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medical-image-segmentation-atrium's Introduction

Medical-Image-Segmentation-Atrium

Constructing UNET and FCN8 models for left atrium segmentation

Project Summary:

My Goal is to create two image segmentation models that can identify the left atrium segmentation from MRI scans. These models are Fully Convolutional Network (FCN-8) and UNET. The accuracy of the model will be measured using the binary_crossentropy loss and both predicted results will be compiled to GIFs.
Side Note: Model structures are learned from Coursera Course, Advanced Techniques TensorFlow

Data Source:

Source: http://medicaldecathlon.com/
License: https://creativecommons.org/licenses/by-sa/4.0/

Project Steps:

Step 1

Extract mri and segmentation labels using nibabel.

Step 2

Covert extractednumpy arrays to TF-Records, a data format that is believed to be the best for training when using TensorFlow Keras
Additionally, this format saves a lot of storage space on your PC :D! (70~80% storage savings)

Step 3

Build models, FCN-8 and UNET with
Final Output Layer: "Sigmoid"
Loss: "Binary CrossEntropy"
Optimizer: "Adam"
Side Note: These structures can also be used for multi-class segmentation problem but changes need to apply accordingly

Results:

Ground Truth:

FCN-8 Predicted Result:

UNET Predicted Result:

medical-image-segmentation-atrium's People

Contributors

cjsgit-tech avatar

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