
 - **Tracks/acquisitions:** 8 tracks per file; 96 acquisitions total.
 - **Frames:** 100 per track; 9,600 frames total.
 - **Raw-data tensor:** `(100, 80, 2304, 80, 1)` per track.
 
-## Subject Metadata
-
-The dataset contains 12 distinct adult healthy volunteers aged 26–33 years.
-They were recruited from among the contributor's researcher colleagues, and no
-known pathologies were reported. Only sequential pseudonyms and the shared
-`healthy_volunteer` cohort classification are stored in the HDF5 files. The age
-range is reported only in aggregate; individual ages are not stored. Sex was
-intentionally not reported or encoded. The shared anatomy/view label is cardiac
-attempted PLAX, and individual diagnostic labels are not included.
-
 ## Data Validation
 
 Four saved zea pipeline configurations are provided under `pipelines/`:
@@ -213,35 +209,17 @@ Four saved zea pipeline configurations are provided under `pipelines/`:
 | `pipeline_hadamard.yaml` | `hadamard` | Adjoint REFoCUS decoding before beamforming |
 | `pipeline_random.yaml` | `random` | Tikhonov-regularized REFoCUS decoding before beamforming |
 
-All configurations perform RF filtering, demodulation, delay-and-sum
-beamforming, envelope detection, normalization, log compression, and scan
-conversion. `reconstruct.py` selects the appropriate configuration from the
-requested track label; `--pipeline` can still override that selection.
-
-Example reconstruction:
-
-```bash
-python reconstruct.py data/subject-001.hdf5 \
-  --track focused_fund --frame 0
-```
+All configurations perform RF filtering, demodulation, delay-and-sum beamforming, envelope detection, normalization, log compression, and scan conversion.
 
 ## Known Issues
 
 - A good PLAX view is not always available for all recordings.
-- Some transmit types, like random apodization recordings, do not give a
-  good quality B-mode. They are not intended to be used for imaging, but
-  for comparison.
-- The two harmonic tracks are pulse-inversion-accumulated nonlinear
-  measurements and should not be treated as linear equivalents of the
-  fundamental tracks.
-- Accumulated harmonic data may lack per-transmit timing arrays; the measured
-  frame rate is documented instead.
-- Hadamard and random tracks require REFoCUS decoding before conventional
-  beamforming.
-- A Verasonics scalar lens-delay correction is retained under `/custom` for
-  provenance, but it is not equivalent to zea's refractive lens model.
+- Some transmit types, like random apodization recordings, do not give a good quality B-mode. They are not intended to have the best quality, but for comparison.
+- The two harmonic tracks are pulse-inversion-accumulated nonlinear measurements and should not be treated as linear equivalents of the fundamental tracks.
+- Accumulated harmonic data may lack per-transmit timing arrays; the measured frame rate is documented instead.
+- Hadamard and random tracks require REFoCUS decoding before conventional beamforming.
+- A Verasonics scalar lens-delay correction is retained under `/custom` for provenance, but it is not equivalent to zea's refractive lens model.
 
 ## Ethical Considerations
 
-Approval was obtained from the Ethical Review Board TU/e (Eindhoven University of Technology).
-Reference: ERB2023EE7 Contact details for the Ethical Review Board TU/e: T +31 (0)40 247 6259 <ethics@tue.nl> <intranet.tue.nl/ethics>
+Approval was obtained from the Ethical Review Board TU/e (Eindhoven University of Technology). Reference: ERB2023EE7 Contact details for the Ethical Review Board TU/e: T +31 (0)40 247 6259 <ethics@tue.nl> <intranet.tue.nl/ethics>