| # 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](https://doi.org/10.1038/s41597-023-02003-7). Download the submitted dataset from [CIL:54816](https://doi.org/10.7295/W9CIL54816), 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: |
|
|
| ```bash |
| 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. |
|
|
| ```text |
| 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. |
|
|
