Abstract: Disclosed herein is a computer programmed to carry out a method for reducing directional error in scanned intensity values. The method includes scanning some rows of a substrate in a first direction, and some rows of the substrate in a second, different, direction, in order to obtain intensity values exhibited by various regions of the various rows. The intensity values from rows scanned in the first direction are analyzed, and the intensity values from rows scanned in the second direction are analyzed, in order to determine the directional error. The intensity values from rows scanned in the first direction and the intensity values from rows scanned in the second direction are then adjusted to reduce the directional error.

Abstract: A reader is provided that, itself, addresses the issue of damage or degradation to arrays within the reader by virtue of air exposure. In doing so, experimental variability is reduced, and read/scan signal strength degradation is minimized for arrays/slides scanned or otherwise read toward the end of a run. The subject scanners employ a filter that reduces the amount of chemicals in the air inside the device that are harmful to the array, or the dye on the array. The implementation of adding a chemical filter to the reader device may be such that air is either drawn into or, alternatively, pushed through the filter into the same. It is possible that the entirety of the device may be provided with filtered air, or just the region holding slides to be scanned. Array readers so-constructed as well as associated methodology involving filtering incoming air while reading arrays are covered.

Abstract: A method of processing one or more detected signal images each acquired from a field of view of a chemical array reader. A location correction is determined based on different detected signals at different image regions which represent regions in the field of view having the same actual signal. Alternatively or additionally, a location correction is applied to a detected signal at an image region. The location correction reduces detected signal discrepancy between different regions in an acquired image which represent different regions in the field of view having the same actual signal. An array reading system and computer program products are also provided.

Abstract: A method of using a chemical array reader, chemical array readers, and computer program products for use with a chemical array reader. The chemical array reader may include a holder to mount an array and hold the array at a reading position. A light system illuminates a mounted array when at a reading position. A detection system having a focal plane, to detect light from different regions across the array emitted in response to the illumination, when at the reading position, and which generates a resulting signal for each of the regions across the array. An autofocus system which detects and reduces offset between the different regions of an array at the reading position and a determined position of the focal plane.

Abstract: An optical scanning system adapted to physically adjust scanner settings in response to control feature readings is disclosed. The scanner and methodology finds particular use in reading of biopolymer arrays. The system may operate in any of a number of ways such that optimal data from scans is obtained. It may also be possible to use the system as a tool to aid in manufacture of arrays by providing feedback to a manufacturer regarding the signal produce for a given batch of samples tested.

Abstract: A method of interrogating an addressable array unit having a transparent substrate with a back surface, and an array with a plurality of different chemical features on a front surface. The method may include illuminating the features while the array is dry, with an interrogating light which is directed through the substrate from the back surface and onto the chemical features on the front surface. The light emitted from respective features in response to the interrogating light may be detected, which detected light has passed from the front surface, through the substrate and out the back surface. In one arrangement the light is emitted from locations of the features which are spaced from the front surface a distance of less than one-eighth of the wavelength of the illuminating light in a gas or a vacuum which is in contact with the dry array. Other methods and a package containing an addressable array are also provided.

Abstract: The light detection system includes at least two light detection elements. Each element is responsive to a selected light color in a first mode, and each element has a different sensitivity and is responsive to a single color in a second mode for enhanced dynamic range. A preferred embodiment includes four light detectors for responding to four separate colors or for responding with enhanced dynamic range to two colors. Embodiments are disclosed using a mirror/beam splitter arrangement to switch between modes and an embodiment including dichroic filters serving as fractional beam splitters.

Abstract: A method and system for calibrating molecular arrays to a reference molecular array, and for subsequently calibrating the molecular arrays to maintain a constant signal-intensity-to-label-concentration ratio. In the first step of the two-step calibration method, a reference array coated with the fluorophore or chromophore used to label probe molecules is employed, while in the second step of the two-step method, a reference array coated with a stable dye is employed.

Abstract: A method and system for preventing signal clipping in a molecular array scanner by adding an offset signal to the signal generated by the photodetectors and initial stages of signal processing within a molecular array scanner in order to promote the signal above the level where signal information is lost during analog-to-digital signal conversion and/or digital signal integration. A portion of the offset is then subtracted from the digital signal or integrated digital signals, leaving a smaller, constant offset that is reported to the user, stored in a data file, or otherwise made available for further correction during later molecular array data processing.

Abstract: A method and system for determining a biopolymer array substrate thickness dependent optimal focus distance for scanning a molecular array by a molecular array scanner are disclosed. Also disclosed are methods of determining the thickness of a biopolymer array substrate using a position sensitive device (PSD) component of a biopolymer array scanner. Further methods include determining the thickness of said biopolymeric array and automatically selecting an optimal focus distance using the determined thickness and a calibration function on thickness versus optimal focus distance. The subject invention finds use in a variety of different applications, including both genomic and proteomic applications.

