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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.


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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.

AIM / Automatic Image Processing system for Microarray

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.


Reads paired 16-bit or 8-bit TIFF image files generated by most microarray scanners. TIGR Spotfinder is an image-processing software created for analysis of the image files generated in microarray expression studies. It uses a fast and reproducible algorithm to identify the spots in the array and provide quantification of expression levels. Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression. Spotfinder is part of TM4 Microarray software.


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.


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.