Fluorescence in situ hybridization data analysis software tools
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.
Analyzes molecule FISH and gets the spatial dimension of the transcriptome. FISH-quant first detects and then localizes mature mRNA in three dimensions by fitting Gaussians to fluorescent spots; each mRNA then undergoes a quality test based on the measured point-spread function (PSF). This tool is useful for the automatization of the computation of the detection intensity threshold.
A widely applicable, user-friendly system tailored for the objective and semi-automated visualization, detection and quantification of genomic alterations and protein expression obtained from fluorescence in situ analysis. In a sample set of HER2-positive breast cancers GoIFISH is highly robust in visual analysis and its accuracy compares favorably to other leading image analysis methods.
Deduces models’ parameters from smFISH data. BayFish allows users to provide smFISH data at multiple time points before and after induction in a selected mathematical model of stochastic gene expression. Then it exploits combined numerical methods for evaluating the Bayesian posterior probability, including the uncertainty quantification for supplying the fittest parameters.
A program for high-throughput processing and analysis of 3D fluorescence images, dedicated to the study of nuclear architecture. It allows to perform the complete analysis process starting from the raw images to the processed measurements (plots and statistical tests).
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.
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