a regression system for estimation of errors introduced by confocal imaging into gene expression data in situ回归估计系统误差引入的共焦成像原位基因表达数据.pdfVIP

Myasnikova et al. BMC Bioinformatics 2011, 12:320 /1471-2105/12/320 RESEARCH ARTICLE Open Access A regression system for estimation of errors introduced by confocal imaging into gene expression data in situ 1* 1 2 1 1 Ekaterina Myasnikova , Svetlana Surkova , Grigory Stein , Andrei Pisarev and Maria Samsonova Abstract Background: Accuracy of the data extracted from two-dimensional confocal images is limited due to experimental errors that arise in course of confocal scanning. The common way to reduce the noise in images is sequential scanning of the same specimen several times with the subsequent averaging of multiple frames. Attempts to increase the dynamical range of an image by setting too high values of microscope PMT parameters may cause clipping of single frames and introduce errors into the data extracted from the averaged images. For the estimation and correction of this kind of errors a method based on censoring technique (Myasnikova et al., 2009) is used. However, the method requires the availability of all the confocal scans along with the averaged image, which is normally not provided by the standard scanning procedure. Results: To predict error size in the data extracted from the averaged image we developed a regression system. The system is trained on the learning sample composed of images obtained from three different microscopes at different combinations of PMT parameters, and for each image all the scans are saved. The system demonstrates high prediction accuracy and was applied for correction of errors in the data on segmentation gene expression in Drosophila blastoderm stored in the FlyEx database (http://urchin.spbcas.ru/flyex/, /flyex/). The prediction method is realized