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.
Agronomy : For general plant counting @cite_43 , counting palm trees @cite_39 , plant stalks @cite_48 , fruits @cite_49 @cite_15 and maize tassels @cite_29 . This is a less mainstream application for counting, but a rich domain, that has real impact in people's lives, and this will be the focus of our paper.
@cite_48 @cite_29 @cite_39 @cite_43 @cite_49 @cite_15
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Accurately counting maize tassels is important for monitoring the growth status of maize plants. This tedious task, however, is still mainly done by manual efforts. In the context of modern plant phenotyping, automating this task is required to meet the need of large-scale analysis of genotype and phenotype. In recent years, computer vision technologies have experienced a significant breakthrough due to the emergence of large-scale datasets and increased computational resources. Naturally image-based approaches have also received much attention in plant-related studies. Yet a fact is that most image-based systems for plant phenotyping are deployed under controlled laboratory environment. When transferring the application scenario to unconstrained in-field conditions, intrinsic and extrinsic variations in the wild pose great challenges for accurate counting of maize tassels, which goes beyond the ability of conventional image processing techniques. This calls for further robust computer vision approaches to address in-field variations. This paper studies the in-field counting problem of maize tassels. To our knowledge, this is the first time that a plant-related counting problem is considered using computer vision technologies under unconstrained field-based environment. With 361 field images collected in four experimental fields across China between 2010 and 2015 and corresponding manually-labelled dotted annotations, a novel Maize Tassels Counting (MTC) dataset is created and will be released with this paper. To alleviate the in-field challenges, a deep convolutional neural network-based approach termed TasselNet is proposed. TasselNet can achieve good adaptability to in-field variations via modelling the local visual characteristics of field images and regressing the local counts of maize tassels. Extensive results on the MTC dataset demonstrate that TasselNet outperforms other state-of-the-art approaches by large margins and achieves the overall best counting performance, with a mean absolute error of 6.6 and a mean squared error of 9.6 averaged over 8 test sequences. TasselNet can achieve robust in-field counting of maize tassels with a relatively high degree of accuracy. Our experimental evaluations also suggest several good practices for practitioners working on maize-tassel-like counting problems. It is worth noting that, though the counting errors have been greatly reduced by TasselNet, in-field counting of maize tassels remains an open and unsolved problem. In this paper we address the task of counting crop plants in a field using Convolutional Neural Networks (CNN). The number of plants in an Unmanned Aerial Vehicle (UAV) image of the field is estimated using regression instead of classification. This avoids to need to know (or guess) the maximum expected number of plants. We also describe a method to extract images of sections or “plots” from an orthorectified image of the entire crop field. These images will be used for training and evaluation of the CNN. Our experiments show that we can obtain a Mean Absolute Percentage Error (MAPE) as low as 6.7 with the Inception-v3 CNN architecture. 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. 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. 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. Yield mapping for tree crops by mechanical harvesting requires automatic detection and counting of fruits in tree canopy. However, partial occlusion, shape irregularity, varying illumination, multiple sizes and similarity with the background make fruit identification a very difficult task to achieve. Therefore, immature green citrus-fruit detection within a green canopy is a challenging task due to all the above-mentioned problems. A novel algorithmic technique was used to detect immature green citrus fruit in tree canopy under natural outdoor conditions. Shape analysis and texture classification were two integral parts of the algorithm. Shape analysis was conducted to detect as many fruits as possible. Texture classification by a support vector machine (SVM), Canny edge detection combined with a graph-based connected component algorithm and Hough line detection, were used to remove false positives. Next, keypoints were detected using a scale invariant feature transform (SIFT) algorithm and to further remove false positives. A majority voting scheme was implemented to make the algorithm more robust. The algorithm was able to accurately detect and count 80.4 of citrus fruit in a validation set of images acquired from a citrus grove under natural outdoor conditions. The algorithm could be further improved to provide growers early yield estimation so that growers can manage grove more efficiently on a site-specific basis to increase yield and profit. This paper describes a fruit counting pipeline based on deep learning that accurately counts fruit in unstructured environments. Obtaining reliable fruit counts is challenging because of variations in appearance due to illumination changes and occlusions from foliage and neighboring fruits. We propose a novel approach that uses deep learning to map from input images to