The ability of plants to sense and orient their root growth towards gravity is studied in many laboratories. It is known that manual analysis of image data is subjected to human bias. Several semi-automated tools are available for analysing images from flatbed scanners, but there is no solution to automatically measure root bending angle over time for vertical-stage microscopy images. To address these problems, we developed ACORBA, which is an automated software that can measure root bending angle over time from vertical-stage microscope and flatbed scanner images. ACORBA also has a semi-automated mode for camera or stereomicroscope images. It represents a flexible approach based on both traditional image processing and deep machine learning segmentation to measure root angle progression over time. As the software is automated, it limits human interactions and is reproducible. ACORBA will support the plant biologist community by reducing labour and increasing reproducibility of image analysis of root gravitropism.

Assignment flows denote a class of dynamical models for contextual data labelling (classification) on graphs. We derive a novel parametrisation of assignment flows that reveals how the underlying information geometry induces two processes for assignment regularisation and for gradually enforcing unambiguous decisions, respectively, that seamlessly interact when solving for the flow. Our result enables to characterise the dominant part of the assignment flow as a Riemannian gradient flow with respect to the underlying information geometry. We consider a continuous-domain formulation of the corresponding potential and develop a novel algorithm in terms of solving a sequence of linear elliptic partial differential equations (PDEs) subject to a simple convex constraint. Our result provides a basis for addressing learning problems by controlling such PDEs in future work.

Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. It is even more problematic if these structures continuously grow when recording a time-series of images. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. The program includes a robust binary level-set algorithm modified to use size constraints, edge intensity, and past information. We verify our algorithms using synthetic data, differential interference contrast images of filamentous prokaryotes, and transmission electron microscopy images of bacterial adhesion fimbriae. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available at Sourceforge.

Crystals within volcanic rocks record geochemical and textural signatures during magmatic evolution before eruption. Clues to this magmatic history can be examined using crystal size distribution (CSD) studies. The analysis of CSDs is a standard petrological tool, but laborious due to manual hand-drawing of crystal margins. The trainable Weka segmentation (TWS) plugin in ImageJ is a promising alternative. It uses machine learning and image segmentation to classify an image. We recorded back-scattered electron (BSE) images of three volcanic samples with different crystallinity (35, 50 and ≥85 vol. %), using scanning electron microscopes (SEM) of variable image resolutions, which we then tested using TWS. Crystal measurements obtained from the automatically segmented images are compared with those of the manual segmentation. Samples up to 50 vol. % crystallinity are successfully segmented using TWS. Segmentation at significantly higher crystallinities fails, as crystal boundaries cannot be distinguished. Accuracy performance tests for the TWS classifiers yield high F-scores (>0.930), hence, TWS is a successful and fast computing tool for outlining crystals from BSE images of glassy rocks. Finally, reliable CSD’s can be derived using a low-cost desktop SEM, paving the way for a wide range of research to take advantage of this new petrological method.

This paper presents visual and 3D structure inspection for steel structures and bridges using a developed climbing robot. The robot can move freely on a steel surface, carry sensors, collect data and then send to the ground station in real-time for monitoring as well as further processing. Steel surface image stitching and 3D map building are conducted to provide a current condition of the structure. Also, a computer vision-based method is implemented to detect surface defects on stitched images. The effectiveness of the climbing robot's inspection is tested in multiple circumstances to ensure strong steel adhesion and successful data collection. The detection method was also successfully evaluated on various test images, where steel cracks could be automatically identified, without the requirement of some heuristic reasoning.

In this paper, an automatic exposure compensation method is proposed for image enhancement. For the exposure compensation, a novel image segmentation method based on luminance distribution is also proposed. Most single-image-enhancement methods often cause details to be lost in bright areas in images or cannot sufficiently enhance contrasts in dark regions. The image-enhancement method that uses the proposed compensation method enables us to produce high-quality images which well represent both bright and dark areas by fusing pseudo multi-exposure images generated from a single image. Here, pseudo multi-exposure images are automatically generated by the proposed exposure compensation method. To generate effective pseudo multi-exposure images, the proposed segmentation method is utilized for automatic parameter setting in the compensation method. In experiments, image enhancement with the proposed compensation method outperforms state-of-the-art image enhancement methods including Retinex-based methods, in terms of both entropy and statistical naturalness. Moreover, visual comparison results show that the proposed compensation method is effective in producing images that clearly present both bright and dark areas.

