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Network structures formed by actin filaments are present in many kinds of fluorescence microscopy images. In order to quantify the conformations and dynamics of such actin filaments, we propose a fully automated method to extract actin networks from images and analyze network topology. The method handles well intersecting filaments and, to some extent, overlapping filaments. First we automatically...
While high-content screening is already playing an important role in drug discovery, a growing number of academic laboratories are applying these techniques to conduct a system-level analysis of biological processes. In this context more complex assays and model systems are being imaged at higher throughput. Examples include co-culture assays, tissues, and entire model systems, as for example zebrafish...
HER-2/neu, a protein often giving higher aggressiveness in breast cancers, has been shown that if the gene is expanded for some reason, the Her-2 protein produced by the cells will be over-expressed to enhance the cancer cells reproduced ability, the prognosis will be also relatively less, too. The HER-2 immunohistochemical stained provides a simple and reliable method for pathologist in clinical...
Location proteomics is concerned with the systematic analysis of the subcellular location of proteins. In order to perform comprehensive analysis of all protein location patterns, automated methods are needed. With the goal of extending automated subcellular location pattern analysis methods to high resolution images of tissues, 3D confocal microscope images of polarized CaCo2 cells immunostained...
In confocal microscopy imaging, the target objects are labeled with fluorescent markers in the living specimen, and usually appear as spots in the observed images. Spot detection and analysis is an important task for the biological studies from the observed images. However, while the spots have irregular sizes and positions due to the variant amount of objects on each spot, the quantitative interpretation...
Quantitative colocalization analysis in fluorescent microscopy imaging is a promising procedure used to perform functional protein analysis. Images acquired are degraded, and the features extracted are affected by this degradation. Moreover, the classification of the data becomes uncertain. In this paper, we address an application of SOM to a clustering problem formulated via feature extraction from...
As rapid acquisition of large collections of fluorescence microscopy cell images can be automated, large-scale subcellular localizations of GFP-tagged fusion proteins can be practically accomplished. Semi-supervised learning has the potential of using a large set of unlabeled images for the recognition of subcellular organelle patterns, but the performance still has room for improvement. This paper...
Figures in full science papers contain much information not described in the main text. The use of these figures is an important subject. In this study, we developed a method to classify these biomedical figures into categories using a combination of a bag of keypoints approach and a bag of words approach for the legends. For bag of keypoints, the descriptors of detected interest points are quantized...
We propose an adaptive multiresolution (MR) approach for classification of fluorescence microscopy images of subcellular protein locations, providing biologically relevant information. These images have highly localized features both in space and frequency which naturally leads us to MR tools. Moreover, as the goal of the classification system is to distinguish between various protein classes, we...
Protein subcellular locations, as an important property of proteins, are commonly learned using fluorescence microscopy. Previous work by our group has shown that automated analysis of 2D and 3D static images can recognize all major subcellular patterns in fluorescence micrographs, and that automated methods can be used to distinguish patterns that are subtly different. Since many proteins are in...
The identification of protein-protein interactions along with their spatial and temporal localization is vital data for assigning functional information to proteins. Historically, these data sets obtained from fluorescence microscopy, have been analyzed manually, a process that is both time consuming and tedious. The development of an automated system that can measure the location dynamics of the...
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