total fruit counts. The pipeline utilizes a custom crowdsourcing platform to quickly label large data sets. A blob detector based on a fully convolutional network extracts candidate regions in the images. A counting algorithm based on a second convolutional network then estimates the number of fruits in each region. Finally, a linear regression model maps that fruit count estimate to a final fruit count. We analyze the performance of the pipeline on two distinct data sets of oranges in daylight, and green apples at night, utilizing human generated labels as ground truth. We also show that the pipeline has a short training time and performs well with a limited data set size. Our method generalizes across both data sets and is able to perform well even on highly occluded fruits that are challenging for human labelers to annotate. Clustering at multiple critical scales may be common for plants since many different factors and processes may cause clustering. This is especially true for tropical rain forests for which theories explaining species coexistence and community structure rest heavily on spatial patterns. We used point pattern analysis to analyze the spatial structure of Shorea congestiflora, a dominant species in a 25-ha forest dynamics plot in a rain forest at Sinharaja World Heritage Site (Sri Lanka), which apparently shows clustering at several scales. We developed cluster processes incorporating two critical scales of clustering for exploring the spatial structure of S. congestiflora and interpret it in relation to factors such as competition, dispersal limitation, recruitment limitation, and Janzen-Connell effects. All size classes showed consistent large-scale clustering with a cluster radius of ;25 m. Inside the larger clusters, small-scale clusters with a radius of 8 m were evident for recruits and saplings, weak for intermediates, and disappeared for adults. The pattern of all trees could be divided into two independent patterns: a random pattern (nearest neighbor distance . 8m ) comprising ;12 of the trees and a nested double-cluster pattern. This finding suggests two independent recruitment and or seed dispersal mechanisms. Saplings were several times as abundant as recruits and may accumulate several recruit generations. Recruits were only weakly associated with adults and occupied about half of the large-scale clusters, but saplings almost all. This is consistent with recruitment limitation. For ;70 (95 ) of all juveniles the nearest adult was less than 26 m away (53 m), suggesting a dispersal limitation that may also be related to the critical large-scale clustering. Our example illustrates the manner in which the use of a specific and complex null hypothesis of spatial structure in point pattern analysis can help us better understand the biology of a species and generate specific hypotheses to be further investigated in the field. We are interested in counting the number of instances of object classes in natural, everyday images. Previous counting approaches tackle the problem in restricted domains such as counting pedestrians in surveillance videos. Counts can also be estimated from outputs of other vision tasks like object detection. In this work, we build dedicated models for counting designed to tackle the large variance in counts, appearances, and scales of objects found in natural scenes. Our approach is inspired by the phenomenon of subitizing &#x2013; the ability of humans to make quick assessments of counts given a perceptual signal, for small count values. Given a natural scene, we employ a divide and conquer strategy while incorporating context across the scene to adapt the subitizing idea to counting. Our approach offers consistent improvements over numerous baseline approaches for counting on the PASCAL VOC 2007 and COCO datasets. Subsequently, we study how counting can be used to improve object detection. We then show a proof of concept application of our counting methods to the task of Visual Question Answering, by studying the how many? questions in the VQA and COCO-QA datasets. Plant has plenty use in foodstuff, medicine and industry. And it is also vitally important for environmental protection. However, it is an important and difficult task to recognize plant species on earth. Designing a convenient and automatic recognition system of plants is necessary and useful since it can facilitate fast classifying plants, and understanding and managing them. In this paper, a leaf database from different plants is firstly constructed. Then, a new classification method, referred to as move median centers (MMC) hypersphere classifier, for the leaf database based on digital morphological feature is proposed. The proposed method is more robust than the one based on contour features since those significant curvature points are hard to find. Finally, the efficiency and effectiveness of the proposed method in recognizing different plants is demonstrated by experiments. This paper describes the participation of the Floristic consortium to the LifeCLEF 2016 plant identification challenge[18]. The aim of the task was to produce a list of relevant species for a large set of plant images related to 1000 species of trees, herbs and ferns living in Western Europe, knowing that some of these images belonged to unseen categories in the training set like plant species from other areas, horticultural plants or even off topic images (people, keyboards, animals, etc). To address this challenge, we first experimented as a baseline, without any rejection procedure, a Convolutional Neural Network (CNN) approach based on a slightly