Phenotyping is the process of measuring an organism's observable traits. Manual phenotyping of crops is a labor-intensive, time-consuming, costly, and error prone process. Accurate, automated, high-throughput phenotyping can relieve a huge burden in the crop breeding pipeline. In this paper, we propose a scalable, high-throughput approach to automatically count and segment panicles (heads), a key phenotype, from aerial sorghum crop imagery. Our counting approach uses the image density map obtained from dot or region annotation as the target with a novel deep convolutional neural network architecture. We also propose a novel instance segmentation algorithm using the estimated density map, to identify the individual panicles in the presence of occlusion. With real Sorghum aerial images, we obtain a mean absolute error (MAE) of 1.06 for counting which is better than using well-known crowd counting approaches such as CCNN, MCNN and CSRNet models. The instance segmentation model also produces respectable results which will be ultimately useful in reducing the manual annotation workload for future data.
Counting by detection is a 2-step process that first detects the objects then counts them. Counting by regression uses regression models, such as neural networks, with the object count as a target for the loss function @cite_9 . In Counting by segmentation the image is segmented into foreground and background, and the counts are estimated from the foreground @cite_22 . Recently proposed Detection by regression approaches @cite_32 @cite_24 attempt to reconstruct an image density map @cite_11 as well as detect the cell in microscopy images. This is the closest to our proposed segmentation approach, however, our problem is much more complex since panicles are much more heterogeneous within and across the various varieties of Sorghum compared to cells that are mostly homogeneous in shape and appearance.
@cite_22 @cite_9 @cite_32 @cite_24 @cite_11
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This paper concerns automated cell counting in microscopy images. The approach we take is to adapt Convolutional Neural Networks (CNNs) to regress a cell spatial density map across the image. This is applicable to situations where traditional single-cell segmentation based methods do not work well due to cell clumping or overlap. We make the following contributions: (i) we develop and compare architectures for two Fully Convolutional Regression Networks (FCRNs) for this task; (ii) since the networks are fully convolutional, they can predict a density map for an input image of arbitrary size, and we exploit this to improve efficiency at training time by training end-to-end on image patches; and (iii) we show that FCRNs trained entirely on synthetic data are able to give excellent predictions on real microscopy images without fine-tuning, and that the performance can be further improved by fine-tuning on the real images. We set a new state-of-the-art performance for cell counting on the standard synthetic image benchmarks and, as a side benefit, show the potential of the FCRNs for providing cell detections for overlapping cells. Object detection and instance segmentation are dominated by region-based methods such as Mask RCNN. However, there is a growing interest in reducing these problems to pixel labeling tasks, as the latter could be more efficient, could be integrated seamlessly in image-to-image network architectures as used in many other tasks, and could be more accurate for objects that are not well approximated by bounding boxes. In this paper we show theoretically and empirically that constructing dense pixel embeddings that can separate object instances cannot be easily achieved using convolutional operators. At the same time, we show that simple modifications, which we call semi-convolutional, have a much better chance of succeeding at this task. We use the latter to show a connection to Hough voting as well as to a variant of the bilateral kernel that is spatially steered by a convolutional network. We demonstrate that these operators can also be used to improve approaches such as Mask RCNN, demonstrating better segmentation of complex biological shapes and PASCAL VOC categories than achievable by Mask RCNN alone. A major problem among the elderly involves falling. The recognition of falls from video first requires the segmentation of the individual from the background. To ensure privacy, segmentation should result in a silhouette that is a binary map indicating only the body position of the individual in an image. We have previously demonstrated a segmentation method based on color that can recognize the silhouette and detect and remove shadows. After the silhouettes are obtained, we extract features and train hidden Markov models to recognize future performances of these known activities. In this paper, we present preliminary results that demonstrate the usefulness of this approach for distinguishing between a few common activities, specifically with fall detection in mind. and dynamic environments. High-level knowledge was fused with low-level feature-based classification to handle a time-varying background, and a decision process based on a fuzzy logic inference system was used to detach the moving objects from the human silhouette. One central task in silhouette extraction is background modeling. Once a background model is established, those image regions with significantly different characteristics from the background are considered foreground objects. In (5), a Least Median of Squares method was used to construct a background model, and in (6), a differencing function was proposed to extract moving human silhouettes. (7) demonstrated a non-parametric kernel density estimation method to model and subtract the human from a background. The adaptive background updating handles small motion in the background scene, such as moving tree branches. A slightly