Automated Vigor Estimation on Vineyards

Estimating the balance or vigor in vines, as the yield to pruning weight relation, is a useful parameter that growers use to better prepare for the harvest season and to establish precision agriculture management of the vineyard, achieving specific site planification like pruning, debriefing or budding. Traditionally growers obtain this parameter by first manually weighting the pruned canes during the vineyard dormant season (no leaves); second during the harvest collect the weight of the fruit for the vines evaluated in the first step and then correlate the two measures. Since this is a very manual and time-consuming task, growers usually obtain this number by just taking a couple of samples and extrapolating this value to the entire vineyard, losing all the variability present in theirs fields, which imply loss in information that can lead to specific site management and consequently grape quality and quantity improvement. In this paper we develop a computer vision-based algorithm that is robust to differences in trellis system, varieties and light conditions; to automatically estimate the pruning weight and consequently the variability of vigor inside the lot. The results will be used to improve the way local growers plan the annual winter pruning, advancing in the transformation to precision agriculture. Our proposed solution doesn\textsc{\char13}t require to weight the shoots (also called canes), creating prescription maps (detail instructions for pruning, harvest and other management decisions specific for the location) based in the estimated vigor automatically. Our solution uses Deep Learning (DL) techniques to get the segmentation of the vine trees directly from the image captured on the field during dormant seaso

Liver segmentation using marker controlled watershed transform

The largest organ in the body is the liver and primarily helps in metabolism and detoxification. Liver segmentation is a crucial step in liver cancer detection in computer vision-based biomedical image analysis. Liver segmentation is a critical task and results in under-segmentation and over-segmentation due to the complex structure of abdominal computed tomography (CT) images, noise, and textural variations over the image. This paper presents liver segmentation in abdominal CT images using marker-based watershed transforms. In the pre-processing stage, a modified double stage gaussian filter (MDSGF) is used to enhance the contrast, and preserve the edge and texture information of liver CT images. Further, marker controlled watershed transform is utilized for the segmentation of liver images from the abdominal CT images. Liver segmentation using suggested MDSGF and marker-based watershed transform help to diminish the under-segmentation and over-segmentation of the liver object. The performance of the proposed system is evaluated on the LiTS dataset based on Dice score (DS), relative volume difference (RVD), volumetric overlapping error (VOE), and Jaccard index (JI). The proposed method gives (Dice score of 0.959, RVD of 0.09, VOE of 0.089, and JI of 0.921)

Three-dimensional topology-based analysis segments volumetric and spatiotemporal fluorescence microscopy

Image analysis techniques provide objective and reproducible statistics for interpreting microscopy data. At higher dimensions, three-dimensional (3D) volumetric and spatiotemporal data highlight additional properties and behaviors beyond the static 2D focal plane. However, increased dimensionality carries increased complexity, and existing techniques for general segmentation of 3D data are either primitive, or highly specialized to specific biological structures. Borrowing from the principles of 2D topological data analysis (TDA), we formulate a 3D segmentation algorithm that implements persistent homology to identify variations in image intensity. From this, we derive two separate variants applicable to spatial and spatiotemporal data, respectively. We demonstrate that this analysis yields both sensitive and specific results on simulated data and can distinguish prominent biological structures in fluorescence microscopy images, regardless of their shape. Furthermore, we highlight the efficacy of temporal TDA in tracking cell lineage and the frequency of cell and organelle replication

A Methodology for Automatic Identification of Units with Ecological Significance in Dehesa Ecosystems

The dehesa is an anthropic complex ecosystem typical of some areas of Spain and Portugal, with a key role in soil and biodiversity conservation and in the search for a balance between production, conservation and ecosystem services. For this reason, it is essential to have tools that allow its characterization, as well as to monitor and support decision-making to improve its sustainability. A multipurpose and scalable tool has been developed and validated, which combines several low-cost technologies, computer vision methods and RGB aerial orthophotographs using open data sources and which allows for automated agroforestry inventories, identifying and quantifying units with important ecological significance such as: trees, groups of trees, ecosystem corridors, regenerated areas and sheets of water. The development has been carried out from images of the national aerial photogrammetry plan of Spain belonging to 32 dehesa farms, representative of the existing variability in terms of density of trees, shrub species and the presence of other ecological elements. First, the process of obtaining and identifying areas of interest was automated using WMS services and shapefile metadata. Then, image analysis techniques were used to detect the different ecological units. Finally, a classification was developed according to the OBIA approach, which stores the results in standardized files for Geographic Information Systems. The results show that a stable solution has been achieved for the automatic and accurate identification of ecological units in dehesa territories. The scalability and generalization to all the dehesa territories, as well as the possibility of segmenting the area occupied by trees and other ecological units opens up a great opportunity to improve the construction of models for interpreting satellite images