modified GoogLeNet model. In a second run, we applied a simple rejection criteria based on probability threshold estimation on the output of the CNN, one for each species, for removing automatically species propositions judged irrelevant. In the third run, rather than definitely eliminating some species predictions with the risk to remove false negative propositions, we applied various attenuation factors in order to revise the probability distributions given by the CNN as confident score expressing how much a query was related or not to the known species. More precisely, for this last run we used the geographical information and several cohesion measures in terms of observation, "organ" tags and taxonomy (genus and family levels) based on a knn similarity search results within the training set. Addressing the challenges of feeding the burgeoning world population with limited resources requires innovation in sustainable, efficient farming. The practice of precision agriculture offers many benefits towards addressing these challenges, such as improved yield and efficient use of such resources as water, fertilizer and pesticides. We describe the design and development of a light-weight, multi-spectral 3D imaging device that can be used for automated monitoring in precision agriculture. The sensor suite consists of a laser range scanner, multi-spectral cameras, a thermal imaging camera, and navigational sensors. We present techniques to extract four key data products — plant morphology, canopy volume, leaf area index, and fruit counts — using the sensor suite. We demonstrate its use with two systems: multi-rotor micro aerial vehicles and on a human-carried, shoulder-mounted harness. We show results of field experiments conducted in collaboration with growers and agronomists in vineyards, apple orchards and orange groves. Sorghum (Sorghum bicolor L. Moench) is a C4 tropical grass that plays an essential role in providing nutrition to humans and livestock, particularly in marginal rainfall environments. The timing of head development and the number of heads per unit area are key adaptation traits to consider in agronomy and breeding but are time consuming and labor intensive to measure. We propose a two-step machine-based image processing method to detect and count the number of heads from high-resolution images captured by unmanned aerial vehicles (UAVs) in a breeding trial. To demonstrate the performance of the proposed method, 52 images were manually labeled; the precision and recall of head detection were 0.87 and 0.98, respectively, and the coefficient of determination (R-2) between the manual and new methods of counting was 0.84. To verify the utility of the method in breeding programs, a geolocationbased plot segmentation method was applied to pre-processed ortho-mosaic images to extract > 1000 plots from original RGB images. Forty of these plots were randomly selected and labeled manually; the precision and recall of detection were 0.82 and 0.98, respectively, and the coefficient of determination between manual and algorithm counting was 0.56, with the major source of error being related to the morphology of plants resulting in heads being displayed both within and outside the plot in which the plants were sown, i.e., being allocated to a neighboring plot. Finally, the potential applications in yield estimation from UAV-based imagery from agronomy experiments and scouting of production fields are also discussed. Plant species classification using leaf samples is a challenging and important problem to solve. This paper introduces a new data set of sixteen samples each of one-hundred plant species; and describes a method designed to work in conditions of small training set size and possibly incomplete extraction of features. This motivates a separate processing of three feature types: shape, texture, and margin; combined using a probabilistic framework. The texture and margin features use histogram accumulation, while a normalised description of contour is used for the shape. Two previously published methods are used to generate separate posterior probability vectors for each feature, using data associated with the k-Nearest Neighbour apparatus. The combined posterior estimates produce the final classification (where missing features could be omitted). We show that both density estimators achieved a 96 mean accuracy of classification when combining the three features in this way (training on 15 samples with unseen cross validation). In addition, the framework can provide an upper bound on the Bayes Risk of the classification problem, and thereby assess the accuracy of the density estimators. Lastly, the high performance of the method is demonstrated for small training set sizes: 91 accuracy is observed with only four training samples. Elliptic Fourier (EF) and discriminant analyses were used to identify young soybean (Glycine max (L.) merrill), sunflower (Helianthus pumilus), redroot pigweed (Amaranthus retroflexus) and velvetleaf (Abutilon theophrasti Medicus) plants, based on leaf shape. Chain encoded, Elliptic Fourier harmonic functions were generated based on leaf boundary. A complexity index of the leaf shape was computed using the variation between consecutive EF functions. Principle component analysis was used to select the Fourier coefficients with the best discriminatory power. Canonical discriminant analysis was used to develop species identification models based on leaf shapes extracted from plant color images during the second and third weeks after germination. The classification results showed that plant species during the third week were successfully identified with an average of correct classification rate of 89.4 . The discriminant model correctly classified on average: 77.9 of redroot pigweed, 93.8 of sunflower, 89.4 of velvetleaf and 96.5 of soybean. Using all of the leaves extracted from the second and the third weeks, the overall classification accuracy was 89.2 . The discriminant model correctly classified 76.4 of redroot pigweed, 93.6 of sunflower, 81.6 of velvetleaf, 91.5 of soybean leaf extracted from trifoliolate and 90.9 of soybean unifoliolate leaves. The Elliptic Fourier shape feature analysis could be an important and accurate tool for weed species identification and mapping. 