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Register a new userWeakly Supervised Volumetric Image Segmentation with Deformed Templates
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Added by
Udaranga Wickramasinghe
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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There are many approaches that use weak-supervision to train networks to segment 2D images. By contrast, existing 3D approaches rely on full-supervision of a subset of 2D slices of the 3D image volume. In this paper, we propose an approach that is truly weakly-supervised in the sense that we only need to provide a sparse set of 3D point on the surface of target objects, an easy task that can be quickly done. We use the 3D points to deform a 3D template so that it roughly matches the target object outlines and we introduce an architecture that exploits the supervision provided by coarse template to train a network to find accurate boundaries. We evaluate the performance of our approach on Computed Tomography (CT), Magnetic Resonance Imagery (MRI) and Electron Microscopy (EM) image datasets. We will show that it outperforms a more traditional approach to weak-supervision in 3D at a reduced supervision cost.
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Medical image annotation is a major hurdle for developing precise and robust machine learning models. Annotation is expensive, time-consuming, and often requires expert knowledge, particularly in the medical field. Here, we suggest using minimal user interaction in the form of extreme point clicks to train a segmentation model which, in effect, can be used to speed up medical image annotation. An initial segmentation is generated based on the extreme points utilizing the random walker algorithm. This initial segmentation is then used as a noisy supervision signal to train a fully convolutional network that can segment the organ of interest, based on the provided user clicks. Through experimentation on several medical imaging datasets, we show that the predictions of the network can be refined using several rounds of training with the prediction from the same weakly annotated data. Further improvements are shown utilizing the clicked points within a custom-designed loss and attention mechanism. Our approach has the potential to speed up the process of generating new training datasets for the development of new machine learning and deep learning-based models for, but not exclusively, medical image analysis.
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