The goal of this survey paper is to overview cellular measurements using optical microscopy imaging followed by automated image segmentation. The cellular measurements of primary interest are taken from mammalian cells and their components. They are denoted as two- or three-dimensional (2D or 3D) image objects of biological interest. In our applications, such cellular measurements are important for understanding cell phenomena, such as cell counts, cell-scaffold interactions, cell colony growth rates, or cell pluripotency stability, as well as for establishing quality metrics for stem cell therapies. In this context, this survey paper is focused on automated segmentation as a software-based measurement leading to quantitative cellular measurements. We define the scope of this survey and a classification schema first. Next, all found and manually filteredpublications are classified according to the main categories: (1) objects of interests (or objects to be segmented), (2) imaging modalities, (3) digital data axes, (4) segmentation algorithms, (5) segmentation evaluations, (6) computational hardware platforms used for segmentation acceleration, and (7) object (cellular) measurements. Finally, all classified papers are converted programmatically into a set of hyperlinked web pages with occurrence and co-occurrence statistics of assigned categories. The survey paper presents to a reader: (a) the state-of-the-art overview of published papers about automated segmentation applied to optical microscopy imaging of mammalian cells, (b) a classification of segmentation aspects in the context of cell optical imaging, (c) histogram and co-occurrence summary statistics about cellular measurements, segmentations, segmented objects, segmentation evaluations, and the use of computational platforms for accelerating segmentation execution, and (d) open research problems to pursue. The novel contributions of this survey paper are: (1) a new type of classification of cellular measurements and automated segmentation, (2) statistics about the published literature, and (3) a web hyperlinked interface to classification statistics of the surveyed papers at https://isg.nist.gov/deepzoomweb/resources/survey/index.html .

In order to facilitate the extraction of quantitative data from live cell image sets, automated image analysis methods are needed. This paper presents an introduction to the general principle of an overlap cell tracking software developed by the National Institute of Standards and Technology (NIST). This cell tracker has the ability to track cells across a set of time lapse images acquired at high rates based on the amount of overlap between cellular regions in consecutive frames. It is designed to be highly flexible, requires little user parameterization, and has a fast execution time.

The perceived texture directionality is an important, not fully explored image characteristic. In many applications texture directionality detection is of fundamental importance. Several approaches have been proposed, such as the fast Fourier-based method. We recently proposed a method based on the interpolated grey-level co-occurrence matrix (iGLCM), robust to image blur and noise but slower than the Fourier-based method. Here we test the applicability of convolutional neural networks (CNNs) to texture directionality detection. To obtain the large amount of training data required, we built a training dataset consisting of synthetic textures with known directionality and varying perturbation levels. Subsequently, we defined and tested shallow and deep CNN architectures. We present the test results focusing on the CNN architectures and their robustness with respect to image perturbations. We identify the best performing CNN architecture, and compare it with the iGLCM, the Fourier and the local gradient orientation methods. We find that the accuracy of CNN is lower, yet comparable to the iGLCM, and it outperforms the other two methods. As expected, the CNN method shows the highest computing speed. Finally, we demonstrate the best performing CNN on real-life images. Visual analysis suggests that the learned patterns generalize to real-life image data. Hence, CNNs represent a promising approach for texture directionality detection, warranting further investigation.