Active Learning and Proofreading for Delineation of Curvilinear Structures

Many state-of-the-art delineation methods rely on supervised machine learning algorithms. As a result, they require manually annotated training data, which is tedious to obtain. Furthermore, even minor classification errors may significantly affect the topology of the final result. In this paper we propose a generic approach to addressing both of these problems by taking into account the influence of a potential misclassification on the resulting delineation. In an Active Learning context, we identify parts of linear structures that should be annotated first in order to train a classifier effectively. In a proofreading context, we similarly find regions of the resulting reconstruction that should be verified in priority to obtain a nearly-perfect result. In both cases, by focusing the attention of the human expert on potential classification mistakes which are the most critical parts of the delineation, we reduce the amount of required supervision. We demonstrate the effectiveness of our approach on microscopy images depicting blood vessels and neurons

Learning Approach to Delineation of Curvilinear Structures in 2D and 3D Images

Detection of curvilinear structures has long been of interest due to its wide range of applications. Large amounts of imaging data could be readily used in many fields, but it is practically not possible to analyze them manually. Hence, the need for automated delineation approaches. In the recent years Computer Vision witnessed a paradigm shift from mathematical modelling to data-driven methods based on Machine Learning. This led to improvements in performance and robustness of the detection algorithms. Nonetheless, most Machine Learning methods are general-purpose and they do not exploit the specificity of the delineation problem. In this thesis, we present learning methods suited for this task and we apply them to various kinds of microscopic and natural images, proving the general applicability of the presented solutions. First, we introduce a topology loss - a new training loss term, which captures higher-level features of curvilinear networks such as smoothness, connectivity and continuity. This is in contrast to most Deep Learning segmentation methods that do not take into account the geometry of the resulting prediction. In order to compute the new loss term, we extract topology features of prediction and ground-truth using a pre-trained network, whose filters are activated by structures at different scales and orientations. We show that this approach yields better results in terms of conventional segmentation metrics and overall topology of the resulting delineation. Although segmentation of curvilinear structures provides useful information, it is not always sufficient. In many cases, such as neuroscience and cartography, it is crucial to estimate the network connectivity. In order to find the graph representation of the structure depicted in the image, we propose an approach for joint segmentation and connection classification. Apart from pixel probabilities, this approach also returns the likelihood of a proposed path being a part of the reconstructed network. We show that segmentation and path classification are closely related tasks and can benefit from the synergy. The aforementioned methods rely on Machine Learning, which requires significant amounts of annotated ground-truth data to train models. The labelling process often requires expertise, it is costly and tiresome. To alleviate this problem, we introduce an Active Learning method that significantly decreases the time spent on annotating images. It queries the annotator only about the most informative examples, in this case the hypothetical paths belonging to the structure of interest. Contrary to conventional Active Learning methods, our approach exploits local consistency of linear paths to pick the ones that stand out from their neighborhood. Our final contribution is a method suited for both Active Learning and proofreading the result, which often requires more time than the automated delineation itself. It investigates edges of the delineation graph and determines the ones that are especially significant for the global reconstruction by perturbing their weights. Our Active Learning and proofreading strategies are combined with a new efficient formulation of an optimal subgraph computation and reduce the annotation effort by up to 80%

Modeling Brain Circuitry over a Wide Range of Scales

If we are ever to unravel the mysteries of brain function at its most fundamental level, we will need a precise understanding of how its component neurons connect to each other. Electron Microscopes (EM) can now provide the nanometer resolution that is needed to image synapses, and therefore connections, while Light Microscopes (LM) see at the micrometer resolution required to model the 3D structure of the dendritic network. Since both the topology and the connection strength are integral parts of the brain's wiring diagram, being able to combine these two modalities is critically important. In fact, these microscopes now routinely produce high-resolution imagery in such large quantities that the bottleneck becomes automated processing and interpretation, which is needed for such data to be exploited to its full potential. In this paper, we briefly review the Computer Vision techniques we have developed at EPFL to address this need. They include delineating dendritic arbors from LM imagery, segmenting organelles from EM, and combining the two into a consistent representation

Delineation of line patterns in images using B-COSFIRE filters

Delineation of line patterns in images is a basic step required in various applications such as blood vessel detection in medical images, segmentation of rivers or roads in aerial images, detection of cracks in walls or pavements, etc. In this paper we present trainable B-COSFIRE filters, which are a model of some neurons in area V1 of the primary visual cortex, and apply it to the delineation of line patterns in different kinds of images. B-COSFIRE filters are trainable as their selectivity is determined in an automatic configuration process given a prototype pattern of interest. They are configurable to detect any preferred line structure (e.g. segments, corners, cross-overs, etc.), so usable for automatic data representation learning. We carried out experiments on two data sets, namely a line-network data set from INRIA and a data set of retinal fundus images named IOSTAR. The results that we achieved confirm the robustness of the proposed approach and its effectiveness in the delineation of line structures in different kinds of images.Comment: International Work Conference on Bioinspired Intelligence, July 10-13, 201

Adjusting the Ground Truth Annotations for Connectivity-Based Learning to Delineate

Deep learning-based approaches to delineating 3D structure depend on accurate annotations to train the networks. Yet, in practice, people, no matter how conscientious, have trouble precisely delineating in 3D and on a large scale, in part because the data is often hard to interpret visually and in part because the 3D interfaces are awkward to use. In this paper, we introduce a method that explicitly accounts for annotation inaccuracies. To this end, we treat the annotations as active contour models that can deform themselves while preserving their topology. This enables us to jointly train the network and correct potential errors in the original annotations. The result is an approach that boosts performance of deep networks trained with potentially inaccurate annotations

Image informatics strategies for deciphering neuronal network connectivity

Brain function relies on an intricate network of highly dynamic neuronal connections that rewires dramatically under the impulse of various external cues and pathological conditions. Among the neuronal structures that show morphologi- cal plasticity are neurites, synapses, dendritic spines and even nuclei. This structural remodelling is directly connected with functional changes such as intercellular com- munication and the associated calcium-bursting behaviour. In vitro cultured neu- ronal networks are valuable models for studying these morpho-functional changes. Owing to the automation and standardisation of both image acquisition and image analysis, it has become possible to extract statistically relevant readout from such networks. Here, we focus on the current state-of-the-art in image informatics that enables quantitative microscopic interrogation of neuronal networks. We describe the major correlates of neuronal connectivity and present workflows for analysing them. Finally, we provide an outlook on the challenges that remain to be addressed, and discuss how imaging algorithms can be extended beyond in vitro imaging studies