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A CNN to segment X-Ray images

Project description

XNet

XNet is a Convolutional Neural Network designed for the segmentation of X-Ray images into bone, soft tissue and open beam regions. Specifically, it performs well on small datasets with the aim to minimise the number of false positives in the soft tissue class.

Architecture

  • Built on a typical encoder-decoder architecture as inspired by SegNet.

  • Additional feature extraction stage, with weight sharing across some layers.

  • Fine and coarse grained feature preservation through concatenation of layers.

  • L2 regularisation at each of the convolutional layers, to decrease overfitting.

The architecture is described in the XNet.py file.

Output

XNet outputs a mask of equal size to the input images.

Training

XNet is trained on a small dataset which has undergone augmention. Examples of this augmentation step can be found in the augmentations.ipynb notebook in the Augmentations folder. Similarly the Training folder contains python scripts that perform the necessary augementations.

Running train.py from the Training folder calls various other scripts to perform one of two possible ways of augmenting the images:

  • 'On the fly augmentation' where a new set of augmentations is generated at each epoch.

  • Pre-augmented images.

Benchmarking

XNet was benchmarked against two of the leading segmentation networks:

  • Simplified SegNet (found in the SimpleSegNet.py file)

  • UNet (found in the UNet.py file)

Data

We trained on a dataset of:

  • 150 X-Ray images.

  • No scatter correction.

  • 1500x1500 .tif image downsampled to 200x200

  • 20 human body part classes.

  • Highly imbalanced.

As this work grew out of work with a corporation we are sadly unable to share the propriatory data we used.

More information

For more information and context see the conference poster Poster.pdf.

Please note that some of the path variables may need to be corrected in order to utilise the current filing system. These are planned to be updated in the future.

Project details


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