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...provide sufficient statistics for shape fitting. Their associations to cells (labels) are also unknown in advance (Fig. 2). To address this issue, we use hard assignment expectation maximization (EM) =-=[10]-=- which iterates between solving two problems—estimating the missing boundary points and segment labels given a set of ellipses (E-step), and estimating an optimum set of ellipses given a completed set...

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...gidity, object topology, and image quality. Many contemporary tracking methods used in microscopy address problems with a subset of these challenges. For example, active contours [4], level sets [5], =-=[21]-=-, [30], [33], and registration based [32] methods address the tracking of a single object with a complex deforming shape but with relatively clear and continuous boundaries. However, they do not addre...

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...ent cells within an embryo, and 3) temporal context between image frames. Common approaches to such temporal tracking are rooted in probabilistic dynamic state space methods such as the Kalman filter =-=[20]-=-, [37], hidden Markov models, or more generally dynamic Bayesian networks [3], [23]. These methods model the joint distribution over a target’s trajectory as the product of a set of conditional probab...

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...cation (ASSC) whose contributions to the human embryo mitosis detection are twofold. First, the framework combines tracking based and tracking free approaches through a conditional random field (CRF) =-=[24]-=- model. Second, the framework performs data driven approximate inference over this model to efficiently deal with the problem’s high dimensionality and make the solution tractable. The CRF integrates ...

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...f human embryo tracking, the solution space is high dimensional and an exact solution is intractable. Thus, approximate inference is needed, which is often performed by sequential Monte Carlo methods =-=[11]-=-. Even then, the tracking results may not be conclusive in a significant portion of cases when using 2-D imaging. Recent work proposed and demonstrated a traditional particle filter for tracking human...

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..., object topology, and image quality. Many contemporary tracking methods used in microscopy address problems with a subset of these challenges. For example, active contours [4], level sets [5], [21], =-=[30]-=-, [33], and registration based [32] methods address the tracking of a single object with a complex deforming shape but with relatively clear and continuous boundaries. However, they do not address the...

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...proaches to such temporal tracking are rooted in probabilistic dynamic state space methods such as the Kalman filter [20], [37], hidden Markov models, or more generally dynamic Bayesian networks [3], =-=[23]-=-. These methods model the joint distribution over a target’s trajectory as the product of a set of conditional probability distributions, known as motion models and observation models. In the case of ...

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...where the likelihood function decomposes into multiple smaller functions, one for each ellipse. This maximization therefore consists of fitting an ellipse to the points , where . We use the method in =-=[14]-=-, which is a direct least squares formulation, and is efficient and robust. 3) Event Inference: The second and final pass of the approximate inference is the event inference. It combines the tracking ...

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...be a standard contour feature detection followed by a merging inference step to reduce the number of segments, as depicted in Fig. 2. We first create a boundary feature image using a Hessian operator =-=[15]-=-. This operator provides bothmagnitude and principal orientation for each pixel. We then extract contour features in a standard fashion by conducting a directed local search for coherent boundary pixe...

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...nd rigidity, object topology, and image quality. Many contemporary tracking methods used in microscopy address problems with a subset of these challenges. For example, active contours [4], level sets =-=[5]-=-, [21], [30], [33], and registration based [32] methods address the tracking of a single object with a complex deforming shape but with relatively clear and continuous boundaries. However, they do not...

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... boundaries as tracking based, and those that try the detection directly from the image pixels and low level features as tracking free. Visual tracking has been studied extensively in computer vision =-=[34]-=-. The difficulty of any visual tracking task is determined by a number of key characteristics of the data, including the number and density of target objects and their mutual interaction, the strength...

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...ct topology, and image quality. Many contemporary tracking methods used in microscopy address problems with a subset of these challenges. For example, active contours [4], level sets [5], [21], [30], =-=[33]-=-, and registration based [32] methods address the tracking of a single object with a complex deforming shape but with relatively clear and continuous boundaries. However, they do not address the data ...

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..., object shape and rigidity, object topology, and image quality. Many contemporary tracking methods used in microscopy address problems with a subset of these challenges. For example, active contours =-=[4]-=-, level sets [5], [21], [30], [33], and registration based [32] methods address the tracking of a single object with a complex deforming shape but with relatively clear and continuous boundaries. Howe...

