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Fluorescence in situ hybridization data analysis software tools | Laser scanning microscopy

Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity.

Source text:
(Shirley et al., 2011) FISH Finder: a high-throughput tool for analyzing FISH images. Bioinformatics.

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SPEX2 / SPatial gene EXpression pattern EXtractor
Allows extraction, transformation, comparison, classification and clustering of spatial gene expression patterns in Drosophila embryos. SPEX2 is an image processing pipeline for automated extraction of bona fide gene expression, from Drosophila embryonic In situ hybridization (ISH) results imaged from the lateral view. The software consists of: (i) embryo standardization, (ii) gene expression pattern extraction and (iii) feature representation.
Oufti
Allows automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti is a standalone that includes routines for subpixel detection of non-diffraction-limited objects. These routines allow quantitative characterization of nucleoids, filamentous structures, and subcellular objects with regular or irregular shapes. It provides plotting tools for data analysis, display of results, as well as various tools for visualization of the cell cycle and for subpixel image alignment and movie construction.
mTRIP / Mitochondrial Transcription and Replication Imaging Protocol
Identifies mitochondrial entities engaged in the mtDNA initiation of replication. mTRIP is able to reveal the mitochondrial RNA (mtRNA) content in single human cells. It can combine recognition of mtDNA initiation of replication, mtRNA content, and proteins in single human cells thanks coupling the tool with immunofluorescence. This tool can assist users to decode mtDNA dynamics and their impact under physiological changes, including stress, and in disease.
IMACULAT / Image Analysis of Chromosomes for computing localization
Obsolete
Computes localization of whole chromosomes. We partition the cell into concentric elliptical compartments of equal areas, and the variance in the quantity of any chromosome is used to determine its movement in the cell. The results are outputted to a text file, and a corresponding gif image showing the elliptical shells is generated for visual comparison with the original image. Automation allows high throughput analysis for deriving statistics that are used to validate a hypothesis regarding the position of any chromosome. The ImageMagick Perl API libraries have been used for pre-processing the images.
Smart 3D-FISH
Obsolete
Automates the process of spot segmentation and distance measurements in images from 3D-FISH experiments. It can handle any number of fluorescent spots and incorporate images of 4',6-diamino-2-phenylindole counterstained nuclei to measure the relative positioning of spot loci in the nucleus and inter-spot distance. Smart 3D-FISH should greatly facilitate image processing and analysis of 3D-FISH images by providing a useful tool to overcome the laborious task of image segmentation based on user-defined parameters and decrease subjectivity in data analysis.
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