Abstract: A multi-chambered deposition pin wash station is provided. The wash station includes a lower chamber and an upper drain basin connected by a plurality of wash tubes. Cleaning fluid is provided to the lower chamber and passes through the cleaning tubes into the upper drain basin. The cleaning tubes are adapted to clean a single deposition pin with a single tube per wash cycle.

Abstract: A multi-chambered deposition pin wash station is provided. The wash station includes a lower chamber and an upper drain basin connected by a plurality of wash tubes. Cleaning fluid is provided to the lower chamber and passes through the cleaning tubes into the upper drain basin. The cleaning tubes are adapted to clean a single deposition pin with a single tube per wash cycle.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Abstract: A multi-chambered deposition pin wash station is provided. The wash station includes a lower chamber and an upper drain basin connected by a plurality of wash tubes. Cleaning fluid is provided to the lower chamber and passes through the cleaning tubes into the upper drain basin. The cleaning tubes are adapted to clean a single deposition pin with a single tube per wash cycle.

Abstract: A multi-chambered deposition pin wash station is provided. The wash station includes a lower chamber and an upper drain basin connected by a plurality of wash tubes. Cleaning fluid is provided to the lower chamber and passes through the cleaning tubes into the upper drain basin. The cleaning tubes are adapted to clean a single deposition pin with a single tube per wash cycle.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Abstract: A multi-chambered deposition pin wash station is provided. The wash station includes a lower chamber and an upper drain basin connected by a plurality of wash tubes. Cleaning fluid is provided to the lower chamber and passes through the cleaning tubes into the upper drain basin. The cleaning tubes are adapted to clean a single deposition pin with a single tube per wash cycle.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Abstract: A multi-chambered deposition pin wash station is provided. The wash station includes a lower chamber and an upper drain basin connected by a plurality of wash tubes. Cleaning fluid is provided to the lower chamber and passes through the cleaning tubes into the upper drain basin. The cleaning tubes are adapted to clean a single deposition pin with a single tube per wash cycle.

Abstract: In one embodiment, a method for correcting feature overlap in biological probe array data is described that comprises (a) receiving a first set of data comprising an intensity value for each of a plurality of features associated with a probe array; (b) calculating a crosstalk parameter for the first set of data using the intensity values of one or more test features and a plurality of features that neighbor each test feature; and (c) applying the crosstalk parameter to each intensity value in the first set of data to produce a second set of data.

Abstract: A method of reconstructing a cell using a raw image of a biological probe array is described that comprises (a) assigning an intensity value to a reconstructed cell of a reconstructed image, where each reconstructed cell comprises a plurality of reconstructed pixels; (b) determining a weighted intensity value for each reconstructed pixel in the reconstructed cell using the intensity value of the reconstructed cell and a weight value; (c) determining an error value for each reconstructed pixel using the weighted intensity value and a raw intensity value corresponding to a pixel in the raw image; (d) updating the intensity value of the reconstructed cell using the error value; and (e) repeating steps (b)-(d) until convergence, wherein the intensity value for the reconstructed cell is representative of light emitted from a corresponding probe feature on the biological probe array.

Abstract: A probe array product is described that comprises a substrate that includes a plurality of biological probes disposed thereon, where at least one of the biological probes is enabled to hybridize a target molecule that comprises a detectable label; and a coating disposed upon a first surface of the substrate, where the coating is substantially reflective at a first wavelength range and is substantially transmissive at a second wavelength range.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Abstract: In one embodiment a method for reducing variation in a plurality of scanners is described. The method comprises directing an excitation beam at a calibration standard in each of the plurality of scanners, where one of the plurality of scanners is a designated scanner; detecting emission data for each of the plurality of scanners from a plurality of fluorescent molecules disposed on the calibration standard, where the emission data is responsive to the excitation beam; determining variation in the emission data of one or more of the plurality of scanners based, at least in part, upon the emission data of the designated scanner; and adjusting one or more parameters in one or more of the plurality of scanners based, at least in part, upon the determined variation.

Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.