Abstract: A method in which a chemical array is read on an array reader and the results saved in a memory linked with a performance characteristic of the array reader. Alternatively or additionally results from reading an array and a linked performance characteristic of a reader which performed the reading are retrieved from a memory. Computer program products and apparatus are also provided.

Abstract: A method of processing one or more detected signal images each acquired from a field of view of a chemical array reader. A location correction is determined based on different detected signals at different image regions which represent regions in the field of view having the same actual signal. Alternatively or additionally, a location correction is applied to a detected signal at an image region. The location correction reduces detected signal discrepancy between different regions in an acquired image which represent different regions in the field of view having the same actual signal. An array reading system and computer program products are also provided.

Abstract: The light detection system includes at least two light detection elements. Each element is responsive to a selected light color in a first mode, and each element has a different sensitivity and is responsive to a single color in a second mode for enhanced dynamic range. A preferred embodiment includes four light detectors for responding to four separate colors or for responding with enhanced dynamic range to two colors. Embodiments are disclosed using a mirror/beam splitter arrangement to switch between modes and an embodiment including dichroic filters serving as fractional beam splitters.

Abstract: Array units and methods are provided which have constructions to reduce or take advantage of Fresnel reflection. The array units may have a subtantially unreflective substrate. In one arrangement a transparent spacer layer is provided while in another an anti-reflective layer is present.

Abstract: An automated method and system for determining an optimal focus distance for scanning a molecular array scanner. Blocks of rows of a reference array are automatically scanned at successively greater distances of the stage from a light gathering medium, such as an optical fiber, or z-positions, to produce data providing a functional relationship between z-position and measured signal intensities. The data is then processed by a peak-height-based, or window-based, focus-finding routine that selects an optimal focus-distance for data scans.

Abstract: Biopolymeric array scanners that are capable of automatically selecting a dye specific scale factor to employ for a plurality of different dyes, as wells as methods for making and using the same, are provided. In many embodiments, the actual dye specific scale factor automatically selected by the scanner is one that is equal to a preset “master” scale factor, so that the scanner reads any supported dye using the same constant scale factor. The dye, specific scale factor selection is typically made by reference to a collection of nominal scale factors for each member of the plurality of dyes. In using the subject scanners, a user simply inputs the one or more dyes being used in a given array assay, and the scanner automatically reads the array using an automatically chosen dye specific scale factor for the selected dyes. Also provided are methods of obtaining collections of nominal scale factors and computer readable mediums comprising the same.

Abstract: An optical scanning system adapted to physically adjust scanner settings in response to control feature readings is disclosed. The scanner and methodology finds particular use in reading of biopolymer arrays. The system may operate in any of a number of ways such that optimal data from scans is obtained. It may also be possible to use the system as a tool to aid in manufacture of arrays by providing feedback to a manufacturer regarding the signal produce for a given batch of samples tested.

Abstract: A method and system for accurately scanning the features of a molecular array in order to take into account chromophore chemical decomposition, peak broadening, and other spectral changes that can alter the relationship between the density, or concentration, of chromophore label initially present within a feature of a molecular array and the intensity of light emitted from the feature of the molecular array at a wavelength characteristic of fluorescent emission from the chromophore label. In one embodiment, a four-channel molecular array scanner is used to more accurately scan a two-channel molecular array. All four detectors of a four-channel molecular array scanner are employed to measure signal from a two-channel array.

Abstract: An optical scanner system scheme is described that enables better detection limits to be reached at the highest resolution of a fluorescent imager. In a scanner that has asymmetric scan qualities, measurement errors are eliminated by a factor that is greater than expected for simply handling random errors through additional sampling. Systematic asymmetries in scan direction are factored out by averaging pixel results obtained from opposite direction scans of the same line and binning them together at the same resolution.

Abstract: A biopolymer array optical scanner system that is configured to accommodate the needs of its working environment, but offer extended life over common scanners as typically used, is provided. The scanner is programmed to allow a user to set times or adopt a schedule by which the scanner will automatically power up and/or power down. The activity of the scanner can be controlled by setting a timer or selecting a given time/event, a custom schedule and/or a preselected schedule to trigger action by a software switch at the appointed time. The switch automatically takes such action as previously directed. The activity may be selected from powering up (turning on or going to standby), powering down (turning off or going to standby) and/or initiating a scan run. Myriad combinations or permutations of activities and their respective timing are possible.