Abstract: A scanning system is calibrated to correct for possible panel misalignments errors. A reference slide or data point is used to obtain a series of measurements with the scanning system. These measurements are compared with the expected results to determine systematic alignment errors in the scanning system. A model is created to correct the alignment errors during the scanning process, thus providing a plurality of more accurate scans. The plurality of scans may then be assembled to create a complete image of the scan area.

Abstract: Expression profiling using DNA microarrays is an important new method for analyzing cellular physiology. In “spotted” microarrays, fluorescently labeled cDNA from experimental and control cells is hybridized to arrayed target DNA and the arrays imaged at two or more wavelengths. Statistical analysis is performed on microarray images and show that non-additive background, high intensity fluctuations across spots, and fabrication artifacts interfere with the accurate determination of intensity information. The probability density distributions generated by pixel-by-pixel analysis of images can be used to measure the precision with which spot intensities are determined. Simple weighting schemes based on these probability distributions are effective in improving significantly the quality of microarray data as it accumulates in a multi-experiment database. Error estimates from image-based metrics should be one component in an explicitly probabilistic scheme for the analysis of DNA microarray data.

Abstract: A system and method of image processing employ mathematical deconvolution to estimate the magnitude and location of a target object within an image. Both the nature of internal reflections and the convolution process by which each internal reflection contributes to blurring of the acquired image data may be measured and modeled. In accordance with mathematical deconvolution techniques, the combined effects of these internal reflections may be reduced to the extent that respective contributions of the target object and each individual reflection may be distinguished and quantified.

Abstract: A fluorescence microscopy system and method allow selective and repeatable switching between Köhler illumination, providing a relatively large field of view, and Critical Illumination, providing a relatively higher axial resolution. This switching or toggle function may be facilitated by a feature associated with an alignment module that allows the focus of the fiber tip, for example, to be selectively and repeatably transitioned between the back aperture of the objective lens and the object plane without losing optical alignment.

Abstract: An image acquisition system and method employing multi-axis integration (MAI) may incorporate both optical axis integration (OAI) and time-delay integration (TDI) techniques. Disclosed MAI systems and methods may integrate image data in the z direction as the data are acquired, projecting the image data prior to deconvolution. Lateral translation of the image plane during the scan in the z direction may allow large areas to be imaged in a single scan sequence.

Abstract: Successive portions of an array of small biological specimens are imaged using a CCD camera. The x,y coordinates of each successive portion within the array are also determined. The array is moved by a precision staging system to accurately locate each successive portion in the array. The separate data portions are then arranged together using the coordinates of each portion to produce a complete data image of the array, without any mathematical smoothing or matching necessary between successive portions.

Abstract: A biological sample is scanned with Time-Delay Integration (TDI) by a CCD camera having columns and rows. When the light from a location of the sample falls onto a picture element (pixel) on the camera, the photons of the light are converted to electrons. The electrons within that pixel are shifted down one row to the pixel directly beneath it. The shifts occur in the columnar direction of the camera while the sample is moved synchronously with the electrons. The electrons shifted off the bottom row of the camera are measured and converted into a digital value for that picture element in the sample image.

Abstract: Expression profiling using DNA microarrays is an important new method for analyzing cellular physiology. In “spotted” microarrays, fluorescently labeled cDNA from experimental and control cells is hybridized to arrayed target DNA and the arrays imaged at two or more wavelengths. Statistical analysis is performed on microarray images and show that non-additive background, high intensity fluctuations across spots, and fabrication artifacts interfere with the accurate determination of intensity information. The probability density distributions generated by pixel-by-pixel analysis of images can be used to measure the precision with which spot intensities are determined. Simple weighting schemes based on these probability distributions are effective in improving significantly the quality of microarray data as it accumulates in a multi-experiment database. Error estimates from image-based metrics should be one component in an explicitly probabilistic scheme for the analysis of DNA microarray data.

Abstract: A scanning system is calibrated to correct for possible panel misalignments errors. A reference slide or data point is used to obtain a series of measurements with the scanning system. These measurements are compared with the expected results to determine systematic alignment errors in the scanning system. A model is created to correct the alignment errors during the scanning process, thus providing a plurality of more accurate scans. The plurality of scans may then be assembled to create a complete image of the scan area.

Abstract: The method of illumination of a microarray sample may contribute to the signal-to-background ratio. An oblique illumination technique is used to reduce the reflections from the sample to the detector. The sample may also be moved to the backside of the sample support to reduce the reflections caused by the sample support. In addition, a parallel scanning technique may be used to ensure proper alignment of the sample.

Abstract: A plurality of panels are assembled into a single image. Each of the panels may have different intensities throughout the panel, as well as non-uniformities between panels. The panels are modified using flat-field calibration, panel flattening, and panel connecting techniques. These techniques correct for non-uniformities and provide a cleaner, single image.