Emergence of Object Segmentation in Perturbed Generative Models

We introduce a novel framework to build a model that can learn how to segment objects from a collection of images without any human annotation. Our method builds on the observation that the location of object segments can be perturbed locally relative to a given background without affecting the realism of a scene. Our approach is to first train a generative model of a layered scene. The layered representation consists of a background image, a foreground image and the mask of the foreground. A composite image is then obtained by overlaying the masked foreground image onto the background. The generative model is trained in an adversarial fashion against a discriminator, which forces the generative model to produce realistic composite images. To force the generator to learn a representation where the foreground layer corresponds to an object, we perturb the output of the generative model by introducing a random shift of both the foreground image and mask relative to the background. Because the generator is unaware of the shift before computing its output, it must produce layered representations that are realistic for any such random perturbation. Finally, we learn to segment an image by defining an autoencoder consisting of an encoder, which we train, and the pre-trained generator as the decoder, which we freeze. The encoder maps an image to a feature vector, which is fed as input to the generator to give a composite image matching the original input image. Because the generator outputs an explicit layered representation of the scene, the encoder learns to detect and segment objects. We demonstrate this framework on real images of several object categories.Comment: 33rd Conference on Neural Information Processing Systems (NeurIPS 2019), Spotlight presentatio

What makes for effective detection proposals?

Current top performing object detectors employ detection proposals to guide the search for objects, thereby avoiding exhaustive sliding window search across images. Despite the popularity and widespread use of detection proposals, it is unclear which trade-offs are made when using them during object detection. We provide an in-depth analysis of twelve proposal methods along with four baselines regarding proposal repeatability, ground truth annotation recall on PASCAL, ImageNet, and MS COCO, and their impact on DPM, R-CNN, and Fast R-CNN detection performance. Our analysis shows that for object detection improving proposal localisation accuracy is as important as improving recall. We introduce a novel metric, the average recall (AR), which rewards both high recall and good localisation and correlates surprisingly well with detection performance. Our findings show common strengths and weaknesses of existing methods, and provide insights and metrics for selecting and tuning proposal methods.Comment: TPAMI final version, duplicate proposals removed in experiment

Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models

The health and function of tissue rely on its vasculature network to provide reliable blood perfusion. Volumetric imaging approaches, such as multiphoton microscopy, are able to generate detailed 3D images of blood vessels that could contribute to our understanding of the role of vascular structure in normal physiology and in disease mechanisms. The segmentation of vessels, a core image analysis problem, is a bottleneck that has prevented the systematic comparison of 3D vascular architecture across experimental populations. We explored the use of convolutional neural networks to segment 3D vessels within volumetric in vivo images acquired by multiphoton microscopy. We evaluated different network architectures and machine learning techniques in the context of this segmentation problem. We show that our optimized convolutional neural network architecture, which we call DeepVess, yielded a segmentation accuracy that was better than both the current state-of-the-art and a trained human annotator, while also being orders of magnitude faster. To explore the effects of aging and Alzheimer's disease on capillaries, we applied DeepVess to 3D images of cortical blood vessels in young and old mouse models of Alzheimer's disease and wild type littermates. We found little difference in the distribution of capillary diameter or tortuosity between these groups, but did note a decrease in the number of longer capillary segments ($>75\mu m$) in aged animals as compared to young, in both wild type and Alzheimer's disease mouse models.Comment: 34 pages, 9 figure

Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus