Data preparation
Dataset 2
The public images and original XML annotations are described in An open dataset of annotated metaphase cell images for chromosome identification. Download the submitted dataset from CIL:54816, then extract the archive. The required folder is 24_chromosomes_object/, containing annotations/ and JEPG/ (the spelling in the original archive).
Use the included split index to reconstruct the exact COCO files used for evaluation:
python tools/prepare_dataset2.py \
--source /path/to/24_chromosomes_object \
--output /path/to/dataset2/coco
python tools/check_dataset.py /path/to/dataset2/coco
The output directory must be new or empty. The tool copies the original images, preserves the XML box coordinates without a one-pixel shift, and assigns the image and category IDs in dataset2_split.json. No random splitting, resizing or augmentation is performed. Reconstructed image records, categories and annotations were compared with the evaluated COCO files and matched exactly for all three splits.
coco/
├── train/
│ ├── _annotations.coco.json
│ └── image files
├── valid/
│ ├── _annotations.coco.json
│ └── image files
└── test/
├── _annotations.coco.json
└── image files
| Split | Images | Annotations |
|---|---|---|
| Train | 3,500 | 160,888 |
| Validation | 500 | 22,984 |
| Test | 1,000 | 45,980 |
All splits use the same 24 chromosome classes. Keep the provided split, image IDs and category ordering when comparing with the reported results. check_dataset.py verifies image IDs, filenames, categories, annotation counts and image availability. The preparation check used the archived original dataset; it was not a new download from the hosting service.
The small image set under figures/data/ and demo/data/ contains Dataset 2 examples used in the manuscript and demonstrations. Attribution: J.-J. Tseng and colleagues, the dataset publication above and CIL:54816. The original dataset's terms apply to these images; the software license does not replace them.
Dataset 1
Dataset 1 is an in-house cohort. Images are not distributed with this repository. Its test set contains 340 images; use the source-group split and annotations supplied by the data custodian. The configurations document transforms and class ordering. --data-root selects the local dataset directory. The public repository alone does not provide access to this cohort.