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 and detection in microscopy images. The approach we take is to use convolutional neural networks (CNNs) to regress a cell spatial density map across the ... 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. 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. The ability to accurately quantitate specific populations of cells is important for precision diagnostics in laboratory medicine. For example, the quantization of positive tumor cells can be used clinically to determine the need for chemotherapy in a cancer patient. In this paper, we describe a supervised learning framework with Convolutional Neural Network (CNN) and cast the cell counting task as a regression problem, where the global cell count is taken as the annotation to supervise training, instead of following the classification or detection framework. To further decrease the prediction error of counting, we tune several cutting-edge CNN architectures (e.g. Deep Residual Network) into the regression model. As the final output, not only the cell count is estimated for an image, but also its spatial density map is provided. The proposed method is evaluated with three state-of-the-art approaches on three cell image datasets and obtain superior performance. We propose a novel object detection framework for partially-occluded small instances, such as pedestrians in low resolution surveillance video, cells under a microscope, flocks of small animals (e.g. birds, fishes), or even tiny insects like honeybees and flies. These scenarios are very challenging for traditional detectors, which are typically trained on individual instances. In our approach, we first estimate the object density map of the input image, and then divide it into local regions. For each region, a sliding window (ROI) is passed over the density map to calculate the instance count within each ROI. 2D integer programming is used to recover the locations of object instances from the set of ROI counts, and the global count estimate of the density map is used as a constraint to regularize the detection performance. Finally, the bounding box for each instance is estimated using the local density map. Compared with current small-instance detection methods, our proposed approach achieves state-of-the-art performance on several challenging datasets including fluorescence microscopy cell images, UCSD pedestrians, small animals and insects. In this paper we address the problem of counting objects instances in images. Our models are able to precisely estimate the number of vehicles in a traffic congestion, or to count the humans in a very crowded scene. Our first contribution is the proposal of a novel convolutional neural network solution, named Counting CNN (CCNN). Essentially, the CCNN is formulated as a regression model where the network learns how to map the appearance of the image patches to their corresponding object density maps. Our second contribution consists in a scale-aware counting model, the Hydra CNN, able to estimate object densities in different very crowded scenarios where no geometric information of the scene can be provided. Hydra CNN learns a multiscale non-linear regression model which uses a pyramid of image patches extracted at multiple scales to perform the final density prediction. We report an extensive experimental evaluation, using up to three different object counting benchmarks, where we show how our solutions achieve a state-of-the-art performance. An approach to the problem of estimating the size of inhomogeneous crowds, which are composed of pedestrians that travel in different directions, without using explicit object segmentation or tracking is proposed. Instead, the crowd is segmented into components of homogeneous motion, using the mixture of dynamic-texture motion model. A set of holistic low-level features is extracted from each segmented region, and a function that maps features into estimates of the number of people per segment is learned with Bayesian regression. Two Bayesian regression models are examined. The first is a combination of Gaussian process regression with a compound kernel, which accounts for both the global and local trends of the count mapping but is limited by the real-valued outputs that do not match the discrete counts. We address this limitation with a second model, which is based on a Bayesian treatment of Poisson regression that introduces a prior distribution on the linear weights of the model. Since exact inference is analytically intractable, a closed-form approximation is derived that is computationally efficient and kernelizable, enabling the representation of nonlinear functions. An approximate marginal likelihood is also derived for kernel hyperparameter learning. The two regression-based crowd counting methods are evaluated on a large pedestrian data set, containing very distinct camera views, pedestrian traffic, and outliers, such as bikes or skateboarders. Experimental results show that regression-based counts are accurate regardless of the crowd size, outperforming the count estimates produced by state-of-the-art pedestrian detectors. Results on 2 h of video demonstrate the efficiency and robustness of the regression-based crowd size estimation over long periods of time. Cell counting is a ubiquitous, yet tedious task that would greatly benefit from automation. From basic biological questions to clinical trials, cell counts provide key quantitative feedback that drive