Lior Shamir

Abstract The cosmological principle (CP)—the notion that the Universe is spatially isotropic and homogeneous on large scales—underlies a century of progress in cosmology. It is conventionally formulated through the Friedmann-Lemaître-Robertson-Walker (FLRW) cosmologies as the spacetime metric, and culminates in the successful and highly predictive Λ-Cold-Dark-Matter (ΛCDM) model. Yet, tensions have emerged within the ΛCDM model, most notably a statistically significant discrepancy in the value of the Hubble constant, H 0 . Since the notion of cosmic expansion determined by a single parameter is intimately tied to the CP, implications of the H 0 tension may extend beyond ΛCDM to the CP itself. This review surveys current observational hints for deviations from the expectations of the CP, highlighting synergies and disagreements that warrant further study. Setting aside the debate about individual large structures, potential deviations from the CP include variations of cosmological parameters on the sky, discrepancies in the cosmic dipoles, and mysterious alignments in quasar polarizations and galaxy spins. While it is possible that a host of observational systematics are impacting results, it is equally plausible that precision cosmology may have outgrown the FLRW paradigm, an extremely pragmatic but non-fundamental symmetry assumption.

We describe a method for automated detection of radiographic osteoarthritis (OA) in knee X-ray images. The detection is based on the Kellgren-Lawrence (KL) classification grades, which correspond to the different stages of OA severity. The classifier was built using manually classified X-rays, representing the first four KL grades (normal, doubtful, minimal, and moderate). Image analysis is performed by first identifying a set of image content descriptors and image transforms that are informative for the detection of OA in the X-rays and assigning weights to these image features using Fisher scores. Then, a simple weighted nearest neighbor rule is used in order to predict the KL grade to which a given test X-ray sample belongs. The dataset used in the experiment contained 350 X-ray images classified manually by their KL grades. Experimental results show that moderate OA (KL grade 3) and minimal OA (KL grade 2) can be differentiated from normal cases with accuracy of 91.5% and 80.4%, respectively. Doubtful OA (KL grade 1) was detected automatically with a much lower accuracy of 57%. The source code developed and used in this study is available for free download at www.openmicroscopy.org.

BACKGROUND: Biological imaging is an emerging field, covering a wide range of applications in biological and clinical research. However, while machinery for automated experimenting and data acquisition has been developing rapidly in the past years, automated image analysis often introduces a bottleneck in high content screening. METHODS: Wndchrm is an open source utility for biological image analysis. The software works by first extracting image content descriptors from the raw image, image transforms, and compound image transforms. Then, the most informative features are selected, and the feature vector of each image is used for classification and similarity measurement. RESULTS: Wndchrm has been tested using several publicly available biological datasets, and provided results which are favorably comparable to the performance of task-specific algorithms developed for these datasets. The simple user interface allows researchers who are not knowledgeable in computer vision methods and have no background in computer programming to apply image analysis to their data. CONCLUSION: We suggest that wndchrm can be effectively used for a wide range of biological image analysis tasks. Using wndchrm can allow scientists to perform automated biological image analysis while avoiding the costly challenge of implementing computer vision and pattern recognition algorithms.

The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays. ''can these groups of images be distinguished?''. In this context, the input to a PR algorithm may be an entire image, a sub-image region identified with segmentation algorithms, or simply image samples in the form of rectangular tiles. Thus, in contrast to selecting and tuning a segmen-