Therefore, to achieve high throughput and objectivity, the method of data acquisition should be standardized as well as automated so less manual work is required from the investigator and data are objectively acquired. The process of manual data acquisition is time consuming and subjective due to inconsistency of an investigator's decisions. Thus, FISH provides a way to visually locate a gene within the nucleus using fluorescence microscopy. FISH incorporates fluorescently labeled probes that bind only to the segment of the genome with which they have a high degree of sequence similarity. The program is freely available from: įluorescence in situ Hybridization (FISH) is a technique used to visualize the location of specific DNA sequences within the nucleus.
Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes.Īvailability: FISH Finder is a standalone MATLAB application and platform independent software. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction.
To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold-based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus segmentation. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis.
Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus.