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Ultrasound Nerve Segmentation

Introduction of ultrasound nerve dataset

We join this task on Kaggle [1]. Surgery inevitably brings discomfort, and oftentimes involves significant post-surgical pain. In the past, the way to decrease the pain is to inject an anesthetic but bring a bevy of unwanted side effects. This competition's sponsor committed to improving pain management through the use of indwelling catheters that block or mitigate pain at the source. Pain management catheters reduce dependence on narcotics and speed up patient recovery. It is a critical step in finding the exact location so can assist to install the device. The task in this competition is to segment a collection of nerves called the Brachial Plexus (BP) in ultrasound images. We are dealing with ultrasound images dataset which contained 5635 training images with 2323 BP and 5508 test images.

example

Getting the code

You can download all the files in this repository by cloning this repository:

https://github.com/Jia-Wei-Liao/Ultrasound_Nerve_Segmentation.git

Repository structure

      .
      ├──checkpoint
      |   └──2021-12-31-02-33-20-best
      ├──dataset
      |   ├──train
      |   |   ├──X_X.tif
      |   |   └──X_X_mask.tif
      |   ├──test
      |   |   └──X.tif
      |   ├──train_masks.csv
      |   ├──clean_masks.csv
      |   ├──Train_X.csv
      |   └──Valid_X.csv
      ├──src
      |   ├──configs.py
      |   ├──dataset.py
      |   ├──transforms.py
      |   ├──model.py
      |   ├──metric.py
      |   ├──logger.py      
      |   ├──trainer.py
      |   ├──RLE.py
      |   └──utils.py
      ├──create_EMS.py
      ├──visualize_mask.py
      ├──train.py
      └──inference.py

Requirements

tqdm==4.55.1
numpy==1.18.5
pandas==1.2.0
matplotlib==3.3.2
pillow==8.1.0
opencv-python==4.5.4.58
torch==1.10.0
torchvision==0.11.1
monai==0.7.0
segmentation_models_pytorch==0.2.1
libtiff=0.4.2

Dataset

You can download the dataset on the Kaggle or our Google Drive:

  1. Download the dataset from Kaggle
    https://www.kaggle.com/c/ultrasound-nerve-segmentation/data

  2. Download the dataset from Google
    https://drive.google.com/drive/folders/1-mmhwFzC-fS9hthWoyu7zdjmu9sxiUut?usp=sharing

Pre-trained weight

You can download the weight and checkpoint of our model and config on the Google Drive: https://drive.google.com/drive/folders/1AlgIqtetFxAl9lOGYcZrd96YLTiMTyX2?usp=sharing

Data preparation

1. Split the train validation set
After downloading the dataset and put them into right place (see repo. structure above, train folder, test folder and train_masks.csv), we first cleaning up the redundant training data by running

python clean_dataset.py

This step will generate clean_masks.csv, then we can split training and validation dataset by running

python split_train_valid.py

This step will generate Train_X.csv and Valid_X.csv.

2. Erosion Mask Smoothing
If you want to implement the erosion mask smoothing, you might run the program python create_EMS.py . Then it will create train_mask folder in dataset.

We also write a code to visualize the train_mask image python visualize_mask.py pair

Training

To train the model, you can run this command:

python train.py \
-bs <batch size of training step> \
-ep <epochs of training step> \
--weight_num <number of save weight> \
  • dataset: 1, 2, 3, 4, 5
  • model: smp_unet, smp_unetpp, deeplabv3pp
  • pretrain: resnet{34, 50}, resnext50_32x4d, efficientnet-b{0, 1, 2}, timm-resnest{14, 26, 50}d
  • activation: RELU, LRELU, SILU, MISH
  • loss: DL, GDL, DCEL, DFL
  • optim: sgd, adam, adamw
  • scheduler: step, cos
  • device: cpu or cuda:0

Inference

To inference the results, you can run this command:

python inference.py \
--adaptive <use adaptive ensemble>
--checkpoint <checkpoint's filename> \
--ensem_num <number of ensemble weight> \

This step will output a csv file, which can be found in checkpoint/{checkpoint you have used}/answer.csv

Reproducing submission

To reproduce our submission, please do the following steps:

  1. Getting the code
  2. Install the package
  3. Download the dataset
  4. Download the weight of model
  5. Inference

Experiments

method backbone private score
UNet ResNet34 0.71031
UNet ResNet50 0.70857
UNet EfficientNet-b0 0.70233
UNet EfficientNet-b1 0.72341

Citation

@misc{
    title = {nuclear_dataset_segmentation},
    author = {Jia-Wei Liao, Kuok-Tong Ng, Yi-Cheng Hung},
    url = {https://github.com/Jia-Wei-Liao/Ultrasound_Nerve_Segmentation},
    year = {2022}
}

Reference

[1] Kaggle: https://www.kaggle.com/c/ultrasound-nerve-segmentation

[2] MONAI: https://github.com/Project-MONAI/MONAI

[3] Segmentation Models: https://github.com/qubvel/segmentation_models.pytorch