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: 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.

Abstract: Methods, systems and computer readable media for automatically feature extracting array images in batch mode. At least two images to be feature extracted are loaded into a batch project, and the system automatically and sequentially feature extracts the images in the batch project. At least one of the images may be feature extracted based upon a different grid template or protocol than at least one other of the images. Methods, systems and computer readable media are provided to automatically feature extract a single array image having an identifier indicating that it is a multipack, multiple array image. A system provided for feature extracting array images in batch mode includes a user interface with a feature enabling a user to select images to be loaded into a batch project; and based upon the loaded images in the batch project, the system may automatically assign a grid template to each image loaded into the batch project.

Abstract: A method and system for quantify random errors, sequence-dependent trends, and spatial-intensity trends in one or more channels of microarray data sets. The method and system of one embodiment of the present invention is directed to a method for quantifying random errors, sequence-dependent trends, and spatial-intensity trends present in microarray data sets. An additive error equation is employed to quantify background noise present in feature intensities due to random errors, sequence-dependent trends, and spatial-intensity trends.

Abstract: Methods for identifying feature boundary pixels are provided. In general, the subject methods involve evaluating a pixel signal to identify any difference in amplitude between a first part of the signal and a second part of the signal. If the difference is significant, the pixel signal may be indicated as a pixel representing a feature boundary. Also provided are systems and programming for performing the subject methods, and an array scanner containing these systems and programming.

Abstract: Methods for evaluating a pixel signal produced during scanning of a chemical array are provided. In general, the subject methods involve identifying a set of conformant digital signals for a pixel, and integrating those signals. Also provided are systems and programming for performing the subject methods, and an array scanner containing these systems and programming.

Abstract: Methods for producing data for a partially saturated pixel produced during scanning of a chemical array are provided. In general, an analog signal for a partially saturated pixel is sampled to obtain a set of non-saturated digital signals and a set of saturated digital signals. The saturated digital signals are then processed to produce data for the pixel. Also provided are computer program products comprising programming for performing the subject methods, and a chemical array scanner containing this programming. The invention finds use in a variety of different applications, including both genomics and proteomics applications.

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 quantifying and correcting spatial-intensity trends for each channel of a microarray data set having one or more channels. The method and system of one embodiment of the present invention selects a set of features from each channel of the microarray data set. Based on the selected set of features, a surface is used to determine the intensities for all features in each channel of the microarray data set. Spatial-intensity trends within the microarray data set are quantified, based on the surface to the intensities for each channel of the microarray data set. After the surface has been determined, the spatial-intensity trend can be removed from the microarray data set.

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 and system for determining a biopolymer array substrate thickness dependent optimal focus distance for scanning a molecular array by a molecular array scanner are provided. A reference substrate is 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 an array substrate thickness dependent focus-finding routine that selects an optimal focus-distance for data scans which is optimized for the thickness of the reference substrate. Also provided are methods of determining the thickness of a biopolymer array substrate using a position sensitive device (PSD) component of a biopolymer array scanner.

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: An automated method and system for determining an optimal focus distance for scanning a molecular array by 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: A method and system for estimating a global background-signal correction for each channel of a microarray data set. The method and system of one embodiment of the present invention is directed to a method for calculating background corrected signals for a microarray data set by receiving a non-negative constant and selects a set of low-combined-intensity features from the microarray data set. Based on the low-combined-intensity features, a representation that describes a central-trend of the selected set of low-combined-intensity features is determined in signal-intensity space. The method adjusts the microarray data set parallel to the determined representation based on the non-negative constant.

Abstract: A set of chemical arrays held together by a common carrier with one or more arrays of the set having been previously exposed to a sample. In one embodiment the common carrier optionally includes an indication of locations along which the carrier should be separated so as to separate the set of chemical arrays into multiple sub-sets each with one or more arrays. A method of use may include separating the set of chemical arrays into multiple sub-sets each with one or more arrays.

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