| --- |
| license: cc-by-4.0 |
| task_categories: |
| - image-segmentation |
| tags: |
| - medical |
| - fundus |
| - retina |
| - glaucoma |
| - optic-disc |
| - optic-cup |
| size_categories: |
| - 1K<n<10K |
| --- |
| |
| # Chaksu |
|
|
| Optic **disc** and optic **cup** segmentation in colour fundus photographs, for |
| glaucoma assessment. Mirror of the Chákṣu database for the MedOtter benchmark suite. |
|
|
| | | | |
| |---|---| |
| | Modality | Colour fundus photography (2D RGB) | |
| | Task | Optic disc + optic cup segmentation (also carries a glaucoma decision label) | |
| | Images | **1,345** — train 1,009 / test 336 | |
| | Cameras | Remidio FoP 2448×3264 (1,074) · Bosch 1920×1440 (145) · Forus 3Nethra 2048×1536 (126) | |
| | Ground truth | **STAPLE** fusion of 5 expert annotators | |
| | License | CC BY 4.0 | |
|
|
| ## Ground truth |
|
|
| Five ophthalmologists annotated every image. The source release ships four fusions |
| of those annotations; the paper designates **STAPLE** as the gold standard, having |
| the highest agreement with the individual experts: |
|
|
| | Fusion | OD Dice | Role here | |
| |---|---|---| |
| | **STAPLE** | **0.9764** | **primary** → `mask`, `disc_mask`, `cup_mask` | |
| | Majority (≥3 of 5) | 0.9732 | secondary → `*_mask_majority` | |
| | Median | 0.9706 | secondary → `*_mask_median` | |
| | Mean (all 5 agree) | 0.9503 | not mirrored (lowest agreement) | |
|
|
| `mask` is a disjoint label map at native image resolution: |
|
|
| | value | class | |
| |---|---| |
| | 0 | background | |
| | 1 | neuroretinal rim (disc minus cup) | |
| | 2 | optic cup | |
|
|
| so `disc = mask > 0` and `cup = mask == 2`. |
|
|
| STAPLE masks are stored anti-aliased upstream; they are binarised at >127. In a |
| small number of images the cup exceeded the disc by a handful of edge pixels, so |
| `disc_mask` is stored as *disc ∪ cup* to guarantee cup ⊆ disc. |
|
|
| ## Columns |
|
|
| | column | notes | |
| |---|---| |
| | `image` | original fundus photograph, native resolution, unmodified bytes | |
| | `mask` | disjoint 0/1/2 label map (STAPLE) | |
| | `disc_mask`, `cup_mask` | binary 0/255 (STAPLE) | |
| | `disc_mask_majority`, `cup_mask_majority` | binary 0/255 (Majority fusion) | |
| | `disc_mask_median`, `cup_mask_median` | binary 0/255 (Median fusion) | |
| | `image_id`, `camera`, `split`, `height`, `width` | identifiers / geometry | |
| | `glaucoma_decision` | majority vote of 5 experts: `NORMAL` / `GLAUCOMA SUSPECT` | |
| | `decision_expert_1..5` | per-expert decision (whitespace/spelling normalised) | |
| | `disc_area`, `cup_area`, `rim_area`, `cup_height`, `cup_width`, `disc_height`, `disc_width` | pixel measurements from the source CSVs | |
| | `acdr`, `vcdr`, `hcdr` | area / vertical / horizontal cup-to-disc ratio | |
|
|
| ## Scope of this mirror |
|
|
| This is a **subset** of the full figshare release, restricted to what a |
| segmentation benchmark needs. Present: tier 1.0 (original images), tier 5.0 |
| STAPLE/Majority/Median fusions, tier 6.0 metrics and decisions. **Not mirrored:** |
| tier 2.0 (expert contour markups), tier 3.0 (per-expert binary masks — note |
| Expert 3 has no Bosch folder), tier 4.0 (OD+OC fusion images), and the Mean and |
| Overlay variants of tier 5.0. Those total ~200 GB of mostly uncompressed TIFF and |
| are available from the original figshare deposit. |
|
|
| ## Caveats |
|
|
| - **Patient overlap across the official split.** Only the Bosch subset carries |
| patient IDs, and at least one patient straddles the boundary (`P10_Image1` in |
| train, `P10_Image2` in test). Forus and Remidio splits are sequential cuts by |
| capture order, not patient-aware, so fellow-eye pairs may also straddle it. |
| The official split is preserved as published. |
| - Source tier-6 CSVs are partly duplicated across the train and test folders |
| (the Bosch CSV is dataset-wide in both); they are merged by `(camera, image_id)`. |
| - Expert decision strings upstream include a misspelling (`GLAUCOMA SUSUPECT`); |
| these are normalised to `GLAUCOMA SUSPECT`. |
| - No overlap with REFUGE, DRISHTI-GS, RIM-ONE, ORIGA, PAPILA, IDRiD, DRIVE or |
| RAVIR — Chaksu was newly acquired at KMC/MIT Manipal. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @article{kumar2023chaksu, |
| title = {Chaksu: A glaucoma specific fundus image database}, |
| author = {Kumar, J. R. Harish and Seelamantula, Chandra Sekhar and |
| Gagan, J. H. and Kamath, Yogish S. and Kuzhuppilly, Neetha I. R. and |
| Vivekanand, U. and Gupta, Preeti and Patil, Shilpa}, |
| journal = {Scientific Data}, |
| volume = {10}, number = {1}, pages = {70}, year = {2023}, |
| doi = {10.1038/s41597-023-01943-4} |
| } |
| ``` |
|
|
| Original data: <https://doi.org/10.6084/m9.figshare.20123135> (CC BY 4.0). |
|
|