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...ts. Meanwhile, many point tracking methods exist that address data association for multiple interacting point targets with occlusions and false positives with the help of spatial and temporal context =-=[19]-=-, [22], [28], but they do not deal with deforming shapes or changing topology. Human embryo tracking faces a diverse set of challenges, and to the best of our knowledge, has not yet been solved in a f...

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...numbers of cells are localized and tracked over time [25]. Many have successfully integrated segmentation with classification and target association to accomplish tracking and lineage reconstructions =-=[1]-=-, [35]. Often fluorescent markers are deployed to help localize cells [39], but this is not an option for human embryos, which must not be tagged with contrast agents. Spatial temporal segmentation ba...

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...anwhile, many point tracking methods exist that address data association for multiple interacting point targets with occlusions and false positives with the help of spatial and temporal context [19], =-=[22]-=-, [28], but they do not deal with deforming shapes or changing topology. Human embryo tracking faces a diverse set of challenges, and to the best of our knowledge, has not yet been solved in a fully a...

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...cells [39], but this is not an option for human embryos, which must not be tagged with contrast agents. Spatial temporal segmentation based tracking approaches with level sets have also been proposed =-=[40]-=-. Recently, probabilistic graphical models have been used in a tracking free approach for mitosis phase labeling in human adenocarcinoma cells [13] as well as automatic mitosis detection in mesenchyma...

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...r the work in this paper. Prior efforts in embryonic and stem cell tracking have often focused on estimating trajectories and lineage, where large numbers of cells are localized and tracked over time =-=[25]-=-. Many have successfully integrated segmentation with classification and target association to accomplish tracking and lineage reconstructions [1], [35]. Often fluorescent markers are deployed to help...

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...rs of cells are localized and tracked over time [25]. Many have successfully integrated segmentation with classification and target association to accomplish tracking and lineage reconstructions [1], =-=[35]-=-. Often fluorescent markers are deployed to help localize cells [39], but this is not an option for human embryos, which must not be tagged with contrast agents. Spatial temporal segmentation based tr...

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...n a tracking free approach for mitosis phase labeling in human adenocarcinoma cells [13] as well as automatic mitosis detection in mesenchymal stem cells, which are relatively 2-D in culture [26] and =-=[18]-=-. These studies suggest that tracking free approaches may be preferable to potentially intractable tracking based approaches if our primary interest is to detect mitosis events and not cell morphology...

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...en used in a tracking free approach for mitosis phase labeling in human adenocarcinoma cells [13] as well as automatic mitosis detection in mesenchymal stem cells, which are relatively 2-D in culture =-=[26]-=- and [18]. These studies suggest that tracking free approaches may be preferable to potentially intractable tracking based approaches if our primary interest is to detect mitosis events and not cell m...

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...e, many point tracking methods exist that address data association for multiple interacting point targets with occlusions and false positives with the help of spatial and temporal context [19], [22], =-=[28]-=-, but they do not deal with deforming shapes or changing topology. Human embryo tracking faces a diverse set of challenges, and to the best of our knowledge, has not yet been solved in a fully automat...

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...ell stages: (a) raw images; (b) overlaid with boundary segment features; and (c) overlaid with inferred cell boundaries. to four or five cells) can help predict downstream embryo fate [7], [9], [17], =-=[27]-=-. Early development—from fertilization to the four cell stage—typically lasts up to 48 h. Some examples of TLM images from a dark field microscope are shown in Fig. 1. In recent years, a number of com...

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...y. Many contemporary tracking methods used in microscopy address problems with a subset of these challenges. For example, active contours [4], level sets [5], [21], [30], [33], and registration based =-=[32]-=- methods address the tracking of a single object with a complex deforming shape but with relatively clear and continuous boundaries. However, they do not address the data association problem inherent ...

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...se microscopy (TLM) has recently emerged as a powerful noninvasive method to assess human embryo development. Quantitative image analysis on such images has also enhanced this modality’s capabilities =-=[2]-=-, [12], [16]. TLM can provide insights into how human embryos reach critical developmental milestones [38] and respond to chromosomal abnormalities [6]. Many recent studies have shown that cell divisi...

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...croscopy (TLM) has recently emerged as a powerful noninvasive method to assess human embryo development. Quantitative image analysis on such images has also enhanced this modality’s capabilities [2], =-=[12]-=-, [16]. TLM can provide insights into how human embryos reach critical developmental milestones [38] and respond to chromosomal abnormalities [6]. Many recent studies have shown that cell division tim...

