Semantic segmentation using convolutional neural networks to facilitate motion tracking of feet : For real-time analysis of perioperative microcirculation images in patients with critical limb thretening ischemia

University essay from Linköpings universitet/Avdelningen för medicinsk teknik

Abstract: This thesis investigates the use of Convolutional Neural Networks (CNNs) toperform semantic segmentation of feet during endovascular surgery in patientswith Critical Limb Threatening Ischemia (CLTI). It is currently being investigatedwhether objective assessment of perfusion can aid surgeons during endovascularsurgery. By segmenting feet, it is possible to perform automatic analysis of perfusion data which could give information about the impact of the surgery in specificRegions of Interest (ROIs). The CNN was developed in Python with a U-net architecture which has shownto be state of the art when it comes to medical image segmentation. An imageset containing approximately 78 000 images of feet and their ground truth segmentation was manually created from 11 videos taken during surgery, and onevideo taken on three healthy test subjects. All videos were captured with a MultiExposure Laser Speckle Contrast Imaging (MELSCI) camera developed by Hultman et al. [1]. The best performing CNN was an ensemble model consisting of10 sub-models, each trained with different sets of training data. An ROI tracking algorithm was developed based on the Unet output, by takingadvantage of the simplicity of edge detection in binary images. The algorithmconverts images into point clouds and calculates a transformation between twopoint clouds with the use of the Iterative Closest Point (ICP) algorithm. The resultis a system that perform automatic tracking of manually selected ROIs whichenables continuous measurement of perfusion in the ROIs during endovascularsurgery. 

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