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ulmshare/README.md

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+---
+pretty_name: "OpenH-RF — ULMShare (in vivo mouse transcranial ULM)"
+license: cc-by-4.0
+task_categories:
+  - image-to-image
+tags:
+  - ultrasound
+  - iq
+  - openh-rf
+  - ulm
+  - super-resolution
+  - microbubbles
+  - in-vivo
+  - mouse
+  - brain
+language:
+  - en
+size_categories:
+  - 10K<n<100K
+---
+
+# ULMShare — in vivo mouse transcranial ULM
+
+## Dataset Description
+
+Pre-beamformed, plane-wave **IQ channel data** from transcranial ultrasound
+localization microscopy (ULM) of the mouse brain, converted from the public
+[ULMShare](https://arxiv.org/abs/2606.07851) release into the zea format. Each
+acquisition is a contrast-enhanced (microbubble) plane-wave sequence over the
+intact skull of an anesthetized mouse; compounding the transmits gives a
+Power-Doppler movie of the cerebral microvasculature, and localizing and
+tracking individual microbubbles across frames gives a super-resolved density
+map of the vessels.
+
+This is **in vivo animal data**, not phantom or simulated. It is a conversion of the upstream release, which holds 99 acquisitions from 61 mice
+(~30 TB of raw data) recorded between March 2022 and March 2025 at the Provost
+Ultrasound Lab (Polytechnique Montréal) and partner sites.
+
+## Dataset Contributor(s)
+
+**Original dataset (ULMShare).** Brice Rauby, Nin Ghigo, Gerardo
+Ramos-Palacios, Alexis Leconte, Stephen A. Lee, Alice Wu, Paul Xing, Oleksandra
+Gulenko, Louis Caron, Antoine Malescot, Eric Martineau, Jonathan Porée, Maxime
+Gasse, Ravi L. Rungta, Abbas F. Sadikot, and Jean Provost — Provost Ultrasound
+Lab, Polytechnique Montréal.
+
+**zea conversion and reconstruction (this submission).** Oisín Nolan
+<o.i.nolan@tue.nl>, Eindhoven University of Technology.
+
+## Dataset Creation Date
+
+08/21/2026 (zea conversion). The underlying acquisitions were recorded between
+March 2022 and March 2025.
+
+## License / Terms of Use
+
+CC BY 4.0. See [LICENSE](./LICENSE).
+
+## Intended Usage
+
+Ultrasound localization microscopy: microbubble detection and localization,
+frame-to-frame tracking, super-resolved vascular density and velocity mapping,
+and clutter filtering / tissue suppression.
+
+## Dataset Characterization
+
+- **Data Collection Method:** in vivo animal (mouse), contrast-enhanced.
+- **Labeling Method:** none. A reference ULM density map rendered by the
+  original authors is stored alongside the acquisitions as a
+  `density_map` custom element — a visualization, not a ground-truth label.
+- **Acquisition system:** Verasonics Vantage 256. See files for further acquisition details.
+
+## Dataset Format
+
+zea (HDF5), written with zea v0.1.3.
+
+Each acquisition is **one HDF5 file with a single track**.
+
+```
+/
+├── probe/                       name, type, probe_geometry, probe_center_frequency
+├── metadata/
+│   ├── credit                   DOI of the ULMShare publication
+│   ├── subject/                 id, type, sex, genetic_strain, weight
+│   └── text_report              procedure notes (where recorded)
+├── custom/                      acquisition context (see table below)
+└── tracks/track_0/
+    ├── data/raw_data            (n_frames, n_tx, n_ax, n_el, 2) int16
+    ├── scan/                    sampling_frequency, center_frequency,
+    │                            demodulation_frequency, sound_speed,
+    │                            initial_times, t0_delays, polar_angles,
+    │                            azimuth_angles, focus_distances,
+    │                            transmit_origins, tx_apodizations,
+    │                            tgc_gain_curve
+    └── transmit_only            False
+```
+
+**Large acquisitions split for upload:** The HuggingFace file-size limit is 500 GB. Four
+acquisitions are near or above it, so each one is split into two parts. These are
+`mouse_58/acquisition_1` (616 GB) and `mouse_59/acquisition_1` to `acquisition_3` (499 GB each).
+The split is at frame 240,000, into `_part1of2.hdf5` and `_part2of2.hdf5`. Both parts hold the
+same metadata: probe geometry, subject information, and clinical fields. To rebuild an
+acquisition, join `raw_data` from the two parts along axis 0.