Image processing and analysis is an effective tool for monitoring and fault diagnosis of activated sludge (AS) wastewater treatment plants. The AS image comprise of flocs (microbial aggregates) and filamentous bacteria. In this paper, nine different approaches are proposed for image segmentation of phase-contrast microscopic (PCM) images of AS samples. The proposed strategies are assessed for their effectiveness from the perspective of microscopic artifacts associated with PCM. The first approach uses an algorithm that is based on the idea that different color space representation of images other than red-green-blue may have better contrast. The second uses an edge detection approach. The third strategy, employs a clustering algorithm for the segmentation and the fourth applies local adaptive thresholding. The fifth technique is based on texture-based segmentation and the sixth uses watershed algorithm. The seventh adopts a split-and-merge approach. The eighth employs Kittler’s thresholding. Finally, the ninth uses a top-hat and bottom-hat filtering-based technique. The approaches are assessed, and analyzed critically with reference to the artifacts of PCM. Gold approximations of ground truth images are prepared to assess the segmentations. Overall, the edge detection-based approach exhibits the best results in terms of accuracy, and the texture-based algorithm in terms of false negative ratio. The respective scenarios are explained for suitability of edge detection and texture-based algorithms.

Image segmentation is a key process in analyzing biological images. However, it is difficult to detect the differences between foreground and background when the image is unevenly illuminated. The unambiguous segmenting of multi-well plate microscopy images with various uneven illuminations is a challenging problem. Currently, no publicly available method adequately solves these various problems in bright-field multi-well plate images. Here, we propose a new method based on contrast values which removes the need for illumination correction. The presented method is effective enough to distinguish foreground and therefore a model organism (Caenorhabditis elegans) from an unevenly illuminated microscope image. In addition, the method also can solve a variety of problems caused by different uneven illumination scenarios. By applying this methodology across a wide range of multi-well plate microscopy images, we show that our approach can consistently analyze images with uneven illuminations with unparalleled accuracy and successfully solve various problems associated with uneven illumination. It can be used to process the microscopy images captured from multi-well plates and detect experimental subjects from an unevenly illuminated background.

Image segmentation is a fundamental problem in both image processing and computer vision with numerous applications. In this paper, we propose a two-stage image segmentation scheme based on inexact alternating direction method. Specifically, we first solve the convex variant of the Mumford-Shah model to get the smooth solution, the segmentation are then obtained by apply the K-means clustering method to the solution. Some numerical comparisons are arranged to show the effectiveness of our proposed schemes by segmenting many kinds of images such as artificial images, natural images, and brain MRI images.

This paper introduces a two-stage model for multi-channel image segmentation, which is motivated by minimal surface theory. Indeed, in the first stage, we acquire a smooth solution u from a convex variational model related to minimal surface property and different data fidelity terms are considered. This minimization problem is solved efficiently by the classical primal-dual approach. In the second stage, we adopt thresholding to segment the smoothed image u. Here, instead of using K-means to determine the thresholds, we propose a more stable hill-climbing procedure to locate the peaks on the 3D histogram of u as thresholds, in the meantime, this algorithm can also detect the number of segments. Finally, numerical results demonstrate that the proposed method is very robust against noise and superior to other image segmentation approaches.

A feature-dependent variational level set formulation is proposed for image segmentation. Two second order directional derivatives act as the external constraint in the level set evolution, with the directional derivative across the image features direction playing a key role in contour extraction and another only slightly contributes. To overcome the local gradient limit, we integrate the information from the maximal (in magnitude) second-order directional derivative into a common variational framework. It naturally encourages the level set function to deform (up or down) in opposite directions on either side of the image edges, and thus automatically generates object contours. An additional benefit of this proposed model is that it does not require manual initial contours, and our method can capture weak objects in noisy or intensity-inhomogeneous images. Experiments on infrared and medical images demonstrate its advantages.

