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Wndchrm – an open source utility for biological image analysisAbstract: 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.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.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.In the past few years, pipelines providing high-throughput biological imaging have been becoming increasingly important, and are supported by automated microscopy and high-performance computing and storage devices. Applications include profiling drug responses, screening for small molecules, classification of subcellular localization, and more. While image acquisition systems, network bandwidths, and storage devices are capable of supporting vast pipelines of biological images, human analysis can be impractically slow. Therefore, machine vision algorithms for analysis of biological images are necessary to complete a fully automated process for interpreting biological experiments.Some highly useful applications have been proposed and made available to the scientific community. OME [1,2], as well as its derivative product OMERO [3], provide a widely used enterprise solution to storing, handling and processing biological and medical images. Another useful application is Ce
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