research. Unfortunately, cell counting is most commonly a manual task and can be time-intensive. The task is made even more difficult due to overlapping cells, existence of multiple focal planes, and poor imaging quality, among other factors. Here, we describe a convolutional neural network approach, using a recently described feature pyramid network combined with a VGG-style neural network, for segmenting and subsequent counting of cells in a given microscopy image. Recently, a body of computer vision research has studied the task of high-throughput plant phenotyping (measurement of plant attributes). The goal is to more rapidly and more accurately estimate plant properties as compared to conventional manual methods. In this work, we develop a method to measure two primary yield attributes of interest; stalk count and stalk width that are important for many broad-acre annual crops (sorghum, sugarcane, corn, maize for example). Prior work of using convolutional deep neural networks for plant analysis has either focused on object detection or dense image segmentation. In our work, we develop a novel pipeline that accurately extracts both detected object regions and dense semantic segmentation for extracting both stalk counts and stalk width. A ground-robot called the Robotanist is used to deploy a high-resolution stereo imager to capture dense image data of experimental plots of Sorghum plants. We ground-truth validate data extracted using two humans who assess the traits independently and we compare both accuracy and efficiency of human versus robotic measurements. Our method yields R-squared correlation of 0.88 for stalk count and a mean absolute error of 2.77 mm where average stalk width is 14.354 mm. Our approach is 30 times faster for stalk count and 270 times faster for stalk width measurement. In real-world crowd counting applications, the crowd densities vary greatly in spatial and temporal domains. A detection based counting method will estimate crowds accurately in low density scenes, while its reliability in congested areas is downgraded. A regression based approach, on the other hand, captures the general density information in crowded regions. Without knowing the location of each person, it tends to overestimate the count in low density areas. Thus, exclusively using either one of them is not sufficient to handle all kinds of scenes with varying densities. To address this issue, a novel end-to-end crowd counting framework, named DecideNet (DEteCtIon and Density Estimation Network) is proposed. It can adaptively decide the appropriate counting mode for different locations on the image based on its real density conditions. DecideNet starts with estimating the crowd density by generating detection and regression based density maps separately. To capture inevitable variation in densities, it incorporates an attention module, meant to adaptively assess the reliability of the two types of estimations. The final crowd counts are obtained with the guidance of the attention module to adopt suitable estimations from the two kinds of density maps. Experimental results show that our method achieves state-of-the-art performance on three challenging crowd counting datasets. This paper proposes a novel method to address the problem of estimating the number of people in surveillance scenes with people gathering and waiting. The proposed method combines a MID (mosaic image difference) based foreground segmentation algorithm and a HOG (histograms of oriented gradients) based head-shoulder detection algorithm to provide an accurate estimation of people counts in the observed area. In our framework, the MID-based foreground segmentation module provides active areas for the head-shoulder detection module to detect heads and count the number of people. Numerous experiments are conducted and convincing results demonstrate the effectiveness of our method. 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. We address the problem of counting cells in time-lapse microscopy images of developing human embryos. Cell counting is considered as an important step in analyzing biological phenomenon such as embryo viability. Traditional approaches to counting cells rely on hand crafted features and cannot fully take advantage of the growth in data set sizes. In this paper, we propose a framework to automatically count the number of cells in developing human embryos. The framework employs a deep convolutional neural network model trained to count cells from raw microscopy images. We demonstrate the effectiveness of our approach on a data set of 265 human embryos. The results show that the proposed framework provides robust estimates of the number of cells in a developing embryo up to the 5-cell stage (i.e., 48 h post fertilization). 