Amy Tabb

United States Department of Agriculture | USDA · Agricultural Research Service (ARS)

Significance Trees’ branches grow against the pull of gravity and toward light. Although gravity and light perception have been studied in model species, much is unknown about how trees detect and respond to these signals. Here, we report the identification of a gene ( WEEP ) that controls lateral branch orientations and is directly or indirectly r...

The segmentation of plant roots from soil and other growing media in X-ray computed tomography images is needed to effectively study the root system architecture without excavation. However, segmentation is a challenging problem in this context because the root and non-root regions share similar features. In this paper, we describe a method based o...

We consider the problem of extracting curve skeletons of three-dimensional, elongated objects given a noisy surface, which has applications in agricultural contexts such as extracting the branching structure of plants. We describe an efficient and robust method based on breadth-first search that can determine curve skeletons in these contexts. Our...

The autonomous measurement of tree traits, such as branching structure, branch diameters, branch lengths, and branch angles, is required for tasks such as robotic pruning of trees as well as structural phenotyping. We propose a robotic vision system called the Robotic System for Tree Shape Esti- mation (RoTSE) to determine tree traits in field sett...

Historically, anecdotal observations support the likelihood of human-assisted invasive insect dispersal to new environments. No previous studies have investigated the ability of insects to remain attached to moving vehicles; however, such information is critical for prioritizing research, mitigation activities and understanding anthropogenic effect...

Grape ( Vitis ) production and fruit quality traits such as cluster size, berry shape, and timing of fruit development are key aspects when selecting cultivars for commercial production. Molecular markers for some, but not all, of these traits have been identified using biparental or association mapping populations. Previously identified markers we...

Agricultural production is a key economic activity providing a growing world population with resources such as food, fibers, fuels, and chemical basic components. Yet, agriculture also plays a crucial role in the depletion of resources, including fresh water, fossil fuels, and nutrients (e.g., phosphate), and has a significant impact on our living...

Measurements of insect external morphology are important to understanding species ecology, biology, and systematics. Precise measurement of width and length can be laborious and time-consuming. Here, we explored an automated approach to insect measurement using an image-based method with adult Halyomorpha halys (Stl) (Heteroptera: Pentatomidae) as...

Grape production and fruit quality traits such as cluster size, berry shape, and timing of fruit development are key aspects in selecting cultivars for commercial production. Molecular markers for some, but not all, of these traits have been identified using bi-parental or association mapping populations. Previously identified markers were tested f...

Convolutional neural networks trained using manually generated labels are commonly used for semantic or instance segmentation. In precision agriculture, automated flower detection methods use supervised models and post-processing techniques that may not perform consistently as the appearance of the flowers and the data acquisition conditions vary....

Convolutional neural networks trained using manually generated labels are commonly used for semantic or instance segmentation. In precision agriculture, automated flower detection methods use supervised models and post-processing techniques that may not perform consistently as the appearance of the flowers and the data acquisition conditions vary....

Images are used frequently in plant phenotyping to capture measurements. This chapter offers a repeatable method for capturing two-dimensional measurements of plant parts in field or laboratory settings using a variety of camera styles (cellular phone, DSLR), with the addition of a printed calibration pattern. The method is based on calibrating the...

Reliable phenotyping methods that are simple to operate and inexpensive to deploy are critical for studying quantitative traits in plants. Traditional fruit shape phenotyping relies on human raters or 2D analyses to assess form, e.g., size and shape. Systems for 3D imaging using multi‐view stereo have been implemented, but frequently rely on commer...

Reliable phenotyping methods that are simple to operate and inexpensive to deploy are critical for studying quantitative traits in plants. Traditional fruit shape phenotyping relies on human raters or 2D analyses to assess form, e.g., size and shape. Systems for 3D imaging using multi-view stereo have been implemented, but frequently rely on commer...

We claim, and present evidence, that allowing arXiv publication before a conference or journal submission benefits researchers, especially early career, as well as the whole scientific community. Specifically, arXiving helps professional identity building, protects against independent re-discovery, idea theft and gate-keeping; it facilitates open r...

