mosaic-intelligence: sync data card and per-acquisition figures with GitHub

mosaic-intelligence/README.md

@@ -1,5 +1,6 @@
 ---
-name: "OpenH-RF — Mosaic Intelligence / NuevoSono IVUS"
+name: mosaic-intelligence
+pretty_name: "Mosaic Intelligence / NuevoSono IVUS"
 license: cc-by-4.0
 task_categories:
   - image-segmentation
@@ -9,38 +10,27 @@ tags:
   - openh-rf
   - IVUS
   - tracked-ultrasound
+language:
+  - en
 ---
 
-# Data Card — Mosaic Intelligence / NuevoSono in-vivo IVUS
+# Mosaic Intelligence / NuevoSono In-vivo IVUS
 
-This data card consists of a collection of in-vivo intravascular ultrasound (IVUS) acquisitions from a porcine study. Each acquisition is saved in the *zea* file format.  The general dataset sections below (contributors, license, characterization, etc.) apply to all acquisitions, with individual subsections detailing each dataset's specific dimensions and which optional groups are present.
+![IVUS pullback: B-mode, segmentation overlay and pullback trajectory](assets/pullback.gif)
 
-There are 9 acquisitions in total:
-
-**Group 1: `15_*` acquisitions (untracked, counterclockwise rotation):**
-- `15_10_18_21`
-- `15_10_50_19`
-- `15_16_45_06`
-
-**Group 2: `22_*` acquisitions (tracked, linear encoder pullback, clockwise rotation):**
-- `22_12_10_52`
-- `22_12_29_46`
-- `22_12_38_45`
-- `22_13_10_16`
-- `22_13_56_43`
-- `22_14_29_54`
+*Pullback through [`data/22_12_10_52.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/mosaic-intelligence/data/22_12_10_52.hdf5), reconstructed from the raw channel data. Left to right: B-mode, the same frame with the lumen and intima-media segmentation, and the linear-encoder pullback position with the current frame marked.*
 
 ## Dataset Description
 
-Each dataset is an IVUS acquisition collected in a porcine animal study. The source data consists of raw IVUS RF frames and a pre-computed (scan-converted) B-mode image. Six of the acquisitions have time-sampled linear encoder pullback positions of the IVUS probe at each frame. For each acquisition and for every frame, per-class segmentation masks are provided for the vessel lumen, intima-media, and guidewire.
+Nine in-vivo intravascular ultrasound (IVUS) acquisitions from a porcine study, each in the *zea* file format with per-frame lumen, intima-media and guidewire segmentation. Per-acquisition dimensions are in [Acquisitions](#acquisitions).
 
-## Dataset Contributors
+Each dataset is an IVUS acquisition collected in a porcine animal study. The source data consists of raw IVUS RF frames and a pre-computed (scan-converted) B-mode image. Six of the acquisitions have time-sampled linear encoder pullback positions of the IVUS probe at each frame. For each acquisition and for every frame, per-class segmentation masks are provided for the vessel lumen, intima-media, and guidewire.
 
-Mosaic Intelligence Labs in collaboration with NuevoSono
+## Dataset Contributor(s)
 
-Primary points of contact:
-Brian Boitnott (1): brian@mosaicintelligence.xyz
-Ali Mackanic (1): ali@mosaicintelligence.xyz
+- Brian Boitnott <brian@mosaicintelligence.xyz> (Mosaic Intelligence Labs; primary point of contact)
+- Ali Mackanic <ali@mosaicintelligence.xyz> (Mosaic Intelligence Labs; primary point of contact)
+- Mosaic Intelligence Labs, in collaboration with NuevoSono
 
 ## Dataset Creation Date
 
@@ -48,31 +38,31 @@ Ali Mackanic (1): ali@mosaicintelligence.xyz
 
 ## License / Terms of Use
 
-All contributed data, labels, and metadata is released by Mosaic Intelligence Labs
-and NuevoSono under CC BY 4.0.
-Pre-existing hardware, software, simulation, and platform intellectual property
-remain the property of their respective owners. The team agrees to comply with
-OpenH-RF governance, publication, and data-sharing policies. The license is also
-recorded in each file's `metadata/credit` field.
+[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
 
-Intended for IVUS tracking and segmentation applications, including lesion
-detection and image-guided intervention.
+Intended for IVUS tracking and segmentation applications, including lesion detection and image-guided intervention.
 