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...g approaches with level sets have also been proposed [40]. Recently, probabilistic graphical models have been used in a tracking free approach for mitosis phase labeling in human adenocarcinoma cells =-=[13]-=- as well as automatic mitosis detection in mesenchymal stem cells, which are relatively 2-D in culture [26] and [18]. These studies suggest that tracking free approaches may be preferable to potential...

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...py (TLM) has recently emerged as a powerful noninvasive method to assess human embryo development. Quantitative image analysis on such images has also enhanced this modality’s capabilities [2], [12], =-=[16]-=-. TLM can provide insights into how human embryos reach critical developmental milestones [38] and respond to chromosomal abnormalities [6]. Many recent studies have shown that cell division timings d...

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...lls within an embryo, and 3) temporal context between image frames. Common approaches to such temporal tracking are rooted in probabilistic dynamic state space methods such as the Kalman filter [20], =-=[37]-=-, hidden Markov models, or more generally dynamic Bayesian networks [3], [23]. These methods model the joint distribution over a target’s trajectory as the product of a set of conditional probability ...

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...g embryo tracking with automated software. The first generation of Eeva has been clinically validated for outcome prediction in a prospective, multi-center clinical in vitro fertilization (IVF) study =-=[8]-=-. The framework used to provide the timing measurements that led to these results was first reported in [29], and is expanded upon in this paper. The measurement of mitosis events is challenged by the...

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...ertain desirable division timing parameters. This task significantly increases their already heavy workload. Expert measurement can also be prone to high inter-observer and intra-observer variability =-=[31]-=-. Automated mitosis detection algorithms have the potential to overcome this bottleneck and introduce a higher level of objectivity. In order to be 0278-0062 © 2014 IEEE. Personal use is permitted, bu...

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...ent. Quantitative image analysis on such images has also enhanced this modality’s capabilities [2], [12], [16]. TLM can provide insights into how human embryos reach critical developmental milestones =-=[38]-=- and respond to chromosomal abnormalities [6]. Many recent studies have shown that cell division timings during early development (up Manuscript received January 23, 2014; revised April 07, 2014; acce...

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...s has also enhanced this modality’s capabilities [2], [12], [16]. TLM can provide insights into how human embryos reach critical developmental milestones [38] and respond to chromosomal abnormalities =-=[6]-=-. Many recent studies have shown that cell division timings during early development (up Manuscript received January 23, 2014; revised April 07, 2014; accepted April 11, 2014. Date of publication Apri...

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... 3-cell, and 4-cell stages: (a) raw images; (b) overlaid with boundary segment features; and (c) overlaid with inferred cell boundaries. to four or five cells) can help predict downstream embryo fate =-=[7]-=-, [9], [17], [27]. Early development—from fertilization to the four cell stage—typically lasts up to 48 h. Some examples of TLM images from a dark field microscope are shown in Fig. 1. In recent years...

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...ll, and 4-cell stages: (a) raw images; (b) overlaid with boundary segment features; and (c) overlaid with inferred cell boundaries. to four or five cells) can help predict downstream embryo fate [7], =-=[9]-=-, [17], [27]. Early development—from fertilization to the four cell stage—typically lasts up to 48 h. Some examples of TLM images from a dark field microscope are shown in Fig. 1. In recent years, a n...

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...nd 4-cell stages: (a) raw images; (b) overlaid with boundary segment features; and (c) overlaid with inferred cell boundaries. to four or five cells) can help predict downstream embryo fate [7], [9], =-=[17]-=-, [27]. Early development—from fertilization to the four cell stage—typically lasts up to 48 h. Some examples of TLM images from a dark field microscope are shown in Fig. 1. In recent years, a number ...

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...owever, in our experiments we found the simple maximum criterion to work well. 2) Tracking Free Features: The tracking free portion of our framework uses a two-level embryo stage classification model =-=[36]-=- that classifies each frame of an embryo video to one of four stages (i.e., 1-cell, 2-cell, 3-cell, and 4-or-more-cell). The features for this portion are intended for training a classifier that direc...

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...essfully integrated segmentation with classification and target association to accomplish tracking and lineage reconstructions [1], [35]. Often fluorescent markers are deployed to help localize cells =-=[39]-=-, but this is not an option for human embryos, which must not be tagged with contrast agents. Spatial temporal segmentation based tracking approaches with level sets have also been proposed [40]. Rece...