resolvestroke: sync data cards, pipelines and assets with GitHub

resolvestroke/README.md

@@ -1,24 +1,67 @@
-# OpenH-RF - Resolve Stroke datasets
-
-[Resolve Stroke](https://www.resolvestroke.com/) develops SYLVER, a
-software-driven ultrasound platform, that supports clinical assessment in
-patients suspected of, or at risk for, cerebral perfusion abnormalities by
-improving visualization of cerebral vasculature and providing complementary
-information on cerebral perfusion.
-SYLVER images with a 32×32 matrix array probe at 2 MHz
-using diverging-wave transmits. CE and FDA clearances are expected in 2026.
-This directory holds the data Resolve Stroke contributes to OpenH-RF: pre-beamformed
-RF/IQ channel data from an imaging phantom, a flow phantom, and in-vivo transcranial
-acquisitions, all de-identified and released under CC BY 4.0. The in-vivo data comes
-from the CPP-approved SCULPT clinical study. Two transmit sequences are included: a
-saddle sequence that images a 2D plane for real-time B-mode, and a 4 kHz
-single-aperture volume sequence for CEUS and blood-flow measurement.
-
-Each dataset directory is a self-contained data card: an HDF5 file, a
-B-mode preview PNG, a `reconstruct.py` + `pipeline.yaml` beamforming recipe, a
-`README.md`, and a `LICENCE` (CC BY 4.0).
-
-## OpenH-RF Release Inventory
+---
+name: resolvestroke
+pretty_name: "Resolve Stroke Transcranial CEUS, Flow and Imaging Phantom Channel Data"
+license: cc-by-4.0
+task_categories:
+  - other
+tags:
+  - ultrasound
+  - iq
+  - openh-rf
+  - 3d
+  - matrix-probe
+  - diverging-wave
+  - contrast-enhanced
+  - power-doppler
+  - transcranial
+  - clinical
+  - phantom
+language:
+  - en
+size_categories:
+  - 100K<n<1M
+---
+
+# Resolve Stroke Transcranial CEUS, Flow and Imaging Phantom Channel Data
+
+<a href="assets/main_image.png"><img src="assets/main_image_small.png" alt="Transcranial contrast-enhanced power Doppler of a human subject (SP03-Left, bolus +10 s), x-z maximum-intensity projection" width="360"></a>
+
+*3D power Doppler of the transcranial CEUS acquisition [`clinical/SP03-Left/SP03-Left.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/resolvestroke/clinical/SP03-Left/SP03-Left.hdf5) at bolus +10 s, x-z maximum-intensity projection, reconstructed from the released channel data.*
+
+## Dataset Description
+
+[Resolve Stroke](https://www.resolvestroke.com/) develops SYLVER, a software-driven ultrasound platform that supports clinical assessment in patients suspected of, or at risk for, cerebral perfusion abnormalities by improving visualization of cerebral vasculature and providing complementary information on cerebral perfusion. SYLVER images with a 32×32 matrix array probe at 2 MHz using diverging-wave transmits. CE and FDA clearances are expected in 2026. This directory holds the data Resolve Stroke contributes to OpenH-RF: pre-beamformed RF/IQ channel data from an imaging phantom, a flow phantom, and in-vivo transcranial acquisitions, all de-identified and released under CC BY 4.0. The in-vivo data comes from the CPP-approved SCULPT clinical study. Two transmit sequences are included: a saddle sequence that images a 2D plane for real-time B-mode, and a 4 kHz single-aperture volume sequence for CEUS and blood-flow measurement.
+
+Each dataset directory holds its data card (`README.md`), a `reconstruct.py` + `pipeline.yaml` beamforming recipe and, for the CEUS datasets, a power-Doppler reconstruction; the HDF5 files are on the Hub and the preview images in [`assets/`](assets/).
+
+## Dataset Contributor(s)
+
+- Aitana Waelbroeck
+- Carl Ferlay
+- Arthur Chavignon
+- Maxence Reberol <maxence.reberol@resolvestroke.com> (contact)
+- Vincent Hingot
+- Resolve Stroke, 29 Rue du Faubourg Saint-Jacques, 75014 Paris
+
+## Dataset Creation Date
+
+01/23/2026 – 07/09/2026 (per sub-dataset; see each data card).
+
+## License / Terms of Use
+
+[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.
+
+## Processing the Dataset
+
+Each sub-dataset has its own `reconstruct.py` and `pipeline.yaml`, as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF/tree/main/datasets/resolvestroke), built on the [zea library](https://github.com/tue-bmd/zea); the CEUS datasets add a power-Doppler reconstruction. See the data card of each sub-dataset for how to run them.
+
+The Python scripts carry their own `SPDX-License-Identifier: Apache-2.0` header; the dataset itself is CC BY 4.0.
+
+## Dataset Format
+
+[zea v0.1.6](https://github.com/tue-bmd/zea)
+
+## Dataset Quantification
 
