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2/306 Top1% 肺腺癌病理切片影像之腫瘤氣道擴散偵測競賽 II:運用影像分割作法於切割STAS輪廓

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STAS_segmentation

Competition URL: https://tbrain.trendmicro.com.tw/Competitions/Details/22
Private Leaderboard: 2 / 307 (Top 1%)

Method

In this competition, we refer to the popular model "Deeplab-v3-plus" on the segmentation task. The model architecture is shown below:

In the inference phase, we use the Test-Time Augmentation(TTA) to make our model more robust. The procedure of TTA is demonstrated below:

Predicted results

Here, we take a few figures from the prediction results as examples.

Getting started

  • Clone this repo to your local
git clone https://github.com/come880412/STAS_segmentation
cd STAS_segmentation

Computer Equipment

  • System: Ubuntu20.04

  • Pytorch version: Pytorch 1.7 or higher

  • Python version: Python 3.7

  • Testing:
    CPU: AMR Ryzen 7 4800H with Radeon Graphics RAM: 32GB
    GPU: NVIDIA GeForce RTX 1660Ti 6GB

  • Training (TWCC):
    CPU: Intel(R) Xeon(R) Gold 6154 CPU @ 3.00GHz
    RAM: 180 GB
    GPU: Tesla V100 32 GB * 4

Packages

Please read the "requirement.txt" for the details.

Download & preprocess dataset

  • You should prepare the dataset from here, and put the dataset on the folder ../dataset. After doing so, please use the following command to do data preprocessing.
python3 preprocessing.py 
  • Note: please modify the dataset path on the script preprocessing.py.

Download pretrained models

  • Please download the pretrained models from here, and put the models on the folder ./checkpoint.

Inference

  • After downloading the pretrained models and preparing the datasets, you could use the following command to test the best results on the public/private leaderboard.
python3 test.py --root path/to/dataset --load ./checkpoint/deeplab_1280_900/model.pth --threshold 0.35
  • The result will be saved on the folder ./publicFig_deeplab automatically.

Training

  • You should download the COCO pretrained models on [1]. And put the model on the folder ./pretrained. After that, please use the following script to train the best model used in this competition.
bash train.sh
  • Furthermore, the following figures are our model's learning curve:

Where the top two figures are the training phase, and the two down figures are the validation phase.

Reference

[1] https://github.com/jfzhang95/pytorch-deeplab-xception

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2/306 Top1% 肺腺癌病理切片影像之腫瘤氣道擴散偵測競賽 II:運用影像分割作法於切割STAS輪廓

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