| --- |
| 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 |
| (approximately 30 TB of original-source raw data, distinct from the stored HF release below) 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), current release `zea_version` 0.1.4. |
|
|
| 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 |
|
|
| **Current OpenH-RF release:** 103 HDF5 files; 20.74 TB (20,735,658,275,478 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. |
|
|
| - **Acquisitions:** 99, from 61 mice — one zea HDF5 file per acquisition. |
| - **Stored HDF5 size:** 20.74 TB (20,735,658,275,478 bytes). |
| - **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. |
|
|