different approach outlined in (8) is based on processing in the YUV color space, and is capable of detecting shadows and extracting Contour detection has been a fundamental component in many image segmentation and object detection systems. Most previous work utilizes low-level features such as texture or saliency to detect contours and then use them as cues for a higher-level task such as object detection. However, we claim that recognizing objects and predicting contours are two mutually related tasks. Contrary to traditional approaches, we show that we can invert the commonly established pipeline: instead of detecting contours with low-level cues for a higher-level recognition task, we exploit object-related features as high-level cues for contour detection. We achieve this goal by means of a multi-scale deep network that consists of five convolutional layers and a bifurcated fully-connected sub-network. The section from the input layer to the fifth convolutional layer is fixed and directly lifted from a pre-trained network optimized over a large-scale object classification task. This section of the network is applied to four different scales of the image input. These four parallel and identical streams are then attached to a bifurcated sub-network consisting of two independently-trained branches. One branch learns to predict the contour likelihood (with a classification objective) whereas the other branch is trained to learn the fraction of human labelers agreeing about the contour presence at a given point (with a regression criterion). We show that without any feature engineering our multi-scale deep learning approach achieves state-of-the-art results in contour detection. The objective of this work is the detection of object classes, such as airplanes or horses. Instead of using a model based on salient image fragments, we show that object class detection is also possible using only the object's boundary. To this end, we develop a novel learning technique to extract class-discriminative boundary fragments. In addition to their shape, these “codebook” entries also determine the object's centroid (in the manner of [19]). Boosting is used to select discriminative combinations of boundary fragments (weak detectors) to form a strong “Boundary-Fragment-Model” (BFM) detector. The generative aspect of the model is used to determine an approximate segmentation. We demonstrate the following results: (i) the BFM detector is able to represent and detect object classes principally defined by their shape, rather than their appearance; and (ii) in comparison with other published results on several object classes (airplanes, cars-rear, cows) the BFM detector is able to exceed previous performances, and to achieve this with less supervision (such as the number of training images). Abstract This paper pertains to the detection of objects located in complex backgrounds. A feature-based segmentation approach to the object detection problem is pursued, where the features are computed over multiple spatial orientations and frequencies. The method proceeds as follows: a given image is passed through a bank of even-symmetric Gabor filters. A selection of these filtered images is made and each (selected) filtered image is subjected to a nonlinear (sigmoidal like) transformation. Then, a measure of texture energy is computed in a window around each transformed image pixel. The texture energy (“Gabor features”) and their spatial locations are inputted to a squared-error clustering algorithm. This clustering algorithm yields a segmentation of the original image—it assigns to each pixel in the image a cluster label that identifies the amount of mean local energy the pixel possesses across different spatial orientations and frequencies. The method is applied to a number of visual and infrared images, each one of which contains one or more objects. The region corresponding to the object is usually segmented correctly, and a unique signature of “Gabor features” is typically associated with the segment containing the object(s) of interest. Experimental results are provided to illustrate the usefulness of this object detection method in a number of problem domains. These problems arise in IVHS, military reconnaissance, fingerprint analysis, and image database query. In this paper, we propose an approach that exploits object segmentation in order to improve the accuracy of object detection. We frame the problem as inference in a Markov Random Field, in which each detection hypothesis scores object appearance as well as contextual information using Convolutional Neural Networks, and allows the hypothesis to choose and score a segment out of a large pool of accurate object segmentation proposals. This enables the detector to incorporate additional evidence when it is available and thus results in more accurate detections. Our experiments show an improvement of 4.1 in mAP over the R-CNN baseline on PASCAL VOC 2010, and 3.4 over the current state-of-the-art, demonstrating the power of our approach. Ground vehicles equipped with monocular vision systems are a valuable source of high-resolution image data for precision agriculture applications in orchards. This paper presents an image processing framework for fruit detection and counting using orchard image data. A general-purpose image segmentation approach is used, including two feature learning algorithms; multiscale multilayered perceptrons (MLP) and convolutional neural networks (CNN). These networks were extended by including contextual information about how the image data was captured (metadata), which correlates with some of the appearance variations and or class distributions observed in the data. The pixel-wise fruit segmentation output is processed using the watershed segmentation (WS) and circular Hough transform (CHT) algorithms to detect and count individual fruits. Experiments were conducted in a commercial apple