Citing imagej software
#Citing imagej software manual#
In addition, the segmentation method used here provides theoretical performance and robustness guarantees, is independent of manual initialization and directly corrects for microscope blur and detector noise, yielding optimally deconvolved segmentations Limitations of Squassh The quality and reliability of Squassh analysis mainly depends on the success of image segmentation. This allows the same method to be applied to a wide spectrum of images by adjusting the prior knowledge (i.e., changing parameter values). Squassh makes use of a segmentation method that directly connects the image-segmentation task with biological reality through prior knowledge about the imaged objects, the image-formation process and the noise present in the image. An overview of Squassh and its advantages Here we present a protocol for Squassh and the colocalization of subcellular shapes. However, recent progress in computer vision has provided well-founded theories that can give justification to the methodology 12. Object detection and image segmentation are still frequently done by hand or by using ad hoc heuristics such as thresholding or hand-crafted pipelines of filters. However, object-based methods require that the objects in the image be first detected and delineated, which is a nontrivial task that involves image segmentation. This allows interactions between objects to be inferred and statistical hypotheses about their distribution (e.g., random versus nonrandom) to be tested 9.
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Object-based methods first detect and delineate the objects represented in the image and then quantify their overlap Object-based analysis provides access to additional features of biological relevance, such as the spatial distribution of objects within the cell and the shapes and sizes of objects. Pixel-based methods compute an overlap measure between the pixel intensities of the different color channels and include the following: Pearson's correlation coefficient 3 the overlap and Manders' overlap coefficients 4 intensity correlation 5 cross-correlation 6 and techniques correcting for unspecific (random) colocalization 7. Colocalization of objects between different color channels can be quantified by various methods that are either pixel-based or object-based 2. Quantification of the shapes and spatial distributions of subcellular objects is an important task, as the fluorescent probes are usually related to cellular markers. In addition, the ability to observe and quantify multiple fluorescent markers in the same cell under various conditions and over time opens doors for spatiotemporal modeling of biological processes 1. Although it is possible to distinguish obvious phenotypes by eye, computational analyses enable the following: the processing of large data sets the generation of quantitative and less biased results and the detection of subtler changes in phenotype by statistical analysis. IntroDuctIon An increasing amount of biological and medical research relies on single-cell imaging to obtain information about the phenotypic response of cells to a variety of chemical, mechanical and genetic perturbations. Together, our data indicate that mosquito-specific viruses may encode RNAi antagonists to suppress antiviral RNAi. Finally, we show that the RNAi-suppressive activity of VP3 is con-served in Drosophila X virus, a birnavirus that per-sistently infects Drosophila cell cultures. Slicing of tar-get RNAs by pre-assembled RNA-induced silencing complexes was not affected by VP3.
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VP3 was found to bind long dsRNA as well as siRNAs and interfered with Dicer-2-mediated cleavage of long dsRNA into siRNAs. We demonstrate that VP3 can functionally replace B2, the well-characterized RNAi suppressor of Flock House virus.
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Furthermore, we show that RNAi is suppressed in CYV-infected cells and that the vi-ral VP3 protein is responsible for RNAi antagonism. We found that the Culex RNAi machinery processes CYV double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNAs).
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We therefore set out to study RNAi sup-pression by Culex Y virus (CYV), a mosquito-specific virus of the Birnaviridae family that was recently iso-lated from Culex pipiens mosquitoes. However, whether mosquito-specific viruses suppress RNAi remains unclear. To counteract the potent antiviral RNAi pathway, insect viruses encode RNAi suppressors. RNA interference (RNAi) is a crucial antiviral defense mechanism in insects, including the major mosquito species that transmit important human viruses.