Dual network extraction algorithm to investigate multiple transport processes in porous materials: Image-based modeling of pore and grain scale processes

The final publication is available at Elsevier via https://doi.org/10.1016/j.compchemeng.2018.12.025 © 2018 This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Image processing of 3D tomographic images to extract structural information of porous materials has become extremely important in porous media research with the commoditization of x-ray tomography equipment to the lab scale. Extracted pore networks from images using image analysis techniques enable transport properties calculation for bigger domains at a low computational cost, allowing pore-scale investigation of porous media over meaningful macroscopic length scales. The present study reports a pore network extraction algorithm to simultaneously extract void and solid networks from tomographic images of porous materials using simple image analysis techniques. Crucially, it includes connectivity and geometrical information of both void and solid phases as well as the interlinking of these phases with each other. Validation was obtained on networks extracted from simple cubic and random sphere packings over a range of porosities. The effective diffusivity in the void phase and thermal conductivity in the solid phase was then calculated and found to agree well with direct numerical simulation results on the images, as well as a range of experimental data. One important outcome of this work was a novel and accurate means of calculating interfacial areas between grains and voids directly from digital images, which is critical to many phenomena where phase interactions occur. The efficient ‘dual network’ algorithm is written in PYTHON using open source tools and provides a new way to study critical processes that depend on transport in both void and solid phase such as catalytic reactors and electrochemical systems.University of Engineering and Technology Lahore, PakistanNatural Sciences and Engineering Research Council of Canad

Structural Characterization of Toxoplasma gondii Brain Cysts in a Model of Reactivated Toxoplasmosis Using Computational Image Analysis

Toxoplasma gondii is an obligate intracellular parasite existing in three infectious life stages—tachyzoites, bradyzoites, and sporozoites. Rupture of tissue cysts and re-conversion of bradyzoites to tachyzoites leads to reactivated toxoplasmosis (RT) in an immunocompromised host. The aim of this study was to apply ImageJ software for analysis of T. gondii brain cysts obtained from a newly established in vivo model of RT. Mice chronically infected with T. gondii (BGD1 and BGD26 strains) were treated with cyclophosphamide and hydrocortisone (experimental group—EG) or left untreated as infection controls (ICs). RT in mice was confirmed by qPCR (PCR+); mice remaining chronically infected were PCR−. A total of 90 images of cysts were analyzed for fractal dimension (FD), lacunarity (L), diameter (D), circularity (C), and packing density (PD). Circularity was significantly higher in PCR+ compared to IC mice (p < 0.05 for BGD1, p < 0.001 for the BGD26 strain). A significant negative correlation between D and PD was observed only in IC for the BGD1 strain (ρ = −0.384, p = 0.048), while fractal parameters were stable. Significantly higher D, C, and PD and lower lacunarity, L, were noticed in the BGD1 compared to the more aggressive BGD26 strain. In conclusion, these results demonstrate the complexity of structural alterations of T. gondii cysts in an immunocompromised host and emphasize the application potential of ImageJ in the experimental models of toxoplasmosis

Biologically inspired robotic perception-action for soft fruit harvesting in vertical growing environments

Multiple interlinked factors like demographics, migration patterns, and economics are presently leading to the critical shortage of labour available for low-skilled, physically demanding tasks like soft fruit harvesting. This paper presents a biomimetic robotic solution covering the full ‘Perception-Action’ loop targeting harvesting of strawberries in a state-of-the-art vertical growing environment. The novelty emerges from both dealing with crop/environment variance as well as configuring the robot action system to deal with a range of runtime task constraints. Unlike the commonly used deep neural networks, the proposed perception system uses conditional Generative Adversarial Networks to identify the ripe fruit using synthetic data. The network can effectively train the synthetic data using the image-to-image translation concept, thereby avoiding the tedious work of collecting and labelling the real dataset. Once the harvest-ready fruit is localised using point cloud data generated by a stereo camera, our platform’s action system can coordinate the arm to reach/cut the stem using the Passive Motion Paradigm framework inspired by studies on neural control of movement in the brain. Results from field trials for strawberry detection, reaching/cutting the stem of the fruit, and extension to analysing complex canopy structures/bimanual coordination (searching/picking) are presented. While this article focuses on strawberry harvesting, ongoing research towards adaptation of the architecture to other crops such as tomatoes and sweet peppers is briefly described

Mapping urban tree species in a tropical environment using airborne multispectral and LiDAR data

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial TechnologiesAccurate and up-to-date urban tree inventory is an essential resource for the development of strategies towards sustainable urban planning, as well as for effective management and preservation of biodiversity. Trees contribute to thermal comfort within urban centers by lessening heat island effect and have a direct impact in the reduction of air pollution. However, mapping individual trees species normally involves time-consuming field work over large areas or image interpretation performed by specialists. The integration of airborne LiDAR data with high-spatial resolution and multispectral aerial image is an alternative and effective approach to differentiate tree species at the individual crown level. This thesis aims to investigate the potential of such remotely sensed data to discriminate 5 common urban tree species using traditional Machine Learning classifiers (Random Forest, Support Vector Machine, and k-Nearest Neighbors) in the tropical environment of Salvador, Brazil. Vegetation indices and texture information were extracted from multispectral imagery, and LiDAR-derived variables for tree crowns, were tested separately and combined to perform tree species classification applying three different classifiers. Random Forest outperformed the other two classifiers, reaching overall accuracy of 82.5% when using combined multispectral and LiDAR data. The results indicate that (1) given the similarity in spectral signature, multispectral data alone is not sufficient to distinguish tropical tree species (only k-NN classifier could detect all species); (2) height values and intensity of crown returns points were the most relevant LiDAR features, combination of both datasets improved accuracy up to 20%; (3) generation of canopy height model derived from LiDAR point cloud is an effective method to delineate individual tree crowns in a semi-automatic approach

NeuronAlg: An Innovative Neuronal Computational Model for Immunofluorescence Image Segmentation

Background: Image analysis applications in digital pathology include various methods for segmenting regions of interest. Their identification is one of the most complex steps and therefore of great interest for the study of robust methods that do not necessarily rely on a machine learning (ML) approach. Method: A fully automatic and optimized segmentation process for different datasets is a prerequisite for classifying and diagnosing indirect immunofluorescence (IIF) raw data. This study describes a deterministic computational neuroscience approach for identifying cells and nuclei. It is very different from the conventional neural network approaches but has an equivalent quantitative and qualitative performance, and it is also robust against adversative noise. The method is robust, based on formally correct functions, and does not suffer from having to be tuned on specific data sets. Results: This work demonstrates the robustness of the method against variability of parameters, such as image size, mode, and signal-to-noise ratio. We validated the method on three datasets (Neuroblastoma, NucleusSegData, and ISBI 2009 Dataset) using images annotated by independent medical doctors. Conclusions: The definition of deterministic and formally correct methods, from a functional and structural point of view, guarantees the achievement of optimized and functionally correct results. The excellent performance of our deterministic method (NeuronalAlg) in segmenting cells and nuclei from fluorescence images was measured with quantitative indicators and compared with those achieved by three published ML approaches

An innovative image processing-based framework for the numerical modelling of cracked masonry structures

A vital aspect when modelling the mechanical behaviour of existing masonry structures is the accuracy in which the geometry of the real structure is transferred in the numerical model. Commonly, the geometry of masonry is captured with traditional techniques (e.g. visual inspection and manual surveying methods), which are labour intensive and error-prone. Over the last ten years, advances in photogrammetry and image processing have started to change the building industry since it is possible to capture rapidly and remotely digital records of objects and features. Although limited work exists in detecting distinct features from masonry structures, up to now there is no automated procedure leading from image-based recording to their numerical modelling. To address this, an innovative framework, based on image-processing, has been developed that automatically extracts geometrical features from masonry structures (i.e. masonry units, mortar, existing cracks and pathologies, etc.) and generate the geometry for their advanced numerical modelling. The proposed watershed-based algorithm initially deconstructs the features of the segmentation, then reconstructs them in the form of shared vertices and edges, and finally converts them to scalable polylines. The polylines extracted are simplified using a contour generalisation procedure. The geometry of the masonry elements is further modified to facilitate the transition to a numerical modelling environment. The proposed framework is tested by comparing the numerical analysis results of an undamaged and a damaged masonry structures, using models generated through manual and the proposed algorithmic approaches. Although the methodology is demonstrated here for use in discrete element modelling, it can be applied to other computational approaches based on the simplified and detailed micro-modelling approach for evaluating the structural behaviour of masonry structures