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siemens-healthineers: sync data card, pipeline grid and figures with GitHub

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Syncs the siemens-healthineers card, pipeline and figures on the Hub with the reviewed state on GitHub (open-h/OpenH-RF).

`pipeline.yaml` gains the `parameters` block the reference reconstructions were made with: a 36 x 35 mm field of view (the RF runs out at 40.7 mm), `n_ch: 2` for the baseband IQ, all transmits, and a -60 dB dynamic range. The grid is 1014 x 986, which is isotropic at ~35.5 um in both directions; the stored `data/image` is itself exactly isotropic at 0.0791 mm, so the earlier implied grid stretched every reconstruction about 12% vertically against that reference.

Corrects the frame counts: 4,539 frames in total, 4,128 of them from the second acquisition round (Subjects 04-15), not 4,541 and 4,130. Acquisition and subject counts are unchanged.

Adds the four figures. `assets/anatomies.png` is the strip the card now leads with — four anatomies beamformed from `data/raw_data` — and `assets/Subject_03_acq_008.gif` is a ten-frame carotid loop whose caption points out that `custom/contact` marks frame 0 as off-subject, so per-frame flags should drive frame selection. The Data Validation paragraph ended mid-sentence where it referred to the reference B-modes; it now points at `assets/`. `assets/main.png` (release image) and `assets/Subject_01_acq_006_recon.png` come along for parity with the GitHub assets folder and are not embedded in the card.

The card also gains the `zea process` one-liner that renders any acquisition straight from the Hub.

Files changed: 6.

```
+ siemens-healthineers/assets/Subject_01_acq_006_recon.png
+ siemens-healthineers/assets/Subject_03_acq_008.gif
+ siemens-healthineers/assets/anatomies.png
+ siemens-healthineers/assets/main.png
~ siemens-healthineers/README.md
~ siemens-healthineers/pipeline.yaml
```

siemens-healthineers/README.md CHANGED
@@ -18,6 +18,21 @@ size_categories:
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  # Data Card — Siemens In-vivo Raw Ultrasound Channel Data
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  ## Dataset Description
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  This is an in-vivo full-synthetic-aperture (FSA) ultrasound raw channel-data
@@ -112,9 +127,9 @@ All spatial maps carry per-pixel Cartesian `coordinates` in meters, last axis `[
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  **Current OpenH-RF release:** 590 HDF5 files; 228.54 GB (228,538,449,920 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.
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- - **590 acquisitions (4,541 frames) from 15 subjects**, one continuous
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  dataset: 51 acquisitions / 411 frames (Subjects 01–03) from the first
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- acquisition round and 539 acquisitions / 4,130 frames (Subjects 04–15) from
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  the second.
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  - **File naming:** one HDF5 per acquisition, `Subject_XX_acq_NNN.hdf5`
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  (acquisitions numbered per subject in acquisition order).
@@ -141,10 +156,16 @@ single probe and system; no pathology labels are asserted.
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  ## Data Validation
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  [`pipeline.yaml`](pipeline.yaml). `data/image` is produced by this same
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- pipeline at conversion time, so `reconstruct.py` reproduces it exactly — a
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- round-trip check that the probe geometry, transmit description, and timing are
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- recorded correctly. Reference B-modes rendered by this pipeline — one per
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- anatomy (breast, thyroid, axilla, carotid, neck, abdomen) — are in
 
 
 
 
 
 
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  ## Known Issues
 
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  # Data Card — Siemens In-vivo Raw Ultrasound Channel Data
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+ ![DAS B-mode reconstructions of four anatomies from the Siemens FSA channel data](assets/anatomies.png)
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+
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+ Four of the anatomies in this dataset, each beamformed from `data/raw_data`:
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+ `Subject_03_acq_018`, `Subject_02_acq_004`, `Subject_03_acq_008`,
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+ `Subject_05_acq_031`.
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+
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+ `zea` renders any acquisition straight from the Hub with the
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+ `pipeline.yaml` in this folder. Try it out with the following command:
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+
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+ ```bash
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+ zea process \
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+ --dataset hf://nvidia/OpenH-RF/siemens-healthineers/data/Subject_03_acq_008.hdf5 \
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+ --config hf://nvidia/OpenH-RF/siemens-healthineers/pipeline.yaml
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+ ```
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+
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  ## Dataset Description
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  This is an in-vivo full-synthetic-aperture (FSA) ultrasound raw channel-data
 
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  **Current OpenH-RF release:** 590 HDF5 files; 228.54 GB (228,538,449,920 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.
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+ - **590 acquisitions (4,539 frames) from 15 subjects**, one continuous
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  dataset: 51 acquisitions / 411 frames (Subjects 01–03) from the first
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+ acquisition round and 539 acquisitions / 4,128 frames (Subjects 04–15) from
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  the second.
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  - **File naming:** one HDF5 per acquisition, `Subject_XX_acq_NNN.hdf5`
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  (acquisitions numbered per subject in acquisition order).
 
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  ## Data Validation
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  [`pipeline.yaml`](pipeline.yaml). `data/image` is produced by this same
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+ pipeline at conversion time, so `reconstruct.py` reproduces it — a round-trip
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+ check that the probe geometry, transmit description, and timing are recorded
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+ correctly. Reference B-modes rendered by this pipeline are in
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+ [`assets/`](assets), and the strip at the top of this card is four of them.
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+
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+ ![Carotid cineloop, ten frames](assets/Subject_03_acq_008.gif)
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+
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+ Ten frames of `data/Subject_03_acq_008.hdf5`. `custom/contact` marks the first
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+ frame as off-subject — use those per-frame flags when picking frames, rather
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+ than assuming frame 0 is usable.
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  ## Known Issues
siemens-healthineers/assets/Subject_01_acq_006_recon.png ADDED

Git LFS Details

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siemens-healthineers/assets/Subject_03_acq_008.gif ADDED

Git LFS Details

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siemens-healthineers/assets/anatomies.png ADDED

Git LFS Details

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siemens-healthineers/assets/main.png ADDED

Git LFS Details

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  • Pointer size: 131 Bytes
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siemens-healthineers/pipeline.yaml CHANGED
@@ -1,3 +1,14 @@
 
 
 
 
 
 
 
 
 
 
 
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  pipeline:
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  operations:
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  - beamform
 
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+ parameters:
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+ xlims: [-0.018, 0.018]
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+ zlims: [0.0, 0.035] # RF runs out at 40.7 mm
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+ # Isotropic pixels (~35.5 um both ways). The stored data/image is exactly
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+ # isotropic (0.0791 mm over 36 x 40 mm); 1014 x 1100 over 36 x 35 mm is not,
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+ # and stretched every reconstruction ~12% vertically against the reference.
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+ grid_size_x: 1014
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+ grid_size_z: 986
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+ n_ch: 2 # baseband IQ
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+ selected_transmits: all
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+ dynamic_range: [-60, 0]
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  pipeline:
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  operations:
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  - beamform