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VegAnn

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Repository of the VegAnn Dataset

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# VegAnn 
![Alt text](https://raw.githubusercontent.com/simonMadec/VegAnn/main/images/vegann-logo.png "Vegann-logo")

# NEWS! : The dataset is now on HuggingFace : https://huggingface.co/datasets/simonMadec/VegAnn
### **Vegetation Annotation of a large multi-crop RGB Dataset acquired under diverse conditions for image semantic segmentation**

# Table of contents
1. [Keypoints](#key)
2. [Abstract](#abs)
3. [DIY with Google Colab](#colab)
4. [Pytorch Data Loader](#loader)
5. [Baseline Results](#res)
6. [Citing](#cite)
7. [Paper](#paper)
8. [Meta-Information](#meta)
9. [Model inference](#model)
10. [Licence](#licence)
11. [Credits](#credits)

## ⏳ Keypoints <a name="key"></a>
- The dataset can be accessed on Hugging face : https://huggingface.co/datasets/simonMadec/VegAnn and Zenodo https://doi.org/10.5281/zenodo.7636408.
- VegAnn contains 3775 images 
- Images are 512*512 pixels 
- Corresponding binary masks is 0 for soil + crop residues (background) 255 for Vegetation (foreground)
- The dataset includes images of 26+ crop species, which are not evenly represented
- VegAnn was compiled using a variety of outdoor images captured with different acquisition systems and configurations
- For more information about VegAnn, details, labeling rules and potential uses see https://doi.org/10.1038/s41597-023-02098-y

## 📚 Abstract <a name="abs"></a>

Applying deep learning to images of cropping systems provides new knowledge and insights in research and commercial applications. Semantic segmentation or pixel-wise classification, of RGB images acquired at the ground level, into vegetation and background is a critical step in the estimation of several canopy traits. Current state of the art methodologies based on convolutional neural networks (CNNs) are trained on datasets acquired under controlled or indoor environments. These models are unable to generalize to real-world images and hence need to be fine-tuned using new labelled datasets. This motivated the creation of the VegAnn - **Veg**etation **Ann**otation - dataset, a collection of 3795 multi-crop RGB images acquired for different phenological stages using different systems and platforms in diverse illumination conditions. We anticipate that VegAnn will help improving segmentation algorithm performances, facilitate benchmarking and promote large-scale crop vegetation segmentation research.

## Google Colab <a name="colab"></a>
Example code for VegAnn (Unet) inference here : https://t.co/LkI1esLzqu

## 📦 Pytorch Data Loader <a name="loader"></a>
We provide Python dataloader that load the data as PyTorch tensors. With the dataloader, users can select desired images with the metadata information such as species, camera system, and training/validation/test sets.

### 🍲 Example use :

Here is an example use case of the dataloader with our custom dataset class:

```
    from segmentation_models_pytorch.encoders import get_preprocessing_fn
    from utils.dataset import DatasetVegAnn
    from torch.utils.data import DataLoader

train_dataset = DatasetVegAnn(images_dir = veganpath,species = ["Wheat","Maize"], system = ["Handeld Cameras","Phone Camera"], tvt="Training")    
    train_dataloader = DataLoader(train_dataset, batch_size=16, shuffle=True,pin_memory=False, num_workers=10)
```
By using this dataloader, you can easily load the desired images as PyTorch tensors see utils/dataset.py for more details.

## 👀 Baseline Results <a name="res"></a>

Metrics are computed at the dataset level for the 5 Test sets of VegAnn

Method               | Encoder | IOU | F1 
---                  | ---  | ---   | ---                  
Unet       |   ResNet34  | 89.7 ±1.4  |  94.5 ±0.8
DeepLabV3  |   ResNet34  | 89.5 ±0.2  |  94.5 ±0.2

## 📝 Citing  <a name="cite"></a>

If you find this dataset useful, please cite:

@article{madec2023,
  title={VegAnn: Vegetation Annotation of multi-crop RGB images acquired under diverse conditions for segmentation},
  author={Madec, Simon  and Irfan, Kamran and Velumani, Kaaviya and Baret, Frederic and David, Etienne  and Daubige, Gaetan  and Samatan, Lucas   and Serouart, Mario and Smith, Daniel  and James, Chris  and Camacho, Fernando  and Guo, Wei and De Solan, Benoit  and Chapman, Scott and Weiss, Marie },
  url={https://doi.org/10.5281/zenodo.7636408},
  year={2023}
}
## 📖 Paper <a name="paper"></a>
https://doi.org/10.1038/s41597-023-02098-y

## ☸️ Model inference <a name="model"></a>
Model weights here : https://drive.google.com/uc?id=1azagsinfW4btSGaTi0XJKsRnFR85Gtaw (Unet, resnet34 weights initialized on Imagenet fine-tunned on Vegan)
Please open an issue or request for any feature request

##  📑Licence <a name="licence"></a>
The dataset is under the CC-BY licence. 
This repository is under the MIT licence

## 👫 Credits <a name="credits"></a>
This work was supported by the projects Phenome-ANR-11-INBS-0012, P2S2-CNES-TOSCA-4500066524, GRDC UOQ2002-08RTX, GRDC UOQ2003-011RTX, JST AIP Acceleration Research JPMJCR21U3 and French Ministry of Agriculture and food (LITERAL CASDAR project).

We thank all the people involved in the labelling review also including F.Venault, M. Debroux, G. Studer

VegAnn

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