SmartSeg: machine learning infrastructure software for accelerating medical image segmentation in patient-specific applications

Abstract

Patient-specific applications in biomechanics and orthopaedics call for segmentation of volumetric medical images. This task has historically been performed manually or semi-automatically, which entails significant effort by trained experts. Computer vision algorithms based on machine learning have emerged as an effective tool for accelerating medical image processing tasks through automation. The current work describes fully no-code software which supports development of custom machine learning models for automatic segmentation of volumetric medical images. This cloud-integrated desktop application allows researchers and biomedical engineers to define segmentation algorithms, configure annotated datasets, and train personalised machine learning algorithms with cloud compute in just a few clicks. A presented case study demonstrates an ideal workflow in the software using femoral cartilage segmentation from magnetic resonance imaging as a representative use case. Models developed in the software demonstrated mean dice similarity coefficients of up to 0.886 on a test cohort, which is competitive with previously reported methods developed with significantly larger data sets. The mean surface difference between digitised models reconstructed from ground truth and predicted segmentation was 0.33 mm. Results suggest the described software enables creation of accurate machine learning models with limited engineering effort.

Keywords

• Machine learning
• automatic segmentation
• medical images