Semantic Segmentation of Soybean Leaves

This project uses Deeplab version 3+ to semantically segment images of soybean leaves. The project was modified to allow the custom dataset using a partially trained model as the initialization.

The dataset consists of a set of images with corresponding masks. These images show soybean leaves growing against a brown dirt background. The goal is to segment out each leaf to determine the percentage of crop coverage in the image.

Dataset conversion

In the datasets folder, the build_soybean_data.py script can be used to convert the images to the tfrecord needed for the tensorflow model. The dataset meta information, was included into the segmentation_dataset.py script in the datasets directory, needs to be included into the segmentation_dataset.py script.

Slim TF Library

Before the model can be trained, the tensorflow slim library needs to be added.

In the main directory (not the deeplab folder), run this to export the library to the python path:

export PYTHONPATH=$PYTHONPATH:pwd:pwd/slim

Train Model

The run_train.sh script run the training of the model based on the initial checkpoint. I started the model training with the 'deeplabv3_pascal_train_aug' initialization model provided by the deeplab team.

• Checkpoints and frozen inference graphs.
  

For running on a cluster, the cluster-run.sh script submits the training script to a bsf queue for processing. This was used on the ETHZ Leonhard GPU cluster.

Validate and Visualize

The run_vis.sh and run_val.sh run the visualization and validation of the saved model checkpoints.

Original README from Tensorflow

DeepLab: Deep Labelling for Semantic Image Segmentation

DeepLab is a state-of-art deep learning model for semantic image segmentation, where the goal is to assign semantic labels (e.g., person, dog, cat and so on) to every pixel in the input image. Current implementation includes the following features:

1. DeepLabv1 [1]: We use atrous convolution to explicitly control the resolution at which feature responses are computed within Deep Convolutional Neural Networks.

2. DeepLabv2 [2]: We use atrous spatial pyramid pooling (ASPP) to robustly segment objects at multiple scales with filters at multiple sampling rates and effective fields-of-views.

3. DeepLabv3 [3]: We augment the ASPP module with image-level feature [5, 6] to capture longer range information. We also include batch normalization [7] parameters to facilitate the training. In particular, we applying atrous convolution to extract output features at different output strides during training and evaluation, which efficiently enables training BN at output stride = 16 and attains a high performance at output stride = 8 during evaluation.

4. DeepLabv3+ [4]: We extend DeepLabv3 to include a simple yet effective decoder module to refine the segmentation results especially along object boundaries. Furthermore, in this encoder-decoder structure one can arbitrarily control the resolution of extracted encoder features by atrous convolution to trade-off precision and runtime.

If you find the code useful for your research, please consider citing our latest works:

• DeepLabv3+:

@article{deeplabv3plus2018,
  title={Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation},
  author={Liang-Chieh Chen and Yukun Zhu and George Papandreou and Florian Schroff and Hartwig Adam},
  journal={arXiv:1802.02611},
  year={2018}
}

• MobileNetv2:

@inproceedings{mobilenetv22018,
  title={Inverted Residuals and Linear Bottlenecks: Mobile Networks for Classification, Detection and Segmentation},
  author={Mark Sandler and Andrew Howard and Menglong Zhu and Andrey Zhmoginov and Liang-Chieh Chen},
  booktitle={CVPR},
  year={2018}
}

In the current implementation, we support adopting the following network backbones:

1. MobileNetv2 [8]: A fast network structure designed for mobile devices.

2. Xception [9, 10]: A powerful network structure intended for server-side deployment.

This directory contains our TensorFlow [11] implementation. We provide codes allowing users to train the model, evaluate results in terms of mIOU (mean intersection-over-union), and visualize segmentation results. We use PASCAL VOC 2012 [12] and Cityscapes [13] semantic segmentation benchmarks as an example in the code.

Some segmentation results on Flickr images:

Contacts (Maintainers)

• Liang-Chieh Chen, github: aquariusjay
• YuKun Zhu, github: yknzhu
• George Papandreou, github: gpapan

Tables of Contents

Demo:

• Colab notebook for off-the-shelf inference.
  

Running:

• Installation.
  