In this paper the feasibility to extract the proportion of pigs located in different areas of a pig pen by advanced image analysis technique is explored and discussed for possible applications. For example, pigs generally locate themselves in the wet dunging area at high ambient temperatures in order to avoid heat stress, as wetting the body surface is the major path to dissipate the heat by evaporation. Thus, the portion of pigs in the dunging area and resting area, respectively, could be used as an indicator of failure of controlling the climate in the pig environment as pigs are not supposed to rest in the dunging area. The computer vision methodology utilizes a learning based segmentation approach using several features extracted from the image. The learning based approach applied is based on extended state-of-the-art features in combination with a structured prediction framework based on a logistic regression solver using elastic net regularization. In addition, the method is able to produce a probability per pixel rather than form a hard decision. This overcomes some of the limitations found in a setup using grey-scale information only. The pig pen is a difficult imaging environment because of challenging lighting conditions like shadows, poor lighting and poor contrast between pig and background. In order to test practical conditions, a pen containing nine young pigs was filmed from a top view perspective by an Axis M3006 camera with a resolution of 640×480 in three, 10-min sessions under different lighting conditions. The results indicate that a learning based method improves, in comparison with greyscale methods, the possibility to reliable identify proportions of pigs in different areas of the pen. Pigs with a changed behaviour (location) in the pen may indicate changed climate conditions. Changed individual behaviour may also indicate inferior health or acute illness.

X-ray fluorescence (XRF) microscopy is an important tool for studying trace metals in biology, enabling simultaneous detection of multiple elements of interest and allowing quantification of metals in organelles without the need for subcellular fractionation. Currently, analysis of XRF images is often done using manually defined regions of interest (ROIs). However, since advances in synchrotron instrumentation have enabled the collection of very large data sets encompassing hundreds of cells, manual approaches are becoming increasingly impractical. We describe here the use of soft clustering to identify cell ROIs based on elemental contents, using data collected over a sample of the malaria parasite Plasmodium falciparum as a test case. Soft clustering was able to successfully classify regions in infected erythrocytes as “parasite,” “food vacuole,” “host,” or “background.” In contrast, hard clustering using the k-means algorithm was found to have difficulty in distinguishing cells from background. While initial tests showed convergence on two or three distinct solutions in 60% of the cells studied, subsequent modifications to the clustering routine improved results to yield 100% consistency in image segmentation. Data extracted using soft cluster ROIs were found to be as accurate as data extracted using manually defined ROIs, and analysis time was considerably improved.

A mean-shift clustering (MSC) algorithm is introduced as a valuable alternative to perform materials phase classification from multispectral images. As opposed to other multivariate statistical techniques, such as factor analysis or principal component analysis (PCA), clustering techniques directly assign a class label to each pixel, so that their outputs are phase segmented images, i.e., there is no need for an additional segmentation algorithm. On the other hand, as compared to other clustering procedures and classification methods, such as segmentation by thresholding of multiple spectral components, MSC has the advantages of not requiring previous knowledge of the number of data clusters and not assuming any shape for these clusters, i.e., neither the number nor the composition of the phases must be previously known. This makes MSC a particularly useful tool for exploratory research, assisting phase identification of unknown samples. Visualization and interpretation of the results are also simplified, since the information content of the output image does not depend on the particular choice of the content of the color channels. We applied MSC to the analysis of two sets of X-ray maps acquired in scanning electron microscopes equipped with energy-dispersive detection systems. Our results indicate that MSC is capable of detecting additional phases, not clearly identified through PCA or multiple thresholding, with a very low empirical reject rate.

One of the classical optimization models for image segmentation is the well known Markov Random Fields (MRF) model. This model is a discrete optimization problem, which is shown here to formulate many continuous models used in image segmentation. In spite of the presence of MRF in the literature, the dominant perception has been that the model is not effective for image segmentation. We show here that the reason for the non-effectiveness is due to the lack of access to the optimal solution. Instead of solving optimally, heuristics have been engaged. Those heuristic methods cannot guarantee the quality of the solution nor the running time of the algorithm. Worse still, heuristics do not link directly the input functions and parameters to the output thus obscuring what would be ideal choices of parameters and functions which are to be selected by users in each particular application context.

We describe here how MRF can model and solve efficiently several known continuous models for image segmentation and describe briefly a very efficient polynomial time algorithm, which is provably fastest possible, to solve optimally the MRF problem. The MRF algorithm is enhanced here compared to the algorithm in Hochbaum (2001) by allowing the set of assigned labels to be any discrete set. Other enhancements include dynamic features that permit adjustments to the input parameters and solves optimally for these changes with minimal computation time. Several new theoretical results on the properties of the algorithm are proved here and are demonstrated for images in the context of medical and biological imaging. An interactive implementation tool for MRF is described, and its performance and flexibility in practice are demonstrated via computational experiments.

We conclude that many continuous models common in image segmentation have discrete analogs to various special cases of MRF and as such are solved optimally and efficiently, rather than with the use of continuous techniques, such as PDE methods, that restrict the type of functions used and furthermore, can only guarantee convergence to a local minimum.

