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First commit : scripted train/test split with README

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  1. README.md +70 -1
  2. dataset.py +47 -0
  3. test/43_L_1/M0.png +3 -0
  4. test/43_L_1/correlation.png +3 -0
  5. test/43_L_1/diasys.png +3 -0
  6. test/43_L_1/maskArtery.png +3 -0
  7. test/43_L_1/maskVein.png +3 -0
  8. test/43_L_2/M0.png +3 -0
  9. test/43_L_2/correlation.png +3 -0
  10. test/43_L_2/diasys.png +3 -0
  11. test/43_L_2/maskArtery.png +3 -0
  12. test/43_L_2/maskVein.png +3 -0
  13. test/43_R_1/M0.png +3 -0
  14. test/43_R_1/correlation.png +3 -0
  15. test/43_R_1/diasys.png +3 -0
  16. test/43_R_1/maskArtery.png +3 -0
  17. test/43_R_1/maskVein.png +3 -0
  18. test/44_L_1/M0.png +3 -0
  19. test/44_L_1/correlation.png +3 -0
  20. test/44_L_1/diasys.png +3 -0
  21. test/44_L_1/maskArtery.png +3 -0
  22. test/44_L_1/maskVein.png +3 -0
  23. test/44_L_2/M0.png +3 -0
  24. test/44_L_2/correlation.png +3 -0
  25. test/44_L_2/diasys.png +3 -0
  26. test/44_L_2/maskArtery.png +3 -0
  27. test/44_L_2/maskVein.png +3 -0
  28. test/44_R_1/M0.png +3 -0
  29. test/44_R_1/correlation.png +3 -0
  30. test/44_R_1/diasys.png +3 -0
  31. test/44_R_1/maskArtery.png +3 -0
  32. test/44_R_1/maskVein.png +3 -0
  33. test/45_L_1/M0.png +3 -0
  34. test/45_L_1/correlation.png +3 -0
  35. test/45_L_1/diasys.png +3 -0
  36. test/45_L_1/maskArtery.png +3 -0
  37. test/45_L_1/maskVein.png +3 -0
  38. test/45_R_1/M0.png +3 -0
  39. test/45_R_1/correlation.png +3 -0
  40. test/45_R_1/diasys.png +3 -0
  41. test/45_R_1/maskArtery.png +3 -0
  42. test/45_R_1/maskVein.png +3 -0
  43. test/46_L_1/M0.png +3 -0
  44. test/46_L_1/correlation.png +3 -0
  45. test/46_L_1/diasys.png +3 -0
  46. test/46_L_1/maskArtery.png +3 -0
  47. test/46_L_1/maskVein.png +3 -0
  48. test/46_L_2/M0.png +3 -0
  49. test/46_L_2/correlation.png +3 -0
  50. test/46_L_2/diasys.png +3 -0
README.md CHANGED
@@ -1,3 +1,72 @@
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  ---
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- license: cc-by-4.0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  ---
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+ language:
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+ - en
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+ pretty_name: Retinal Vessel Segmentation from Holographic Doppler Imaging
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+ tags:
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+ - medical-imaging
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+ - holography
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+ - retina
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+ - vessel-segmentation
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+ - deep-learning
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+ - artery-vein-segmentation
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+ - doppler-imaging
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+ task_categories:
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+ - image-segmentation
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+ license: cc-by-nc-4.0
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+ size_categories:
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+ - n<1K
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  ---
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+
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+ # Retinal Vessel Segmentation from Holographic Doppler Imaging
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+
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+ This dataset provides paired images and segmentation masks for **retinal vessel segmentation** from **holographic Doppler imaging**.
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+ It is designed for research in **computational imaging**, **retinal blood flow analysis**, and **deep learning-based vessel segmentation**.
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+
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+ ---
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+
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+ ## Dataset Summary
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+
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+ Holographic Doppler imaging enables quantitative blood flow mapping in the retina by analyzing temporal fluctuations in optical interferograms.
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+ This dataset includes **power Doppler images (M0)** and their corresponding **artery and vein segmentation masks**, representing the spatial distribution of retinal blood flow observed through laser Doppler holography.
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+ Temporal informations derived from the arterial signal, namely the correlation map and the diasys image, are also provided.
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+ See the article submitted to ISBI2026 (*linked soon*) for more details
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+
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+ ---
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+
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+ ## Data Description
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+
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+ | Attribute | Description |
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+ |:-----------|:-------------|
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+ | **Imaging modality** | Holographic Laser Doppler imaging of the retina |
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+ | **Input type** | Power Doppler intensity images (M0), Correlation map, Diasys image
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+ | **Target type** | Artery and Vein masks : binary segmentation masks (vessels vs. background) |
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+ | **Classes** | 0: Background, 1: Vessel |
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+ | **File format** | PNG (8-bit grayscale) |
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+ | **Typical image size** | 1023 × 1023 pixels |
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+ | **Sampling** | Retinal field of view from high-speed interferometric acquisitions |
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+ | **Preprocessing** | Temporal SVD filtering, Fresnel reconstruction, power Doppler accumulation |
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+
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+ ---
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+
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+ ## Dataset Structure
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+
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+ HoloDopplerSegISBI/
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+ ├── dataset.py
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+ ├── README.md
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+ ├── train/
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+ │ ├── measure_001/
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+ │ │ ├── M0.png
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+ │ │ ├── correlation.png
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+ │ │ ├── diasys.png
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+ │ │ ├── maskArtery.png
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+ │ │ └── maskVein.png
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+ │ └── ...
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+ └── test/
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+ ├── measure_122/
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+ └── ...
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+
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+
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+ Measures have the following form : *id*\_*eye*\_*\_number*, with:
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+ - *id* corresponding to a unique patient.
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+ - *eye* equals to 'R' or 'L', respectively for right eye or left eye
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+ - *number* indicating which measure of the same eye it is
dataset.py ADDED
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+ import os
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+ from datasets import DatasetBuilder, DatasetInfo, SplitGenerator, Split, Features, Value
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+
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+ class DopplerRetina(DatasetBuilder):
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+ VERSION = "1.0.0"
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+
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+ def _info(self):
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+ return DatasetInfo(
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+ description="Retinal Doppler artery/vein segmentation dataset",
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+ features=Features({
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+ "measure_id": Value("string"),
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+ "m0": Value("string"),
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+ "correlation": Value("string"),
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+ "diasys": Value("string"),
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+ "artery_mask": Value("string"),
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+ "vein_mask": Value("string"),
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+ }),
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+ )
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+
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+ def _split_generators(self, dl_manager):
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+ repo_dir = dl_manager.download_and_extract(self.base_path)
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+
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+ return [
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+ SplitGenerator(
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+ name=Split.TRAIN,
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+ gen_kwargs={"path": os.path.join(repo_dir, "train")},
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+ ),
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+ SplitGenerator(
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+ name=Split.TEST,
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+ gen_kwargs={"path": os.path.join(repo_dir, "test")},
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+ ),
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+ ]
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+
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+ def _generate_examples(self, path):
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+ for measure in sorted(os.listdir(path)):
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+ mdir = os.path.join(path, measure)
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+ if not os.path.isdir(mdir):
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+ continue
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+
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+ yield measure, {
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+ "measure_id": measure,
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+ "m0": os.path.join(mdir, "M0.png"),
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+ "correlation": os.path.join(mdir, "correlation.png"),
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+ "diasys": os.path.join(mdir, "diasys.png"),
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+ "artery_mask": os.path.join(mdir, "maskArtery.png"),
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+ "vein_mask": os.path.join(mdir, "maskVein.png"),
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+ }
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