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. Display Omitted Deep convolutional neural network (CNN) for plant identification focusing on leaf vein patterns.No task-specific feature extractors needed.Improved the state of the art accuracy on a legume species recognition task.Visualization of relevant vein patterns. We propose using a deep convolutional neural network (CNN) for the problem of plant identification from leaf vein patterns. In particular, we consider classifying three different legume species: white bean, red bean and soybean. The introduction of a CNN avoids the use of handcrafted feature extractors as it is standard in state of the art pipeline. Furthermore, this deep learning approach significantly improves the accuracy of the referred pipeline. We also show that the reported accuracy is reached by increasing the model depth. Finally, by analyzing the resulting models with a simple visualization technique, we are able to unveil relevant vein patterns. In this paper, we investigate estimating emergence and biomass traits from color images and elevation maps of wheat field plots. We employ a state-of-the-art deconvolutional network for segmentation and convolutional architectures, with residual and Inception-like layers, to estimate traits via high dimensional nonlinear regression. Evaluation was performed on two different species of wheat, grown in field plots for an experimental plant breeding study. Our framework achieves satisfactory performance with mean and standard deviation of absolute difference of 1.05 and 1.40 counts for emergence and 1.45 and 2.05 for biomass estimation. Our results for counting wheat plants from field images are better than the accuracy reported for the similar, but arguably less difficult, task of counting leaves from indoor images of rosette plants. Our results for biomass estimation, even with a very small dataset, improve upon all previously proposed approaches in the literature. Oil palm trees are important economic crops in Malaysia and other tropical areas. The number of oil palm trees in a plantation area is important information for predicting the yield of palm oil, monitoring the growing situation of palm trees and maximizing their productivity, etc. In this paper, we propose a deep learning based framework for oil palm tree detection and counting using high-resolution remote sensing images for Malaysia. Unlike previous palm tree detection studies, the trees in our study area are more crowded and their crowns often overlap. We use a number of manually interpreted samples to train and optimize the convolutional neural network (CNN), and predict labels for all the samples in an image dataset collected through the sliding window technique. Then, we merge the predicted palm coordinates corresponding to the same palm tree into one palm coordinate and obtain the final palm tree detection results. Based on our proposed method, more than 96 of the oil palm trees in our study area can be detected correctly when compared with the manually interpreted ground truth, and this is higher than the accuracies of the other three tree detection methods used in this study. Plant Diseases and Pests are a major challenge in the agriculture sector. An accurate and a faster detection of diseases and pests in plants could help to develop an early treatment technique while substantially reducing economic losses. Recent developments in Deep Neural Networks have allowed researchers to drastically improve the accuracy of object detection and recognition systems. In this paper, we present a deep-learning-based approach to detect diseases and pests in tomato plants using images captured in-place by camera devices with various resolutions. Our goal is to find the more suitable deep-learning architecture for our task. Therefore, we consider three main families of detectors: Faster Region-based Convolutional Neural Network (Faster R-CNN), Region-based Fully Convolutional Network (R-FCN), and Single Shot Multibox Detector (SSD), which for the purpose of this work are called “deep learning meta-architectures”. We combine each of these meta-architectures with “deep feature extractors” such as VGG net and Residual Network (ResNet). We demonstrate the performance of deep meta-architectures and feature extractors, and additionally propose a method for local and global class annotation and data augmentation to increase the accuracy and reduce the number of false positives during training. We train and test our systems end-to-end on our large Tomato Diseases and Pests Dataset, which contains challenging images with diseases and pests, including several inter- and extra-class variations, such as infection status and location in the plant. Experimental results show that our proposed system can effectively recognize nine different types of diseases and pests, with the ability to deal with complex scenarios from a plant’s surrounding area.