orchard near Melbourne, Australia. The results show an improvement in fruit segmentation performance with the inclusion of metadata on the previously benchmarked MLP network. We extend this work with CNNs, bringing agrovision closer to the state-of-the-art in computer vision, where although metadata had negligible influence, the best pixel-wise F1-score of 0.791 was achieved. The WS algorithm produced the best apple detection and counting results, with a detection F1-score of 0.861. As a final step, image fruit counts were accumulated over multiple rows at the orchard and compared against the post-harvest fruit counts that were obtained from a grading and counting machine. The count estimates using CNN and WS resulted in the best performance for this data set, with a squared correlation coefficient of r2=0.826. In this paper we present a Bayesian framework for parsing images into their constituent visual patterns. The parsing algorithm optimizes the posterior probability and outputs a scene representation as a "parsing graph", in a spirit similar to parsing sentences in speech and natural language. The algorithm constructs the parsing graph and re-configures it dynamically using a set of moves, which are mostly reversible Markov chain jumps. This computational framework integrates two popular inference approaches--generative (top-down) methods and discriminative (bottom-up) methods. The former formulates the posterior probability in terms of generative models for images defined by likelihood functions and priors. The latter computes discriminative probabilities based on a sequence (cascade) of bottom-up tests filters. In our Markov chain algorithm design, the posterior probability, defined by the generative models, is the invariant (target) probability for the Markov chain, and the discriminative probabilities are used to construct proposal probabilities to drive the Markov chain. Intuitively, the bottom-up discriminative probabilities activate top-down generative models. In this paper, we focus on two types of visual patterns--generic visual patterns, such as texture and shading, and object patterns including human faces and text. These types of patterns compete and cooperate to explain the image and so image parsing unifies image segmentation, object detection, and recognition (if we use generic visual patterns only then image parsing will correspond to image segmentation (Tu and Zhu, 2002. IEEE Trans. PAMI, 24(5):657--673). We illustrate our algorithm on natural images of complex city scenes and show examples where image segmentation can be improved by allowing object specific knowledge to disambiguate low-level segmentation cues, and conversely where object detection can be improved by using generic visual patterns to explain away shadows and occlusions. Bourdev and Malik (ICCV 09) introduced a new notion of parts, poselets, constructed to be tightly clustered both in the configuration space of keypoints, as well as in the appearance space of image patches. In this paper we develop a new algorithm for detecting people using poselets. Unlike that work which used 3D annotations of keypoints, we use only 2D annotations which are much easier for naive human annotators. The main algorithmic contribution is in how we use the pattern of poselet activations. Individual poselet activations are noisy, but considering the spatial context of each can provide vital disambiguating information, just as object detection can be improved by considering the detection scores of nearby objects in the scene. This can be done by training a two-layer feed-forward network with weights set using a max margin technique. The refined poselet activations are then clustered into mutually consistent hypotheses where consistency is based on empirically determined spatial keypoint distributions. Finally, bounding boxes are predicted for each person hypothesis and shape masks are aligned to edges in the image to provide a segmentation. To the best of our knowledge, the resulting system is the current best performer on the task of people detection and segmentation with an average precision of 47.8 and 40.5 respectively on PASCAL VOC 2009. In this paper, we address the problems of contour detection, bottom-up grouping, object detection and semantic segmentation on RGB-D data. We focus on the challenging setting of cluttered indoor scenes, and evaluate our approach on the recently introduced NYU-Depth V2 (NYUD2) dataset (, ECCV, 2012). We propose algorithms for object boundary detection and hierarchical segmentation that generalize the @math gPb-ucm approach of (TPAMI, 2011) by making effective use of depth information. We show that our system can label each contour with its type (depth, normal or albedo). We also propose a generic method for long-range amodal completion of surfaces and show its effectiveness in grouping. We train RGB-D object detectors by analyzing and computing histogram of oriented gradients on the depth image and using them with deformable part models (, TPAMI, 2010). We observe that this simple strategy for training object detectors significantly outperforms more complicated models in the literature. We then turn to the problem of semantic segmentation for which we propose an approach that classifies superpixels into the dominant object categories in the NYUD2 dataset. We design generic and class-specific features to encode the appearance and geometry of objects. We also show that additional features computed from RGB-D object detectors and scene classifiers further improves semantic segmentation accuracy. In all of these tasks, we report significant improvements over the state-of-the-art. This paper presents a novel method for detecting and localizing objects of a visual category in cluttered real-world scenes. Our approach considers object categorization and figure-ground segmentation as two interleaved processes that closely collaborate towards a common goal. As