russel0719 / unet-3-plus-pytorch

Unofficial Pytorch Implementation of UNet3Plus: A Full-Scale Connected UNet for Medical Image Segmentation

UNet 3+ Unofficial Pytorch Implementation

This code is Implementation of UNet 3+ in pytorch.

I refered to Tensorflow Implementation of UNet 3+ github.

UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation

Hit star ⭐ if you find my work useful.

Table of Contents

• UNet 3+ for Image Segmentation in Pytorch.
  • Table of Contents
  • Installation
  • Code Structure
  • Config
  • Data Preparation
  • Models
  • Training
  • Inferencing
  • Acknowledgement

Installation

Requirements

• Python >= 3.10
• Pytorch >= 2.2.0
• CUDA 12.0

This code base is tested against above-mentioned Python and Pytorch versions. But it's expected to work for latest versions too.

• Clone code

git clone https://github.com/russel0719/UNet-3-Plus-Pytorch.git UNet3P
cd UNet3P

• Install other requirements.

pip install -r requirements.txt

Code Structure

• checkpoint: Model checkpoint and logs directory
• configs: Configuration file
• data: Dataset files (see Data Preparation) for more details
• data_preparation: For LiTS data preparation and data verification
• losses: Implementations of UNet3+ hybrid loss function and dice coefficient
• models: Unet3+ model files
• utils: Generic utility functions
• data_generator.py: Data generator for training, validation and testing
• predict.py: Prediction script used to visualize model output
• train.py: Training script

Config

Configurations are passed through yaml file. For more details on config file read here.

Data Preparation

• This code can be used to reproduce UNet3+ paper results on LiTS - Liver Tumor Segmentation Challenge.
• You can also use it to train UNet3+ on custom dataset.

For dataset preparation read here.

Models

This repo contains all three versions of UNet3+.

#	Description	Model Name	Training Supported
1	UNet3+ Base model	unet3plus	✓
2	UNet3+ with Deep Supervision	unet3plus_deepsup	✓
3	UNet3+ with Deep Supervision and Classification Guided Module	unet3plus_deepsup_cgm	✓

• But we can train unet3plus_deepsup_cgm only with OUTPUT.CLASSES = 1 option

Here is a sample code for UNet 3+

INPUT_SHAPE = [1, 320, 320]
OUTPUT_CHANNELS = 1

unet_3P = UNet3Plus(INPUT_SHAPE, OUTPUT_CHANNELS, deep_supervision=False, CGM=False)
unet_3P_deep_sup = UNet3Plus(INPUT_SHAPE, OUTPUT_CHANNELS, deep_supervision=True, CGM=False)
unet_3P_deep_sup_cgm = UNet3Plus(INPUT_SHAPE, OUTPUT_CHANNELS, deep_supervision=True, CGM=True)

Here you can find UNet3+ hybrid loss.

Training

To train a model call train.py with required model type and configurations .

e.g. To train on base model run

python train.py MODEL.TYPE=unet3plus

Inferencing

To inference a model call predict.py with required model type and configurations .

e.g. To train on base model run

python train.py MODEL.TYPE=unet3plus

Acknowledgement

• UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation

We appreciate any feedback so reporting problems, and asking questions are welcomed here.

Licensed under MIT License