Variational image segmentation based on the Mumford and Shah model [31], together with implementation by the piecewise constant level-set method (PCLSM) [26], leads to fully nonlinear Total Variation (TV)-Allen-Cahn equations. The commonly-used numerical approaches usually suffer from the difficulties not only with the non-differentiability of the TV-term, but also with directly evolving the discontinuous piecewise constant-structured solutions. In this paper, we propose efficient dual algorithms to overcome these drawbacks. The use of a splitting-penalty method results in TV-Allen-Cahn type models associated with different “double-well” potentials, which allow for the implementation of the dual algorithm of Chambolle [8]. Moreover, we present a new dual algorithm based on an edge-featured penalty of the dual variable, which only requires to solve a vectorial Allen-Cahn type equation with linear ∇(div)-diffusion rather than fully nonlinear diffusion in the Chambolle’s approach. Consequently, more efficient numerical algorithms such as time-splitting method and Fast Fourier Transform (FFT) can be implemented. Various numerical tests show that two dual algorithms are much faster and more stable than the primal gradient descent approach, and the new dual algorithm is at least as efficient as the Chambolle’s algorithm but is more accurate. We demonstrate that the new method also provides a viable alternative for image restoration.

In previous work, a platform was developed for testing computer-vision algorithms for robotic planetary exploration. This platform consisted of a digital video camera connected to a wearable computer for real-time processing of images at geological and astrobiological field sites. The real-time processing included image segmentation and the generation of interest points based upon uncommonness in the segmentation maps. Also in previous work, this platform for testing computer-vision algorithms has been ported to a more ergonomic alternative platform, consisting of a phone camera connected via the Global System for Mobile Communications (GSM) network to a remote-server computer. The wearable-computer platform has been tested at geological and astrobiological field sites in Spain (Rivas Vaciamadrid and Riba de Santiuste), and the phone camera has been tested at a geological field site in Malta. In this work, we (i) apply a Hopfield neural-network algorithm for novelty detection based upon colour, (ii) integrate a field-capable digital microscope on the wearable computer platform, (iii) test this novelty detection with the digital microscope at Rivas Vaciamadrid, (iv) develop a Bluetooth communication mode for the phone-camera platform, in order to allow access to a mobile processing computer at the field sites, and (v) test the novelty detection on the Bluetooth-enabled phone camera connected to a netbook computer at the Mars Desert Research Station in Utah. This systems engineering and field testing have together allowed us to develop a real-time computer-vision system that is capable, for example, of identifying lichens as novel within a series of images acquired in semi-arid desert environments. We acquired sequences of images of geologic outcrops in Utah and Spain consisting of various rock types and colours to test this algorithm. The algorithm robustly recognized previously observed units by their colour, while requiring only a single image or a few images to learn colours as familiar, demonstrating its fast learning capability.

During locomotion, observers respond to objects in the environment that may represent obstacles to avoid or landmarks for navigation. Although much is known about how visual cortical neurons respond to stimulus objects moving against a blank background, nothing is known about their responses when objects are embedded in optic flow fields (the patterns of motion seen during locomotion). We recorded from cells in the lateral suprasylvian visual area (LS) of the cat, an area probably analogous to area MT. In our first experiments, optic flow simulations mimicked the view of a cat trotting across a plain covered with small balls; a black bar lying on the balls served as a target object. In subsequent experiments, optic flow simulations were composed of natural elements, with target objects representing bushes, rocks, and variants of these. Cells did not respond to the target bar in the presence of optic flow backgrounds, although they did respond to it in the absence of a background. However, 273/423 cells responded to at least one of the taller, naturalistic objects embedded in optic flow simulations. These responses might represent a form of image segmentation, in that cells detected objects against a complex background. Surprisingly, the responsiveness of cells to objects in optic flow fields was not correlated with preferred direction as measured with a moving bar or whole-field texture. Because the direction of object motion was determined solely by receptive-field location, it often differed considerably from a cell's preferred direction. About a quarter of the cells responded well to objects in optic flow movies but more weakly or not at all to bars moving in the same direction as the object, suggesting that the optic flow background modified or suppressed direction selectivity.

We have used a simple camera phone to significantly improve an ‘exploration system’ for astrobiology and geology. This camera phone will make it much easier to develop and test computer-vision algorithms for future planetary exploration. We envision that the ‘Astrobiology Phone-cam’ exploration system can be fruitfully used in other problem domains as well.