Halyomorpha halys (Stål), the brown marmorated stink bug, is an invasive and highly polyphagous insect that has caused serious economic injury to specialty and row crops in the United States and Europe. Here, we evaluated the effects of marking adult and nymphal H. halys with four different colors of fluorescent powder (Blaze Orange, Corona Pink, H...

The brain's vascular network dynamically affects its development and core functions. It rapidly responds to abnormal conditions by adjusting properties of the network, aiding stabilization and regulation of brain activities. Tracking prominent arterial changes has clear clinical and surgical advantages. However, the arterial network functions as a...

Background Shape is a critical element of the visual appeal of strawberry fruit and is influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human eye to make categorical assessments. However, fruit shape is an inherently multi-dimensional, continuo...

** Code available at https://github.com/amy-tabb/calico ** Camera network and multi-camera calibration for external parameters is a necessary step for a variety of contexts in computer vision and robotics, ranging from three-dimensional reconstruction to human activity tracking. This paper describes CALICO, a method for camera network and/or multi-...

Background Shape is a critical element of the visual appeal of strawberry fruit and determined by both genetic and non-genetic factors. Current fruit phenotyping approaches for external characteristics in strawberry rely on the human eye to make categorical assessments. However, fruit shape is multi-dimensional, continuously variable, and not adequ...

This example dataset and code are a companion to 2018 paper Segmenting Root Systems in X-Ray Computed Tomography Images Using Level Sets doi: 10.1109/WACV.2018.00070 . The code uses a three-dimensional level-set algorithm (described in the paper) to segment root from non-root regions in X-Ray CT. See the releases below for full details. License,...

Book chapter that summarizes recent research on agricultural robotics in orchard management, including Robotic pruning, Robotic thinning, Robotic spraying, Robotic harvesting, Robotic fruit transportation, and future trends. Full text may be found at arXiv: https://arxiv.org/abs/1907.13114

The reconstruction of fruit shape, and particularly, that of strawberry, is needed for a variety of purposes such as the assessing of market class and informing cultivar release documentation. In this work, we focus on the use of fruit shape for phenotyping and selection in breeding programs [6]. We describe a portable, low-cost turntable system fo...

A key aspect to controlling and reducing the effects invasive insect species have on agriculture is to obtain knowledge about the migration patterns of these species. Current state-of-the-art methods of studying these migration patterns involve a mark-release-recapture technique, in which insects are released after being marked and researchers atte...

Images are used frequently in plant phenotyping to capture measurements. This chapter offers a repeatable method for capturing two-dimensional measurements of plant parts in field or laboratory settings using a variety of camera styles (cellular phone, DSLR), with the addition of a printed calibration pattern. The method is based on calibrating the...

A key aspect to controlling and reducing the effects invasive insect species have on agriculture is to obtain knowledge about the migration patterns of these species. Current state-of-the-art methods of studying these migration patterns involve a mark-release-recapture technique, in which insects are released after being marked and researchers atte...

The brown marmorated stink bug, Halyomorpha halys, is an agricultural and urban pest that has become widely established as an invasive species of major concern in the USA and throughout Europe. The insect forms large aggregations before entering diapause, and it is often these aggregations that are found by biosecurity officials conducting inspecti...

Large-scale annotation of image segmentation datasets is often prohibitively expensive, as it usually requires a huge number of worker hours to obtain high-quality results. Abundant and reliable data has been, however, crucial for the advances on image understanding tasks achieved by deep learning models. In this paper, we introduce FreeLabel, an i...

Large-scale annotation of image segmentation datasets is often prohibitively expensive, as it usually requires a huge number of worker hours to obtain high-quality results. Abundant and reliable data has been, however, crucial for the advances on image understanding tasks achieved by deep learning models. In this paper, we introduce FreeLabel, an i...

Prunus persica (peach) trees carrying the “Pillar” or “Broomy” trait (br) have vertically oriented branches caused by loss-of-function mutations in a gene called TILLER ANGLE CONTROL 1 (TAC1). TAC1 encodes a protein in the IGT gene family that includes LAZY1 and DEEPER ROOTING 1 (DRO1), which regulate lateral branch and root orientations, respectiv...