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. We propose a new supervised learning framework for visual object counting tasks, such as estimating the number of cells in a microscopic image or the number of humans in surveillance video frames. We focus on the practically-attractive case when the training images are annotated with dots (one dot per object). Our goal is to accurately estimate the count. However, we evade the hard task of learning to detect and localize individual object instances. Instead, we cast the problem as that of estimating an image density whose integral over any image region gives the count of objects within that region. Learning to infer such density can be formulated as a minimization of a regularized risk quadratic cost function. We introduce a new loss function, which is well-suited for such learning, and at the same time can be computed efficiently via a maximum subarray algorithm. The learning can then be posed as a convex quadratic program solvable with cutting-plane optimization. The proposed framework is very flexible as it can accept any domain-specific visual features. Once trained, our system provides accurate object counts and requires a very small time overhead over the feature extraction step, making it a good candidate for applications involving real-time processing or dealing with huge amount of visual data. Crowd counting from a single image is a challenging task due to high appearance similarity, perspective changes and severe congestion. Many methods only focus on the local appearance features and they cannot handle the aforementioned challenges. In order to tackle them, we propose a Perspective Crowd Counting Network (PCC Net), which consists of three parts: 1) Density Map Estimation (DME) focuses on learning very local features for density map estimation; 2) Random High-level Density Classification (R-HDC) extracts global features to predict the coarse density labels of random patches in images; 3) Fore- Background Segmentation (FBS) encodes mid-level features to segments the foreground and background. Besides, the DULR module is embedded in PCC Net to encode the perspective changes on four directions (Down, Up, Left and Right). The proposed PCC Net is verified on five mainstream datasets, which achieves the state-of-the-art performance on the one and attains the competitive results on the other four datasets. The source code is available at this https URL. Summary Cell loss and addition is an important biological event in pathology, and it usually provides central information to the changes of biological activity in the histological sections. To develop a reliable and accurate cell counting tools in tissue section, in this paper, we proposed a novel cell nuclei detecting method based on the sliding band filter which is a member of convergence index family. We evaluated the accuracy and performance of our method on density packed retinal outer nuclear layer cell confocal multivariate fluorescence microscopy image datasets. The results show our proposed method exhibited an excellent performance with its accuracy compared with human manual counting. It is worth noting that the proposed cell counting method can clearly benefit for retinal detachment and reattachment visual diagnostics close related to cell loss and addition. Abstract The overall goal of this study is to develop an effective, simple, aptly computer vision algorithm to detect and count citrus on the tree using image processing techniques, to estimate the yield, and to compare the yield estimation results obtained through several methods. This new citrus recognition and counting algorithm was utilized the color features (or schemes) to present an estimate of the citrus yield, and the corresponding models are developed to provide an early estimation of the citrus yield. Citrus images were taken from Jeju, South Korea during daylight and the citrus recognition and counting algorithm were tested on 84 images which were collected from 21 trees. The citrus counting algorithm consisted of the following steps: convert RGB image to HSV, thresholding, orange color detection, noise removal, watershed segmentation, and counting. Distance transform and marker-controlled watershed algorithms were evaluated for automated watershed segmentation in citrus fruits to obtain good result. A correlation coefficient R 2 of 0.93 was obtained between the citrus counting algorithm and counting performed through human observation. The proposed algorithm showed great potential for early prediction of the yield of single citrus trees and the possibility of its uses for further fruit crops. Counting the number of leaves in plants is important for plant phenotyping, since it can be used to assess plant growth stages. We propose a learning-based approach for counting leaves in rosette (model) plants. We relate image-based descriptors learned in an unsupervised fashion to leaf counts using a supervised regression model. To take advantage of the circular and coplanar arrangement of leaves and also to introduce scale and rotation invariance, we learn features in a log-polar representation. Image patches extracted in this log-polar domain are provided to K-means, which builds a codebook in a unsupervised manner. Feature codes are obtained by projecting patches on the codebook using the triangle encoding, introducing both sparsity and specifically designed representation. A global, per-plant image descriptor is obtained by pooling local features in specific regions of the image. Finally, we provide the global descriptors to a support vector regression framework to estimate the number of leaves in a plant. We evaluate our method on datasets of the (LCC), containing images of Arabidopsis and tobacco plants. Experimental results show that on average we reduce absolute counting error by 40 w.r.t. the winner of the 2014 edition of the challenge -a counting via segmentation method. When compared to state-of-the-art density-based approaches to counting, on Arabidopsis image data 75 less counting errors are observed. Our findings suggest that it is possible to treat leaf counting as a regression problem, requiring as input only the total leaf count per training image.