Tuesday, April 21, 2009

Microarray Image Analysis Software

Microarray Image Analysis Software FAQ’s

What are the main features of
Mapix?

The « Gridding »
Mapix lets you define a grid on a scanned image so that you can identify each spot by assigning it unique coordinates. This feature is called spot addressing or gridding. Mapix uses a highly efficient algorithm to automatically insert user-defined or imported grids (in the form of GAL files generated by the NanoPrint or SpotBot microarrayer).

The « Segmentation »
Mapix delimits the area of each spot with respect to the slide. This feature is called foreground segmentation (the foreground containing the spot as opposed to the background noise). Mapix generates the digital mean and median values of the signal from spot pixels and of the local background noise (delimited by the grid), as well as various other parameters such as the standard deviation of spot pixel brightness values and signal-to-noise ratio. The results file generated by Mapix can be exported in text formats to be databased or imported into other programs for analysis and reporting.

The « Flagging »
Mapix lets you pinpoint unusable spots—for example where there is no spot or the slide area is covered by noise—with a flagging system that assigns a numeric quality code to aid filtering out of non-significant data. Mapix also marks spots so that you can sort them when analysing results. The results file contains a “flag” column indicating a value for each spot :

Code = Signification
0 = spot not flagged
100= good spot
–100= bad spot
–50= spot not found
–75= no spot

The « Batch Processing »
The batch mode option lets you automate processing to support high-data-rate microarray analysis. Batch processing consists in setting parameters to scan and analyse large numbers of biochips according to their type, to automatically generate results files.

What data visualization modes does Mapix provide?

The Histogram
Mapix automatically plots a histogram of the pixel brightness distribution for each
wavelength, thereby helping you to define your biochip read settings.

What data import format does Mapix use?

GAL (Gene Array List) file format
Mapix uses a microarray industry-standard import file format containing lists that
describe biochip spot positions and content. GAL files of course do not have to contain genes, many other types of biomolecules are printed into microarrays. The NanoPrint and SpotBot microarrayers provide software for spot map GAL file generation. All commercial microarrays such as H25K come with a GAL file.

What data export format does Mapix use?

GPR file format
Mapix uses a microarray industry-standard export file format containing all spot
quantification data. GPR used to stand for Gene Picture results, however, GPR files are considered standard quantification txt files.

What type of images can Mapix analyze and record?

 TIFF format
Mapix records images in TIFF format (Tagged Image File Format (.tif)). TIFF is a special, lossless format able to record one or more images along with a set of other information stored in “tags”. For example, when Mapix records images acquired at 2 given wavelengths, it creates a single TIFF file containing the 2 images (unless the user configures it to generate 2 separate files). In both cases, the acquisition parameters are stored in the tags.

JPEG format
Mapix can also record images in JPEG format (Joint Photographic Experts Group (.jpg)). This format, which has become popular in particular through increasing use of digital photographic cameras, generates a lossy, compressed image. The file is therefore smaller, which is useful when inserting images in a presentation or report. JPEG images cannot be used to obtain biological experiment results. They are therefore no substitute for acquired TIFF images, which are not compressed and contain usable values.