shown in our work, the tight coupling between those two processes allows them to benefit from each other and improve the combined performance. The core part of our approach is a highly flexible learned representation for object shape that can combine the information observed on different training examples in a probabilistic extension of the Generalized Hough Transform. The resulting approach can detect categorical objects in novel images and automatically infer a probabilistic segmentation from the recognition result. This segmentation is then in turn used to again improve recognition by allowing the system to focus its efforts on object pixels and to discard misleading influences from the background. Moreover, the information from where in the image a hypothesis draws its support is employed in an MDL based hypothesis verification stage to resolve ambiguities between overlapping hypotheses and factor out the effects of partial occlusion. An extensive evaluation on several large data sets shows that the proposed system is applicable to a range of different object categories, including both rigid and articulated objects. In addition, its flexible representation allows it to achieve competitive object detection performance already from training sets that are between one and two orders of magnitude smaller than those used in comparable systems. Background Automated segmentation of fluorescently-labeled cell nuclei in 3D confocal microscope images is essential to many studies involving morphological and functional analysis. A common source of segmentation error is tight clustering of nuclei. There is a compelling need to minimize these errors for constructing highly automated scoring systems. Methods A combination of two approaches is presented. First, an improved distance transform combining intensity gradients and geometric distance is used for the watershed step. Second, an explicit mathematical model for the anatomic characteristics of cell nuclei such as size and shape measures is incorporated. This model is constructed automatically from the data. Deliberate initial over-segmentation of the image data is performed, followed by statistical model-based merging. A confidence score is computed for each detected nucleus, measuring how well the nucleus fits the model. This is used in combination with the intensity gradient to control the merge decisions. Results Experimental validation on a set of rodent brain cell images showed 97 concordance with the human observer and significant improvement over prior methods. Conclusions Combining a gradient-weighted distance transform with a richer morphometric model significantly improves the accuracy of automated segmentation and FISH analysis. Cytometry Part A 56A:23–36, 2003. © 2003 Wiley-Liss, Inc. We propose an approach to the problem of detecting and segmenting generic object classes that combines three "off the shelf" components in a novel way. The components are a generic image segmenter that returns a set of "super pixels" at different scales; a generic classifier that can determine if an image region (such as one or more super pixels) contains (part of) the foreground object or not; and a generic belief propagation (BP) procedure for tree-structured graphical models. Our system combines the regions together into a hierarchical, tree-structured conditional random field, applies the classifier to each node (region), and fuses all the information together using belief propagation. Since our classifiers only rely on color and texture, they can handle deformable (non-rigid) objects such as animals, even under severe occlusion and rotation. We demonstrate good results for detecting and segmenting cows, cats and cars on the very challenging Pascal VOC dataset. In this paper, we address the task of object counting in images. We follow modern learning approaches in which a density map is estimated directly from the input image. We employ CNNs and incorporate two significant improvements to the state of the art methods: layered boosting and selective sampling. As a result, we manage both to increase the counting accuracy and to reduce processing time. Moreover, we show that the proposed method is effective, even in the presence of labeling errors. Extensive experiments on five different datasets demonstrate the efficacy and robustness of our approach. Mean Absolute error was reduced by 20 to 35 . At the same time, the training time of each CNN has been reduced by 50 . We propose a new method to count objects of specific categories that are significantly smaller than the ground sampling distance of a satellite image. This task is hard due to the cluttered nature of scenes where different object categories occur. Target objects can be partially occluded, vary in appearance within the same class and look alike to different categories. Since traditional object detection is infeasible due to the small size of objects with respect to the pixel size, we cast object counting as a density estimation problem. To distinguish objects of different classes, our approach combines density estimation with semantic segmentation in an end-to-end learnable convolutional neural network (CNN). Experiments show that deep semantic density estimation can robustly count objects of various classes in cluttered scenes. Experiments also suggest that we need specific CNN architectures in remote sensing instead of blindly applying existing ones from computer vision. Generic object detection is the challenging task of proposing windows that localize all the objects in an image, regardless of their classes. Such detectors have recently been shown to benefit many applications such as speeding-up class-specific object detection, weakly supervised learning of object detectors and object discovery. In this paper, we introduce a novel and very efficient method for generic object detection based on a randomized version of Prim's algorithm. Using the