• Running DeepLab on PASCAL VOC 2012 semantic segmentation dataset.
  
• Running DeepLab on Cityscapes semantic segmentation dataset.
  
• Running DeepLab on ADE20K semantic segmentation dataset.
  

Models:

• Checkpoints and frozen inference graphs.
  

Misc:

• Please check FAQ if you have some questions before reporting the issues.
  

Getting Help

To get help with issues you may encounter while using the DeepLab Tensorflow implementation, create a new question on StackOverflow with the tag "tensorflow".

Please report bugs (i.e., broken code, not usage questions) to the tensorflow/models GitHub issue tracker, prefixing the issue name with "deeplab".

Change Logs

May 18, 2018

1. Added builders for ResNet-v1 and Xception model variants.
2. Added ADE20K support, including colormap and pretrained Xception_65 checkpoint.
3. Fixed a bug on using non-default depth_multiplier for MobileNet-v2.

March 22, 2018

Released checkpoints using MobileNet-V2 as network backbone and pretrained on PASCAL VOC 2012 and Cityscapes.

March 5, 2018

First release of DeepLab in TensorFlow including deeper Xception network backbone. Included chekcpoints that have been pretrained on PASCAL VOC 2012 and Cityscapes.

References

1. Semantic Image Segmentation with Deep Convolutional Nets and Fully Connected CRFs
   Liang-Chieh Chen+, George Papandreou+, Iasonas Kokkinos, Kevin Murphy, Alan L. Yuille (+ equal contribution).
   [link]. In ICLR, 2015.

2. DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs
   Liang-Chieh Chen+, George Papandreou+, Iasonas Kokkinos, Kevin Murphy, and Alan L Yuille (+ equal contribution).
   [link]. TPAMI 2017.

3. Rethinking Atrous Convolution for Semantic Image Segmentation
   Liang-Chieh Chen, George Papandreou, Florian Schroff, Hartwig Adam.
   [link]. arXiv: 1706.05587, 2017.

4. Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation
   Liang-Chieh Chen, Yukun Zhu, George Papandreou, Florian Schroff, Hartwig Adam. arXiv: 1802.02611.
   [link]. arXiv: 1802.02611, 2018.

5. ParseNet: Looking Wider to See Better
   Wei Liu, Andrew Rabinovich, Alexander C Berg
   [link]. arXiv:1506.04579, 2015.

6. Pyramid Scene Parsing Network
   Hengshuang Zhao, Jianping Shi, Xiaojuan Qi, Xiaogang Wang, Jiaya Jia
   [link]. In CVPR, 2017.

7. Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate shift
   Sergey Ioffe, Christian Szegedy
   [link]. In ICML, 2015.

8. Inverted Residuals and Linear Bottlenecks: Mobile Networks for Classification, Detection and Segmentation
   Mark Sandler, Andrew Howard, Menglong Zhu, Andrey Zhmoginov, Liang-Chieh Chen
   [link]. arXiv:1801.04381, 2018.

9. Xception: Deep Learning with Depthwise Separable Convolutions
   François Chollet
   [link]. In CVPR, 2017.

10. Deformable Convolutional Networks -- COCO Detection and Segmentation Challenge 2017 Entry
    Haozhi Qi, Zheng Zhang, Bin Xiao, Han Hu, Bowen Cheng, Yichen Wei, Jifeng Dai
    [link]. ICCV COCO Challenge Workshop, 2017.

11. Tensorflow: Large-Scale Machine Learning on Heterogeneous Distributed Systems
    M. Abadi, A. Agarwal, et al.
    [link]. arXiv:1603.04467, 2016.

12. The Pascal Visual Object Classes Challenge – A Retrospective,
    Mark Everingham, S. M. Ali Eslami, Luc Van Gool, Christopher K. I. Williams, John Winn, and Andrew Zisserma.
    [link]. IJCV, 2014.

13. The Cityscapes Dataset for Semantic Urban Scene Understanding
    Cordts, Marius, Mohamed Omran, Sebastian Ramos, Timo Rehfeld, Markus Enzweiler, Rodrigo Benenson, Uwe Franke, Stefan Roth, Bernt Schiele.
    [link]. In CVPR, 2016.