+
+### Per-sample feature table
+
+| Feature | Shape | Dtype | Units | Description |
+|---|---|---|---|---|
+| `data/raw_data` | `(n_frames, n_tx, n_ax, n_el, 2)` | `int16` | ADC counts | Baseband IQ channel data, `[I, Q]` (`I + jQ`) |
+| `probe/probe_geometry` | `(n_el, 3)` | `float32` | m | Element positions `(x, y, z)` |
+| `probe/probe_center_frequency` | `()` | `float32` | Hz | Probe center frequency |
+| `scan/sampling_frequency` | `()` | `float32` | Hz | IQ sampling rate (`fc` for BS100BW, `fc/2` for BS50BW) |
+| `scan/center_frequency`, `scan/demodulation_frequency` | `()` | `float32` | Hz | Transmit carrier / demodulation frequency |
+| `scan/sound_speed` | `()` | `float32` | m/s | 1540 |
+| `scan/polar_angles` | `(n_tx,)` | `float32` | rad | Plane-wave steering angles, ping-pong order |
+| `scan/azimuth_angles` | `(n_tx,)` | `float32` | rad | Zero (2D imaging) |
+| `scan/focus_distances` | `(n_tx,)` | `float32` | m | `inf` (unfocused plane waves) |
+| `scan/t0_delays` | `(n_tx, n_el)` | `float32` | s | Transmit delays, min 0 |
+| `scan/initial_times` | `(n_tx,)` | `float32` | s | Zero (MUST adds no per-transmit offset) |
+| `scan/tx_apodizations` | `(n_tx, n_el)` | `float32` | – | Ones (full aperture; see Known Issues) |
+| `scan/transmit_origins` | `(n_tx, 3)` | `float32` | m | Zero |
+| `scan/tgc_gain_curve` | `(n_ax,)` | `float32` | – | 8 source control points interpolated per sample |
+| `metadata/subject/weight` | `()` | `float32` | kg | Mouse body weight |
+| `custom/density_map` | `(H, W, 3)` or `(H, W)` | `uint8` | – | Reference ULM density map PNG |
+
+### Custom elements
+
+Acquisition context with no zea spec field, stored as strings exactly as
+recorded upstream: `anesthesia`, `injection_type`, `mb_dilution`,
+`volume_mb_injected`, `frame_rate_hz`, `npulse`, `voltage`, `mouse_weight`,
+`mouse_age_days`, `mouse_animal_protocol_id`, `flush`, and (where non-blank)
+`procedure_type`, `slice_position`, `temperature`, `syringe_gauge`.
+
+## Dataset Quantification
+
+- **Acquisitions:** 99, from 61 mice — one zea HDF5 file per acquisition.
+- **Total size on disk:** TODO.
+- **Split:** none.
+
+## Subject Metadata
+
+Aggregate only; the subjects are mice, so no PHI applies. Subject attributes
+are counted per mouse (n = 61); probe and imaging plane per acquisition
+(n = 99).
+
+- **Subjects:** 61 mice, 99 acquisitions.
+- **Sex:** 36 female, 22 male, 3 unrecorded.
+- **Strain:** C57BL/6J (48), C57BL/6N (13).
+- **Age:** 22–216 days (recorded for 56 of 61).
+- **Weight:** 11.3–31.0 g (recorded for 55 of 61).
+- **Anatomy:** whole-brain transcranial, through the intact skull. An imaging
+  plane is named for 23 of 99 acquisitions: striatum, hippocampus, midbrain,
+  pons, cerebellum.
+- **Pathology:** none — all animals are healthy.
+- **Probe model:** L22-14v (77), GEL818iD (15), L22-14vX (7).
+- **Sites:** McGill University (43 mice), ICM / Paris Brain Institute (12),
+  Université de Montréal (6).
+
+## Data Validation
+
+- Standard B-mode and B-mode with tissue suppression `zea` pipelines available in `pipeline_bmode.yaml` and `pipeline_tissue_suppression.yaml`, respectively.
+
+## Known Issues
+
+- N/A
+
+## Ethical Considerations
+
+- **Data tier:** in vivo animal (mouse). No human subjects, no protected health
+  information, and no participant-consent or IRB requirement applies.
+- **Animal use approval:** acquisitions were performed under an institutional
+  animal use protocol. `custom/mouse_animal_protocol_id` records the identifier
+  per acquisition. Recording sites are McGill University, the ICM (Institut de cardiologie de Montréal), and Université de Montréal. The approval statements themselves
+  belong to the original ULMShare authors and should be reproduced from their
+  publication when this conversion is published, rather than inferred from the
+  protocol identifiers alone.
+- **Animal welfare (ARRIVE 2.0):** the essential-10 reporting items that this
+  dataset can carry are recorded per acquisition and summarized under Subject
+  Metadata — species and strain, sex, age, weight, health status (all healthy;
+  no disease model), anesthetic protocol, contrast-agent route and dose, and
+  recording site. Items that belong to the original study design rather than
+  the released data — sample-size rationale, randomization, blinding, and
+  outcome definitions — are not reproduced here and should be taken from the
+  ULMShare publication.
+- **De-identification:** not applicable to animal subjects. Subject IDs are
+  coded (`mouse_18`), and no date of birth is carried into the zea files —
+  only age in days.
+- **Procedures:** no terminal procedure is represented; imaging is transcranial
+  through the intact skull.
+
+## Citation
+
+CC BY 4.0 requires attribution to the original authors. Cite the **dataset**:
+
+Rauby, B., Ghigo, N., Ramos-Palacios, G., Leconte, A., Lee, S., Wu, A.,
+Xing, P., Gulenko, O., Caron, L., Malescot, A., Martineau, É., Porée, J.,
+Gasse, M., Rungta, R., Sadikot, A., Provost, J. (2026). *ULMShare: A
+Large-Scale In Vivo Ultrasound Localization Microscopy Dataset for
+Microvascular Imaging.* Federated Research Data Repository.
+[doi:10.20383/103.01550](https://doi.org/10.20383/103.01550)
+
+and, where the methods are relevant, the accompanying preprint:
+[arXiv:2606.07851](https://doi.org/10.48550/arXiv.2606.07851).
+
+Note that `metadata/credit` inside the converted files carries the source
+`acquisition.json`'s `doi_citations` where those are recorded, and otherwise
+falls back to the preprint DOI above; the FRDR dataset DOI is the canonical
+citation target for the data itself.