 ## Dataset Characterization
 
 - **Data Collection Method:** Porcine (in-vivo animal study)
 - **Labeling Method:** derived tracking metadata, semi-automated labeling
-- **Acquisition System:** Single-element IVUS, center frequency 30 MHz,
-  sampling rate 1 GHz
+- **Acquisition System:** Single-element IVUS, center frequency 30 MHz, sampling rate 1 GHz
+
+## Processing the Dataset
+
+The acquisitions can be processed with the `reconstruct.py` [script](https://github.com/open-h/OpenH-RF/blob/main/datasets/mosaic-intelligence/reconstruct.py) as provided in the [OpenH-RF GitHub repository](https://github.com/open-h/OpenH-RF), together with the `pipeline.yaml` definition in this folder and the [zea library](https://github.com/tue-bmd/zea). The script streams the data from the Hugging Face Hub.
+
+The script overlays the segmentation masks on frames spread evenly across the pullback:
+
+![Five frames across the pullback with lumen, intima-media and guidewire overlays](assets/22_12_10_52/overview_5_frames.png)
 
 ## Dataset Format
 
-All acquisitions are submitted in the *zea* file format. The RF data is stored as
-a rotational sequence of A-lines (`n_tx` transmits per frame, one element/channel);
-the accompanying B-mode `image` and `segmentation` masks are pre-computed,
-scan-converted Cartesian frames sharing a per-pixel coordinate grid.
+[zea v0.1.6](https://github.com/tue-bmd/zea)
+
+All acquisitions are submitted in the *zea* file format. The RF data is stored as a rotational sequence of A-lines (`n_tx` transmits per frame, one element/channel); the accompanying B-mode `image` and `segmentation` masks are pre-computed, scan-converted Cartesian frames sharing a per-pixel coordinate grid.
 
 ### Shared per-sample schema
 
@@ -97,111 +87,29 @@ Fields that are in every acquisition:
 | `metadata/rotation/{samples, sampling_frequency, start_time_offset}` | `[1]` / scalar / scalar | float32 | — / Hz / s | Transducer rotation: `samples = +1` clockwise, `-1` counterclockwise |
 | `metadata/pullback_position/{samples, sampling_frequency, start_time_offset}` | `[n_frames]` / scalar / scalar | float32 | m / Hz / s | Linear encoder pullback position per frame (**tracked acquisitions only**) |
 
-## Per-dataset details
-
-One data card per contributed sub-dataset. All fields follow the shared schema above. `n_ax = 8192`, `n_el = 1`, and `n_labels = 4` (`background`, `lumen`,
-`intima_media`, `guidewire`) for every acquisition.
-
-### `15_10_18_21` (untracked, counterclockwise)
-
-- Dimensions: `n_frames = 100`, `n_tx = 540`, `H = 985`, `W = 986`
-- Frame rate: ~3.33 Hz
-- Rotation: `metadata/rotation/samples = -1` (counterclockwise); `metadata/text_report = "Transducer rotation direction: counterclockwise."`
-- Tracking: **none** — no `metadata/pullback_position` group (source has no `frameAttributes.txt`)
-- **Stored HDF5 size:** 1.46 GB (1,456,209,920 bytes).
-- Note: the image/mask grid is non-square (`985 x 986`)
-
-![15_10_18_21 reconstruction overview](../outputs/15_10_18_21/overview_5_frames.png)
-
-### `15_10_50_19` (untracked, counterclockwise)
-
-- Dimensions: `n_frames = 60`, `n_tx = 360`, `H = 985`, `W = 986`
-- Frame rate: ~3.33 Hz
-- Rotation: `metadata/rotation/samples = -1` (counterclockwise)
-- Tracking: **none** — no `metadata/pullback_position` group
-- **Stored HDF5 size:** 592.12 MB (592,117,760 bytes).
-- Note: the image/mask grid is non-square (`985 x 986`)
-
-![15_10_50_19 reconstruction overview](../outputs/15_10_50_19/overview_5_frames.png)
-
-### `15_16_45_06` (untracked, counterclockwise)
-
-- Dimensions: `n_frames = 100`, `n_tx = 540`, `H = 985`, `W = 986`
-- Frame rate: ~3.33 Hz
-- Rotation: `metadata/rotation/samples = -1` (counterclockwise)
-- Tracking: **none** — no `metadata/pullback_position` group
-- **Stored HDF5 size:** 1.46 GB (1,456,275,456 bytes).
-- Note: the image/mask grid is non-square (`985 x 986`)
+## Acquisitions
 
-![15_16_45_06 reconstruction overview](../outputs/15_16_45_06/overview_5_frames.png)
+Nine acquisitions sharing the schema above: `n_ax = 8192`, `n_el = 1`, and four segmentation labels (`background`, `lumen`, `intima_media`, `guidewire`). The `15_*` acquisitions are untracked, rotate counterclockwise and use a non-square image grid; the `22_*` are tracked with a linear-encoder pullback and rotate clockwise.
 
-### `22_12_10_52` (tracked, clockwise)
-
-- Dimensions: `n_frames = 150`, `n_tx = 540`, `H = W = 2048`
-- Frame rate: ~3.33 Hz
-- Rotation: `metadata/rotation/samples = +1` (clockwise)
-- Tracking: includes `metadata/pullback_position` `[150]` (linear encoder position per frame)
-- **Stored HDF5 size:** 2.36 GB (2,356,936,704 bytes).
-
-![22_12_10_52 reconstruction overview](../outputs/22_12_10_52/overview_5_frames.png)
-
-### `22_12_29_46` (tracked, clockwise)
-
-- Dimensions: `n_frames = 100`, `n_tx = 540`, `H = W = 2048`
-- Frame rate: ~8.33 Hz
-- Rotation: `metadata/rotation/samples = +1` (clockwise)
-- Tracking: includes `metadata/pullback_position` `[100]`
-- **Stored HDF5 size:** 1.60 GB (1,602,945,024 bytes).
-
-![22_12_29_46 reconstruction overview](../outputs/22_12_29_46/overview_5_frames.png)
-
-### `22_12_38_45` (tracked, clockwise)
-
-- Dimensions: `n_frames = 150`, `n_tx = 360`, `H = W = 2048`
-- Frame rate: ~8.33 Hz
-- Rotation: `metadata/rotation/samples = +1` (clockwise)
-- Tracking: includes `metadata/pullback_position` `[150]`
-- **Stored HDF5 size:** 1.58 GB (1,576,337,408 bytes).
-
-![22_12_38_45 reconstruction overview](../outputs/22_12_38_45/overview_5_frames.png)
-
-### `22_13_10_16` (tracked, clockwise)
-
-- Dimensions: `n_frames = 100`, `n_tx = 540`, `H = W = 2048`
-- Frame rate: ~8.33 Hz
-- Rotation: `metadata/rotation/samples = +1` (clockwise)
-- Tracking: includes `metadata/pullback_position` `[100]`
-- **Stored HDF5 size:** 1.54 GB (1,535,311,872 bytes).
-
-![22_13_10_16 reconstruction overview](../outputs/22_13_10_16/overview_5_frames.png)
-
-### `22_13_56_43` (tracked, clockwise)
-
-- Dimensions: `n_frames = 100`, `n_tx = 540`, `H = W = 2048`
-- Frame rate: ~8.33 Hz
-- Rotation: `metadata/rotation/samples = +1` (clockwise)
-- Tracking: includes `metadata/pullback_position` `[100]`
-- **Stored HDF5 size:** 1.53 GB (1,527,119,872 bytes).
-
-![22_13_56_43 reconstruction overview](../outputs/22_13_56_43/overview_5_frames.png)
-
-### `22_14_29_54` (tracked, clockwise)
-
-- Dimensions: `n_frames = 150`, `n_tx = 360`, `H = W = 2048`
-- Frame rate: ~3.33 Hz
-- Rotation: `metadata/rotation/samples = +1` (clockwise); `metadata/text_report = "Transducer rotation direction: clockwise."`
-- Tracking: includes `metadata/pullback_position` `[150]`
-- **Stored HDF5 size:** 1.65 GB (1,653,080,064 bytes).
-
-![22_14_29_54 reconstruction overview](../outputs/22_14_29_54/overview_5_frames.png)
+| Acquisition | Tracked | Frames | Transmits | Image grid | Frame rate | Size |
+|---|---|---:|---:|---|---:|---:|
+| `15_10_18_21` | no | 100 | 540 | 985x986 | 3.33 Hz | 1.46 GB |
+| `15_10_50_19` | no | 60 | 360 | 985x986 | 3.33 Hz | 592.12 MB |
+| `15_16_45_06` | no | 100 | 540 | 985x986 | 3.33 Hz | 1.46 GB |
+| `22_12_10_52` | yes | 150 | 540 | 2048x2048 | 3.33 Hz | 2.36 GB |
+| `22_12_29_46` | yes | 100 | 540 | 2048x2048 | 8.33 Hz | 1.60 GB |
+| `22_12_38_45` | yes | 150 | 360 | 2048x2048 | 8.33 Hz | 1.58 GB |
+| `22_13_10_16` | yes | 100 | 540 | 2048x2048 | 8.33 Hz | 1.54 GB |
+| `22_13_56_43` | yes | 100 | 540 | 2048x2048 | 8.33 Hz | 1.53 GB |
+| `22_14_29_54` | yes | 150 | 360 | 2048x2048 | 3.33 Hz | 1.65 GB |
 
 ## Dataset Quantification
 
-**Current OpenH-RF release:** 9 HDF5 files; 13.76 GB (13,756,334,080 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.
+9 HDF5 files; 13.76 GB (13,756,334,080 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.
 
 - Acquisitions: 9 (3 untracked `15_*`, 6 tracked `22_*`)
 - Frames per acquisition: 60–150 (1010 frames total across all acquisitions)
-- Frame rate: ~3.33 Hz or ~8.33 Hz depending on acquisition (see per-dataset table)
+- Frame rate: ~3.33 Hz or ~8.33 Hz depending on acquisition (see the table above)
 - Train / validation / test split: N/A
 - **Stored HDF5 size:** 13.76 GB (13,756,334,080 bytes).
 
@@ -223,17 +131,14 @@ Animal study data — no human subjects.
 
 ## Data Validation
 
-A `zea.Pipeline` reconstructs the IVUS B-mode from the raw channel data
-(RF → envelope → normalization → log compression → scan conversion). See
-[reconstruct.py](../reconstruct.py) and [pipeline.yaml](../pipeline.yaml). Linear encoder position (when applicable) and segmentation masks are overlayed on the B-modes.
+A `zea.Pipeline` reconstructs the IVUS B-mode from the raw channel data (RF → envelope → normalization → log compression → scan conversion), as defined in `pipeline.yaml` and run by `reconstruct.py`. Linear encoder position (when applicable) and segmentation masks are overlayed on the B-modes.
 
 ## Known Issues
 
-- Untracked (`15_*`) acquisitions have no `pullback_position`, so the pullback
-  trajectory panel is omitted during reconstruction.
+- Untracked (`15_*`) acquisitions have no `pullback_position`, so the pullback trajectory panel is omitted during reconstruction.
 
 ## Ethical Considerations
 
-Porcine animal study data only; contains no human subjects or PHI. Collected and
-released in compliance with applicable institutional animal care approvals and
-OpenH-RF governance and data-sharing policies.
+Porcine animal study data only; contains no human subjects or PHI. Collected and released in compliance with applicable institutional animal care approvals and OpenH-RF governance and data-sharing policies.
+
+All contributed data, labels and metadata are released by Mosaic Intelligence Labs and NuevoSono; pre-existing hardware, software, simulation and platform intellectual property remains the property of the respective owners. The license is also recorded in each file's `metadata/credit` field.