connectivity graph of an image's super pixels, with weights modelling the probability that neighbouring super pixels belong to the same object, the algorithm generates random partial spanning trees with large expected sum of edge weights. Object localizations are proposed as bounding-boxes of those partial trees. Our method has several benefits compared to the state-of-the-art. Thanks to the efficiency of Prim's algorithm, it samples proposals very quickly: 1000 proposals are obtained in about 0.7s. With proposals bound to super pixel boundaries yet diversified by randomization, it yields very high detection rates and windows that tightly fit objects. In extensive experiments on the challenging PASCAL VOC 2007 and 2012 and SUN2012 benchmark datasets, we show that our method improves over state-of-the-art competitors for a wide range of evaluation scenarios. A robust and efficient anomaly detection technique is proposed, capable of dealing with crowded scenes where traditional tracking based approaches tend to fail. Initial foreground segmentation of the input frames confines the analysis to foreground objects and effectively ignores irrelevant background dynamics. Input frames are split into non-overlapping cells, followed by extracting features based on motion, size and texture from each cell. Each feature type is independently analysed for the presence of an anomaly. Unlike most methods, a refined estimate of object motion is achieved by computing the optical flow of only the foreground pixels. The motion and size features are modelled by an approximated version of kernel density estimation, which is computationally efficient even for large training datasets. Texture features are modelled by an adaptively grown code-book, with the number of entries in the codebook selected in an online fashion. Experiments on the recently published UCSD Anomaly Detection dataset show that the proposed method obtains considerably better results than three recent approaches: MPPCA, social force, and mixture of dynamic textures (MDT). The proposed method is also several orders of magnitude faster than MDT, the next best performing method. For crowded scenes, the accuracy of object-based computer vision methods declines when the images are low-resolution and objects have severe occlusions. Taking counting methods for example, almost all the recent state-of-the-art counting methods bypass explicit detection and adopt regression-based methods to directly count the objects of interest. Among regression-based methods, density map estimation, where the number of objects inside a subregion is the integral of the density map over that subregion, is especially promising because it preserves spatial information, which makes it useful for both counting and localization (detection and tracking). With the power of deep convolutional neural networks (CNNs) the counting performance has improved steadily. The goal of this paper is to evaluate density maps generated by density estimation methods on a variety of crowd analysis tasks, including counting, detection, and tracking. Most existing CNN methods produce density maps with resolution that is smaller than the original images, due to the downsample strides in the convolution pooling operations. To produce an original-resolution density map, we also evaluate a classical CNN that uses a sliding window regressor to predict the density for every pixel in the image. We also consider a fully convolutional adaptation, with skip connections from lower convolutional layers to compensate for loss in spatial information during upsampling. In our experiments, we found that the lower-resolution density maps sometimes have better counting performance. In contrast, the original-resolution density maps improved localization tasks, such as detection and tracking, compared with bilinear upsampling the lower-resolution density maps. Finally, we also propose several metrics for measuring the quality of a density map, and relate them to experiment results on counting and localization. For crowded scenes, the accuracy of object-based computer vision methods declines when the images are low-resolution and objects have severe occlusions. Taking counting methods for example, almost all the recent state-of-the-art counting methods bypass explicit detection and adopt regression-based methods to directly count the objects of interest. Among regression-based methods, density map estimation, where the number of objects inside a subregion is the integral of the density map over that subregion, is especially promising because it preserves spatial information, which makes it useful for both counting and localization (detection and tracking). With the power of deep convolutional neural networks (CNNs) the counting performance has improved steadily. The goal of this paper is to evaluate density maps generated by density estimation methods on a variety of crowd analysis tasks, including counting, detection, and tracking. Most existing CNN methods produce density maps with resolution that is smaller than the original images, due to the downsample strides in the convolution pooling operations. To produce an original-resolution density map, we also evaluate a classical CNN that uses a sliding window regressor to predict the density for every pixel in the image. We also consider a fully convolutional (FCNN) adaptation, with skip connections from lower convolutional layers to compensate for loss in spatial information during upsampling. In our experiments, we found that the lower-resolution density maps sometimes have better counting performance. In contrast, the original-resolution density maps improved localization tasks, such as detection and tracking, compared to bilinear upsampling the lower-resolution density maps. Finally, we also propose several metrics for measuring the quality of a density map, and relate them to experiment results on counting and localization.