Probabilistic Domain Adapation for Biomedical Image Segmentation

Domain adaptation based on self-training and probabilistic segmentation. This repository implements the methods described in Probabilistic Domain Adaptation for Probabilistic Domain Adaptation (arXiv).

Installation

We recommend to use conda to install all required dependencies. To set up a suitable conda environment and install the additional functionality neeeded follow these steps:

• If you don't have conda installed follow these installation instructions
• Create a new conda environment with the necessary requirements, using the environment file we provide:

  conda env create -f environment.yaml -n <ENV_NAME>
  

• Then activate the environment and install our prob_utils library:

  conda activate <ENV_NAME>
  pip install -e .
  

Please note that you may need to adapt the CUDA version in the environment.yaml file to match your system.

Now you can run all scripts for model training, prediction and evaluation in the <ENV_NAME> environment.

Experiments

We provide the code for all three domain adaptation experiments from the paper, all scripts for the respective experiments are in the respective folders:

LIVECell

Available training frameworks :

• UNet Source
• PUNet Source
• PUNet Target (optional - with Consensus Weighting/Masking)
• PUNet Mean-Teacher - Separate Training (optional - with Consensus Weighting/Masking)
• PUNet FixMatch - Separate Training (optional - with Consensus Weighting/Masking)
• PUNet Mean-Teacher - Joint Training (optional - with Consensus Weighting/Masking)
• PUNet FixMatch - Joint Training (optional - with Consensus Weighting/Masking)

MitoEM

Available training frameworks :

• UNet Source
• PUNet Source
• PUNet Target (optional - with Consensus Weighting/Masking)
• PUNet Mean-Teacher - Separate Training (optional - with Consensus Weighting/Masking)
• PUNet FixMatch - Separate Training (optional - with Consensus Weighting/Masking)
• PUNet Mean-Teacher - Joint Training (optional - with Consensus Weighting/Masking)
• PUNet FixMatch - Joint Training (optional - with Consensus Weighting/Masking)

Lung X-Ray

Available training frameworks :

• UNet Source
• PUNet Source
• PUNet Mean-Teacher - Separate Training (optional - with Consensus Weighting/Masking)
• PUNet Mean-Teacher - Joint Training (optional - with Consensus Weighting/Masking)