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--- |
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license: agpl-3.0 |
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language: |
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- en |
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metrics: |
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- mae |
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- mse |
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- accuracy |
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tags: |
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- biology |
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- plant |
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- vitis |
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- downey mildew |
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- Plasmopara viticola |
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- OIV 452-1 |
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base_model: microsoft/swin-tiny-patch4-window7-224 |
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--- |
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# OIV Leaf Disc Phenotyping |
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Companion repository for the article |
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"Phenotyping grapevine resistance to downy mildew: deep learning as a promising tool to assess sporulation and necrosis" found [Here](https://link.springer.com/article/10.1186/s13007-024-01220-4?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20240613&utm_content=10.1186/s13007-024-01220-4) |
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## Folder Structure |
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### checkpoints |
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Contains checkpoint files for leaf disc detector and OIV 452-1 scorer. |
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### data |
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Contains all datasets data in CSV format |
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#### Leaf Disc Detection Files |
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- ldd_train.csv, ldd_val.csv and ldd_test.csv contain bounding box annotations in Pascal VOC format |
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- train_ld_bounding_boxes.csv contains predictions for all available plates. |
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#### OIV 452-1 Predictions |
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- oiv_train.csv, oiv_val.csv and oiv_test.csv contain OIV 452-1 annotated scores. |
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#### Genotype Differenciation |
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- genotype_differenciation_dataset.csv contains annotated scores and predictions for leaf patches used in to validate model on genptype differenciation. |
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### images |
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Contains all images in three different folders: |
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- plates contains full plate images. |
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- leaf_discs contains full leaf discs. Output folder for predicted leaf discs. |
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- leaf_patches contains extracted patches. Output folder for predicted leaf patches. |
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### src |
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Contains source code under two formats: |
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- *.py files contain base functionality and classes |
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- *.ipynb files contain code to reproduce the article data |
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## Notebooks |
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### repo_manager.ipynb |
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Utility notebook to create this repository |
