Content-based Propagation of User Markings for Interactive Segmentation of Patterned Images

Efficient and easy segmentation of images and volumes is of great practical importance. Segmentation problems that motivate our approach originate from microscopy imaging commonly used in materials science, medicine, and biology. We formulate image segmentation as a probabilistic pixel classification problem, and we apply segmentation as a step towards characterising image content. Our method allows the user to define structures of interest by interactively marking a subset of pixels. Thanks to the real-time feedback, the user can place new markings strategically, depending on the current outcome. The final pixel classification may be obtained from a very modest user input. An important ingredient of our method is a graph that encodes image content. This graph is built in an unsupervised manner during initialisation and is based on clustering of image features. Since we combine a limited amount of user-labelled data with the clustering information obtained from the unlabelled parts of the image, our method fits in the general framework of semi-supervised learning. We demonstrate how this can be a very efficient approach to segmentation through pixel classification.Comment: 9 pages, 7 figures, PDFLaTe

Underwater Fish Detection with Weak Multi-Domain Supervision

Given a sufficiently large training dataset, it is relatively easy to train a modern convolution neural network (CNN) as a required image classifier. However, for the task of fish classification and/or fish detection, if a CNN was trained to detect or classify particular fish species in particular background habitats, the same CNN exhibits much lower accuracy when applied to new/unseen fish species and/or fish habitats. Therefore, in practice, the CNN needs to be continuously fine-tuned to improve its classification accuracy to handle new project-specific fish species or habitats. In this work we present a labelling-efficient method of training a CNN-based fish-detector (the Xception CNN was used as the base) on relatively small numbers (4,000) of project-domain underwater fish/no-fish images from 20 different habitats. Additionally, 17,000 of known negative (that is, missing fish) general-domain (VOC2012) above-water images were used. Two publicly available fish-domain datasets supplied additional 27,000 of above-water and underwater positive/fish images. By using this multi-domain collection of images, the trained Xception-based binary (fish/not-fish) classifier achieved 0.17% false-positives and 0.61% false-negatives on the project's 20,000 negative and 16,000 positive holdout test images, respectively. The area under the ROC curve (AUC) was 99.94%.Comment: Published in the 2019 International Joint Conference on Neural Networks (IJCNN-2019), Budapest, Hungary, July 14-19, 2019, https://www.ijcnn.org/ , https://ieeexplore.ieee.org/document/885190

AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks

Segmentation of axon and myelin from microscopy images of the nervous system provides useful quantitative information about the tissue microstructure, such as axon density and myelin thickness. This could be used for instance to document cell morphometry across species, or to validate novel non-invasive quantitative magnetic resonance imaging techniques. Most currently-available segmentation algorithms are based on standard image processing and usually require multiple processing steps and/or parameter tuning by the user to adapt to different modalities. Moreover, only few methods are publicly available. We introduce AxonDeepSeg, an open-source software that performs axon and myelin segmentation of microscopic images using deep learning. AxonDeepSeg features: (i) a convolutional neural network architecture; (ii) an easy training procedure to generate new models based on manually-labelled data and (iii) two ready-to-use models trained from scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Results show high pixel-wise accuracy across various species: 85% on rat SEM, 81% on human SEM, 95% on mice TEM and 84% on macaque TEM. Segmentation of a full rat spinal cord slice is computed and morphological metrics are extracted and compared against the literature. AxonDeepSeg is freely available at https://github.com/neuropoly/axondeepsegComment: 14 pages, 7 figure

Autonomous monitoring of cliff nesting seabirds using computer vision

In this paper we describe a proposed system for automatic visual monitoring of seabird populations. Image sequences of cliff face nesting sites are captured using time-lapse digital photography. We are developing image processing software which is designed to automatically interpret these images, determine the number of birds present, and monitor activity. We focus primarily on the the development of low-level image processing techniques to support this goal. We first describe our existing work in video processing, and show how it is suitable for this problem domain. Image samples from a particular nest site are presented, and used to describe the associated challenges. We conclude by showing how we intend to develop our work to construct a distributed system capable of simultaneously monitoring a number of sites in the same locality

Automatic Crack Detection in Built Infrastructure Using Unmanned Aerial Vehicles

This paper addresses the problem of crack detection which is essential for health monitoring of built infrastructure. Our approach includes two stages, data collection using unmanned aerial vehicles (UAVs) and crack detection using histogram analysis. For the data collection, a 3D model of the structure is first created by using laser scanners. Based on the model, geometric properties are extracted to generate way points necessary for navigating the UAV to take images of the structure. Then, our next step is to stick together those obtained images from the overlapped field of view. The resulting image is then clustered by histogram analysis and peak detection. Potential cracks are finally identified by using locally adaptive thresholds. The whole process is automatically carried out so that the inspection time is significantly improved while safety hazards can be minimised. A prototypical system has been developed for evaluation and experimental results are included.Comment: In proceeding of The 34th International Symposium on Automation and Robotics in Construction (ISARC), pp. 823-829, Taipei, Taiwan, 201

Whole-brain vasculature reconstruction at the single capillary level

The distinct organization of the brain’s vascular network ensures that it is adequately supplied with oxygen and nutrients. However, despite this fundamental role, a detailed reconstruction of the brain-wide vasculature at the capillary level remains elusive, due to insufficient image quality using the best available techniques. Here, we demonstrate a novel approach that improves vascular demarcation by combining CLARITY with a vascular staining approach that can fill the entire blood vessel lumen and imaging with light-sheet fluorescence microscopy. This method significantly improves image contrast, particularly in depth, thereby allowing reliable application of automatic segmentation algorithms, which play an increasingly important role in high-throughput imaging of the terabyte-sized datasets now routinely produced. Furthermore, our novel method is compatible with endogenous fluorescence, thus allowing simultaneous investigations of vasculature and genetically targeted neurons. We believe our new method will be valuable for future brain-wide investigations of the capillary network

ROAM: a Rich Object Appearance Model with Application to Rotoscoping

Rotoscoping, the detailed delineation of scene elements through a video shot, is a painstaking task of tremendous importance in professional post-production pipelines. While pixel-wise segmentation techniques can help for this task, professional rotoscoping tools rely on parametric curves that offer the artists a much better interactive control on the definition, editing and manipulation of the segments of interest. Sticking to this prevalent rotoscoping paradigm, we propose a novel framework to capture and track the visual aspect of an arbitrary object in a scene, given a first closed outline of this object. This model combines a collection of local foreground/background appearance models spread along the outline, a global appearance model of the enclosed object and a set of distinctive foreground landmarks. The structure of this rich appearance model allows simple initialization, efficient iterative optimization with exact minimization at each step, and on-line adaptation in videos. We demonstrate qualitatively and quantitatively the merit of this framework through comparisons with tools based on either dynamic segmentation with a closed curve or pixel-wise binary labelling