Official code for our Pattern Recognition paper Improving image segmentation with contextual and structural similarity.

In this paper, we propose a contextual similarity loss and a structural similarity loss for measuring the high-level similarity between segmentation model predictions and the corresponding ground-truth. These two loss functions complement and can be used together with pixel/voxel-level loss functions, e.g., cross-entropy loss and dice loss, for improved segmentation performance.

In the released code, we demonstrate the use of our method for pancreas segmentation using publicly available NIH pancreas dataset. However, the same method can be used for other organs accurately and efficiently. To use the code, follow the 3 steps below.

Step1: Data preprocessing

   Don't worry about it! Only spatial normalization and intensity clipping are needed.
   
   Images are named as "image0001.nii.gz", while labels are named as "label0001.nii.gz".
   
   After processing, save them where you can access and change the paths in training.py and testing.py

Step2: Training

   Command: python training

Step3: Inference

   Command: python testing

A pretrained a model is previded in checkpoints folder. It is trained with images from 21 to 82. When using it for inference, you can expect an average DSC of 85.4% on the first fold.