| | --- |
| | license: agpl-3.0 |
| | language: |
| | - en |
| | metrics: |
| | - mae |
| | - mse |
| | - accuracy |
| | tags: |
| | - biology |
| | - plant |
| | - vitis |
| | - downey mildew |
| | - Plasmopara viticola |
| | - OIV 452-1 |
| | base_model: microsoft/swin-tiny-patch4-window7-224 |
| | --- |
| | # OIV Leaf Disc Phenotyping |
| |
|
| | Companion repository for the article |
| | "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) |
| |
|
| | ## Folder Structure |
| |
|
| | ### checkpoints |
| | Contains checkpoint files for leaf disc detector and OIV 452-1 scorer. |
| |
|
| | ### data |
| | Contains all datasets data in CSV format. All files are semicolon separated. |
| |
|
| | #### Leaf Disc Detection Files |
| | - ldd_train.csv, ldd_val.csv and ldd_test.csv contain bounding box annotations in Pascal VOC format. |
| | - train_ld_bounding_boxes.csv contains predictions for all available plates. |
| |
|
| | #### OIV 452-1 Annotation |
| | - oiv_annotation.csv fully annotated dataset created with the UI in leaf_patch_annotation.ipynb. |
| | - oiv_annotation_empty.csv empty annotation CSV, use it to familiarize yoursel with the annotation process. |
| | |
| | #### OIV 452-1 Predictions |
| | - oiv_train.csv, oiv_val.csv and oiv_test.csv contain OIV 452-1 annotated scores. |
| |
|
| | #### Genotype Differenciation |
| | - genotype_differenciation_dataset.csv contains annotated scores and predictions for leaf patches used in to validate model on genptype differenciation. |
| |
|
| | ### images |
| |
|
| |  |
| |
|
| | Contains all images in three different folders: |
| | - plates contains full plate images. |
| | - leaf_discs contains full leaf discs. Output folder for predicted leaf discs. |
| | - leaf_patches contains extracted patches. Output folder for predicted leaf patches. |
| |
|
| | ### src |
| | Contains source code under two formats: |
| | - *.py files contain base functionality and classes. |
| | - *.ipynb files contain code to reproduce the article data. |
| |
|
| | ## Notebooks |
| |
|
| |  |
| |
|
| | ### repo_manager.ipynb |
| | Utility notebook to create this repository |