 **Current OpenH-RF release:** 43 HDF5 files; 110.62 GB (110,619,394,048 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.
 
@@ -26,15 +69,59 @@ B-mode preview PNG, a `reconstruct.py` + `pipeline.yaml` beamforming recipe, a
 
 | Path | What's inside |
 |------|---------------|
-| `clinical/` | 20 clinical transcranial CEUS acquisitions (SCULPT study, subjects `SP01`–`SP10`, Left/Right). Each subdirectory holds one acquisition's HDF5 (five 1 s bolus wash-in clips), reconstruction scripts, and B-mode / power-Doppler / reference montages. |
-| `phantom_flow/` | Flow-phantom CEUS (CIRS 769 + ATS523A) with microbubble contrast: five 1 s clips capturing a flow-on/flow-off bolus wash-in. Single combined HDF5 + 3D power-Doppler reconstruction. |
-| `phantom_mp/` | Multi-tissue imaging phantom (CIRS 040GSE), pre-beamformed channel data, 1000 volumetric frames of the same static scene (wire targets, cysts, tissue-mimicking background). |
-| `saddle/` | Single-frame anatomical reference B-modes (21 files: the 20 clinical acquisitions + 1 imaging phantom) from the wide-angle "saddle" sequence. These are the structural companion to the clinical CEUS clips. |
+| [`clinical/`](clinical/) | 20 clinical transcranial CEUS acquisitions (SCULPT study, subjects `SP01`–`SP10`, Left/Right), one HDF5 per acquisition (five 1 s bolus wash-in clips) under `clinical/<name>/`. All 20 share the same probe, sequence and layout, so one data card, the reconstruction scripts and the pipeline YAMLs live at the `clinical/` root (pick the acquisition with `SUBJECT` at the top of each script). |
+| [`phantom_flow/`](phantom_flow/) | Flow-phantom CEUS (CIRS 769 + ATS523A) with microbubble contrast: five 1 s clips capturing a flow-on/flow-off bolus wash-in. Single combined HDF5 + 3D power-Doppler reconstruction. |
+| [`phantom_mp/`](phantom_mp/) | Multi-tissue imaging phantom (CIRS 040GSE), pre-beamformed channel data, 1000 volumetric frames of the same static scene (wire targets, cysts, tissue-mimicking background). |
+| [`saddle/`](saddle/) | Single-frame anatomical reference B-modes (21 files: the 20 clinical acquisitions + 1 imaging phantom) from the wide-angle "saddle" sequence. These are the structural companion to the clinical CEUS clips. |
+
+## `clinical/` — transcranial CEUS, 20 acquisitions
+
+Ten human subjects of the SCULPT study, two acquisitions each (other side and/or second session), imaged through the temporal acoustic window during a microbubble bolus. Each file holds 20 000 frames of diverging-wave IQ channel data at 4 kHz: five 1 s clips taken before the bolus and at +5, +10, +15 and +20 s. Every file also carries reference maps computed by SYLVER from the complete bolus passage (`custom/computed_references/`: microvascular image and radial velocities on a 0.6 mm Cartesian grid), provided as targets, not as a clinical ground truth.
+
+Power Doppler reconstructed from the released channel data, one x-z projection per acquisition at bolus +10 s:
+
