Image processing software tools | Microarray data analysis
The first step in microarray data analysis consists of image processing intending to estimate the ratio of the fluorescence intensities in two color channels at each spot. This ratio reflects differential gene (cDNA) or protein expression or change in DNA copy number (CGH) between two compared samples.
A package for a quantitative assessment of performance on multiple replicates of genome-wide array-based comparative genomic hybridization experiments. UCSF Spot automatically locates both subarray grids and individual spots. Ratios are computed based on explicit segmentation of each spot. On a typical image of 6000 spots, the entire process takes less than 20 sec. UCSF Spot offers a step toward fast and accurate operator-independent results in the quantification of DNA microarray image data.
A wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size. SpotCaliper is able to automatically find spots of varying size, and gives a precise measurement on their radius. The detections are collected in a table, displaying the following parameters: unique identifier (ID) of the spot, its location (x and y coordinates), radius, confidence, contrast, SNR and type. It is implemented as an ImageJ plugin with a friendly user interface. The user is allowed to edit the results by modifying the measurements (in a semi-automated way), extract data for further analysis. The fine tuning of the detections includes the possibility of adjusting or removing the original detections, as well as adding further spots. The main advantage of the software is its ability to capture the size of spots in a fast and accurate way.
Enables spatial mapping of RNA-seq transcript data onto high resolution tissue images. ST Spot Detector allows automatic spot detection for the positions and selections and positional adjustments. Users can visualize high throughput transcriptome data via high resolution tissue sample images. It facilitates the correction of visualisation but only one pair of images at a time can be uploaded with this tool.
Allows users to collect, manage, and effectively analyze data from microarray experiments. TM4 Microarray Software Suite is composed of a set of four tools: Madam, Spotfinder, Midas and MeV. It offers functions that allow users to record their experimental parameters and data; permit researchers to load the output of a microarray scanning operation and to adjust the placement of each grid cell manually allow for accurate spot detection.
Provides a method for uncalibrated microarray gridding and quantitative image analysis. AIM is a fast suffix array construction algorithm that performs very well even for worst-case strings. This system contains GUI programs to operate the system independently as well as command-line tools. It starts by sorting the suffixes in relation to a prefix of the same length, then refines each bucket of suffixes that share the same prefix by tracking the order of the suffixes already sorted.
A data acquisition and analysis software tool for microarray images which combines ease-of-use, user-friendliness and high performance. Mapix has the most up to date requirements to browse data from microarray experiments quickly with a high level of reliability and optimised productivity. Mapix controls all INNOPSYS InnoScan range of microarray scanners. Saving configurations (reading and analysis settings) allows users to define all protocols appropriately for each of their applications.
Assists users with microarray image analysis. MicroVigene offers signal segmentation and automated grid technology with a graphical interface. Scientists can customize plug-in array modules for functional expression, quantitate and reverse phase protein array. This application supports any image layout up to three levels of hierarchies: mixed orientation of blocks, any type of grid layout, and various sizes of spots or sub grids.
For microarray users who want an easy-to-use software tool that releases them from long hours of manual image processing, Spotxel® is microarray analysis software that facilitates microarray image analysis, automatic batch processing of multiple images, and discovery of important features and samples. Employing powerful spot finding algorithms and an efficient batch processing tool, Spotxel® can for example automatically process a batch of 160 microarray images in 3 hours, saving you 3 weeks of manual array alignment and data quantification. Spotxel® works natively on both Windows and Mac OS X platforms. The software is very affordable, for example a three-month software license costs only 115 EUR. The 14-day trial version with full functionality is free and can be requested at the product website.
Provides statistical tools for visualization and analysis of microarrays. GeneSpring GX offers an interactive environment that promotes investigation and enables understanding of Transcriptomics, Genomics, Metabolomics and Proteomics data within a biological context. It can be used for expression arrays, miRNA, exon arrays and genomics copy number data. It also allows to identify targets of interest that are both statistically and biologically meaningful.
Delivers data and automation to quantify, normalize and analyze experiments. ImaGene is a leading edge microarray image analysis software. It analyzes every spot and the array itself to determine the quality of the array image or individual spots. An optional batch-processing module allows to process any number of images. The software offers flexible options which can provide multiple data normalization options including lowess on entire array, sub-grid or control spots or differential regulation analysis.
Serves for microarray image analysis. Spotfinder is a program that uses an algorithm to identify the spots in the array and provide quantification of expression levels. Moreover, this program is part of TM4 Microarray software.
Allows automated image acquisition and real-time signal quantification. LabArray aims to simplify the process of microarray image analysis in non-equilibrium dissociation studies. It is able to proceed real-time monitoring. This tool made use of the covariance of an image containing periodic objects to calculate the distance between any two given objects or probe spots. It can identify spots that were misaligned during the printing process.
Scans and processes up automatically to 100 microarray raw image files. Agilent's Feature Extraction is a software that locates and places microarray grids, rejects aberrant pixels, accurately determines intensities and characteristic ratios, marks aberrant pixels and calculates statistical confidences. This commercial application is compatible with some non-Agilent scanners. In this software, application-specific QC reports provide metrics targeted to the experiment.
Offers a platform that investigates fluorescent images of microarrays. ScanAnalyze provides a graphic interface which is able to perform complex pixel and spot analyses. The application can produce files compatible with export towards various databases and also supplies features intending to automate tasks such as a semi-automatic definition of grids.