In fruit production, critical crop management decisions are guided by bloom intensity, i.e., the number of flowers present in an orchard. Despite its importance, bloom intensity is still typically estimated by means of human visual inspection. Existing automated computer vision systems for flower identification are based on hand-engineered techniqu...

The segmentation of plant roots from soil and other growing media in X-ray computed tomography images is needed to effectively study the root system architecture without excavation. However, segmentation is a challenging problem in this context because the root and non-root regions share similar features. In this paper, we describe a method based o...

To optimize fruit production, a portion of the flowers and fruitlets of apple trees must be removed early in the growing season. The proportion to be removed is determined by the bloom intensity, i.e., the number of flowers present in the orchard. Several automated computer vision systems have been proposed to estimate bloom intensity, but their ov...

In fruit production, critical crop management decisions are guided by bloom intensity, i.e. the number of flowers present in an orchard. Despite its importance, bloom intensity is still typically estimated by means of human visual inspection. Existing automated computer vision systems for flower identification are based on hand-engineered technique...

Fast and robust curve skeletonization for real-world elongated objects

Segmenting root systems in X-ray computed tomography images using level sets

Video files: robot vision system in operation, results shown.

This code is a companion to the paper, “Fast and robust curve skeletonization for real-world elongated objects,” by Amy Tabb and Henry Medeiros. The code performs curve skeletonization of objects, which have a voxel representation. Curve skeletonization is used to convert a three-dimensional digital object or shape to locally one-dimensional parts;...

Robot-world, hand-eye calibration is the problem of determining the transformation between the robot end-effector and a camera, as well as the transformation between the robot base and the world coordinate system. This relationship has been modeled as AX = ZB , where X and Z are unknown homogeneous transformation matrices. The successful execution...

The attached file gives a link to code and datasets for robot-world, hand-eye(s) calibration. This material is a companion to a paper which was published in May 2017 in Machine Vision and Applications: Solving the robot-world, hand-eye(s) calibration problem with iterative methods. Robot-world, hand-eye calibration is required to determine the tran...

Accurate robot-world, hand-eye calibration is crucial to automation tasks. In this paper, we discuss the robot-world, hand-eye calibration problem which has been modeled as the linear relationship AX = ZB, where X and Z are the unknown calibration matrices composed of rotation and translation components. While there are many different approaches to...

The use of shape from silhouette for reconstruction tasks is plagued by two types of real-world errors: camera calibration error and silhouette segmentation error. When either error is present, we call the problem the Shape from Inconsistent Silhouette (SfIS) problem. In this paper, we show how small camera calibration error can be corrected when u...

This paper considers the problem of reconstructing the shape of thin, texture-less objects such as leafless trees when there is noise or deterministic error in the silhouette extraction step or there are small errors in camera calibration. Traditional intersection-based techniques such as the visual hull are not robust to error because they penaliz...

A unique dry bin filler for apples using a sequenced tray was developed to reduce bruising in packing operations. Research and commercial trials in West Virginia, Pennsylvania, and Washington State demonstrated the ability to fill bins evenly and with low damage. Cultivars with different bruising susceptibility ('Pink Lady,' 'Golden Delicious,' 'Mc...

Artificial neural networks and principal components were used to detect surface defects on apples in near-infrared images. Neural networks were trained and tested on sets of principal components, derived from columns of pixels from images of apples acquired at two wavelengths (740 nm and 950 nm). In an iterative process, different ways of preproces...

A method for locating apples was developed to process real-time video image sequences captured with an over-the-row harvester. The concepts of background modeling in RGB color were used, which is a novel approach to the apple segmentation problem. In background modeling, the distributions of background colors are approximated from real data. The al...

An experimental machine vision system was used to identify surface defects on apples, including bruises. Images were captured through two optical filters at 740 and 950 nm, respectively. In the ensuing grey scale images, defects appeared as dark areas, however, so did shadows and parts of the stem/calyx area. This paper reports a novel approach to...