Software tools: ChipSkipper

ChipSkipper  combines all  tasks required for analysis and quantitation of micro-array data - both DNA or protein arrays.
It's image processing routines may be also applied to automated evaluation and quantiation of microscopic images.


Like an image processing system,
ChipSkipper  can load multiple image files simultaneously, supporting the commonly used file file formats. A set of different views into the data allows to analyze image quality. Basic image manipulation routines enable to optimize the image data.

A variety of digital image processing functions allows in combination with ChipSkippers's scripting ability the analysis and qunatitation of large batches of e.g. microscopic images.

For spot quantitation integration grids can be easily created, or already existing grid templates can be reused within slide batches. Integration grids are semi automatic aligned to the images. Several integration algorithms and options are available.

Statistical analysis of integration results may be used for quality estimates of the whole microarray or in dependance of the spotting pins.

Integration data can be viewed in tabular form or in 2-dimensional or 3-dimensional scatter-plots. Ratio distribution can be visualized in ratio histograms. Several normalization algorithms and modes are available to compensate for experimental effects. Integration data can be saved as tab-separated text files or uploaded as separate tables into databases.

A dynamic ratio thresholding may be performed to select the statistically significant expressed genes in any intensity range.

The data visualization and analysis tools can load data from tab-separated files, clipboard or out of databases.

Spot annotations as well as integration results are searchable. Those spots meeting the search criteria are marked in the data views or can be saved as gene lists. Basic tools for merging and folding of these gene list are available.

Visit the ChipSkipper-page to learn more about this program.