+<a href="assets/clinical_pd_montage.png"><img src="assets/clinical_pd_montage.png" alt="Power Doppler x-z MIP at bolus +10 s for the 20 clinical acquisitions" width="100%"></a>
+
+The reference microvascular image of the same 20 acquisitions, x-z projection:
+
+<a href="assets/clinical_mvi_montage.png"><img src="assets/clinical_mvi_montage.png" alt="Reference microvascular image (mvi), x-z MIP, for the 20 clinical acquisitions" width="100%"></a>
+
+The [data card](clinical/README.md) has the inventory of the 20 acquisitions with the five-clip power Doppler and the reference maps of each, the field table, and the reconstruction scripts.
+
+## `phantom_flow/` — flow phantom CEUS
+
+A CIRS 769 flow phantom with an ATS523A pump, microbubbles flowing through two tubes (4 mm and 2 mm), same sequence and clip structure as the clinical files. The file also carries the tube mask (known geometry, an actual ground truth) and the same computed reference maps as the clinical data.
+
+<a href="assets/phantom_flow_bmode.png"><img src="assets/phantom_flow_bmode.png" alt="phantom_flow B-mode, two perpendicular sectors" width="100%"></a>
+
+*Figure: B-mode of one frame, x-z and y-z sectors.*
+
+<a href="assets/phantom_flow_PD_montage.png"><img src="assets/phantom_flow_PD_montage.png" alt="phantom_flow power Doppler, five clips, next to the reference mvi" width="100%"></a>
+
+*Figure: power Doppler of the five clips, with the reference `mvi` in the last column.*
+
+<a href="assets/phantom_flow_references_montage.png"><img src="assets/phantom_flow_references_montage.png" alt="phantom_flow computed reference maps" width="100%"></a>
+
+*Figure: computed reference maps (tube mask, `mvi`, radial velocities).*
+
+See the [data card](phantom_flow/README.md).
+
+## `phantom_mp/` — multi-tissue imaging phantom
+
+A CIRS 040GSE phantom, 1000 volumetric frames of the same static scene with the 4 kHz diverging-wave sequence: wire targets, cysts and tissue-mimicking background, for beamforming and resolution studies.
+
+<a href="assets/phantom_mp_bmode.png"><img src="assets/phantom_mp_bmode.png" alt="phantom_mp B-mode, two perpendicular sectors" width="100%"></a>
+
+*Figure: B-mode of one frame, x-z and y-z sectors.*
+
+See the [data card](phantom_mp/README.md).
 
-## Contributors
+## `saddle/` — anatomical reference B-modes
 
-Aitana Waelbroeck\*, Carl Ferlay\*, Arthur Chavignon\*, Maxence Reberol\*, Vincent Hingot\*
+One wide-angle diverging-wave frame per acquisition from the "saddle" sequence (9 transmits steered −24° to +24°; each transmit is repeated for four consecutive 256-element receive sub-apertures, so the frame carries the full 1024-element aperture), for the 20 clinical acquisitions and the imaging phantom: the anatomical view at the same probe placement as the CEUS clips.
 
-_\*Resolve Stroke, 29 Rue du Faubourg Saint-Jacques, 75014 Paris_
+<a href="assets/saddle_bmode_montage.png"><img src="assets/saddle_bmode_montage.png" alt="Saddle-array B-modes for the 21 files" width="100%"></a>
 
+*Figure: the 21 saddle B-modes.*
 
+See the [data card](saddle/README.md).