SPOT, a software package for analysing microarray images.
Spot: software for DNA microarray image analysis
Spot is a microarray spot detection and characterisation software package which extracts more meaningful numerical information from cDNA microarrays than other software.
29 October 2010 | Updated 4 January 2013
About Spot software
Spot is a software package for analysing microarray images.
Life scientists use cDNA (complementary DNA) microarrays, or 'DNA chips', to measure the expression levels of genes in cells.
Images of the microarrays have to be analysed to measure the intensity of each labeled cDNA spot.
The cDNA spots are arranged in rows and columns and they are not always round.
Spot software has been developed by CSIRO’s Biotech Imaging specialists, based on well-respected, fundamental research into microarrays.
Spot software extracts a broad range of meaningful numerical information.
The software is very flexible and it:
can accommodate spots that aren’t circular
allows appropriate background adjustment which can substantially improve the precision of low-intensity spot values
offers an automatic grid-finding procedure that minimises manual intervention.
It's features include:
powerful graphical user interface
automatic rotation correction
automatic grid location, with optional user guidance
flexible spot segmentation
morphological background estimation
programmer interface for customization.
Spot software is implemented as a package within the open source statistical environment, 'R'.
The powerful suite of 'R' tools can therefore be used directly on the results produced by Spot software.
How to get an evaluation copy of Spot 3.0
CSIRO provides Spot image analysis software free.
Spot is available for the following platforms:
To download Spot you need to:
read and agree to the terms set out in the Evaluation License Agreement, and
provide some registration details.
After you have registered, an email message will be sent to you with download details.
Download Spot now [external link] or find out more about the work of CSIRO Mathematics, Informatics and Statistics.
Wilson DL, Buckley MJ, Helliwell CA, Wilson IW. 2003. New Normalization Methods for cDNA Microarray Data. In: Bioinformatics. 19(11): 1325-1332. July 2003.
Yang J, Buckley MJ, Dudoit S, Speed T. 2002. Comparison of methods for image analysis on cDNA microarray data. In: Journal of Computational and Graphical Statistics.11(1): 108-136.
Sun C, Buckley MJ. 2001. Discussion on A penalized likelihood approach to image warping. In: Journal of the Royal Statistical Society: Series B. 63(3): 506-507.
Yang YH, Buckley MJ, Speed T. 2001. Analysis of cDNA microarray images. In: Briefings in Bioinformatics. 2(4): 341-349.