Abstract: A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention.

Abstract: An optical system configured to detect optical signals during imaging sessions. The optical system includes an objective lens that has a collecting end that is positioned proximate to a sample and configured to receive optical signals therefrom. The optical system also includes a removable path compensator that is configured to be located at an imaging position between the collecting end of the objective lens and the sample. The path compensator adjusts an optical path of the light emissions when in the imaging position. Also, the optical system includes a transfer device that is configured to move the path compensator. The transfer device locates the path compensator at the imaging position for a first imaging session and removes the path compensator from the imaging position for a second imaging session.

Abstract: The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.

Abstract: The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.

Abstract: A cluster internal routing network for use in a programmable logic device with a cluster-based architecture employs a Clos network-based routing architecture. The routing architecture is a multi-stage blocking architecture, where the number of inputs to the first stage exceeds the number of outputs from the first stage.

Abstract: A logic cluster for a field programmable gate array integrated circuit device is disclosed. The cluster comprises a plurality of functional blocks and three levels of routing multiplexers. External signals enter the logic cluster primarily at the third level multiplexers with a few signals entering at the second level. Combinational outputs are fed back into the first and second level multiplexers while sequential outputs are fed back into the third level multiplexers. The logic function generators have permutable inputs with varying propagation delays. Routing signals between the first and second level multiplexers are grouped into speed classes and coupled to first level multiplexers associated with different logic function generators according to their speed class. Second and third level multiplexers are organized into groups such that routing signals between the second and third level multiplexers can be localized within the area occupied by the group.

Abstract: A logic module for an FPGA includes a LUT formed from an N-level tree of 2:1 multiplexers. Each of the N inputs to the LUT is connected to the select inputs of the multiplexers in one level of the tree. Each of the data inputs at the leaves of the tree is driven by a configuration memory cell that produces either a logic 0 or a logic 1. The output of the single multiplexer at the last level of the tree forms a Y output and is coupled to one input of an XOR gate and to the select input of a two-input carry multiplexer. The 0 input of the carry multiplexer is coupled to a G input. A CI input is coupled to the other input of the XOR gate and to the 1 input of the carry multiplexer.

Abstract: Systems and methods for facilitating focusing of an image scanner, such as a confocal microscope, are disclosed. Measurement of optical characteristics in certain areas of a test sample are compared to stored or baseline optical characteristic profiles to determine an appropriate correction to properly focus the scanner. In one aspect, the method includes obtaining a dynamic profile at a current detection region of a test sample and associating the dynamic profile to a profile selected from a set of stored baseline profiles. Each of the stored baseline profiles is associated with a correction.

Abstract: A line scanning arrangement for imaging microarrays includes a line illuminator that converts output from one or more lasers to a radiation line. The laser output passes through a single mode fiber and a module that converts the laser light to the radiation line. The line is confocally directed to sites on the microarray, and retrobeams returned from the sites are collected on an imaging detector. The microarray is moved in the imaging apparatus so as to progressively illuminate an array or matrix of sites for imaging.

Abstract: A logic module for an FPGA includes a LUT formed from an N-level tree of 2:1 multiplexers. Each of the N inputs to the LUT is connected to the select inputs of the multiplexers in one level of the tree. Each of the data inputs at the leaves of the tree is driven by a configuration memory cell that produces either a logic 0 or a logic 1. The output of the single multiplexer at the last level of the tree forms a Y output and is coupled to one input of an XOR gate and to the select input of a two-input carry multiplexer. The 0 input of the carry multiplexer is coupled to a G input. A CI input is coupled to the other input of the XOR gate and to the 1 input of the carry multiplexer.

Abstract: Systems and methods for facilitating focusing of an image scanner, such as a confocal microscope, are disclosed. Measurement of optical characteristics in certain areas of a test sample are compared to stored or baseline optical characteristic profiles to determine an appropriate correction to properly focus the scanner. In one aspect, the method includes obtaining a dynamic profile at a current detection region of a test sample and associating the dynamic profile to a profile selected from a set of stored baseline profiles. Each of the stored baseline profiles is associated with a correction.

Abstract: The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.

Abstract: A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may, for instance, be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The captured and detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection (TIR) methods may benefit from the techniques of the present invention.

Abstract: The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.

Abstract: An interconnect architecture for a programmable logic device comprises a plurality of interconnect routing lines. The data inputs of a plurality of first-level multiplexers are connected to the plurality of interconnect routing lines such that each interconnect routing line is connected to only one multiplexer. A plurality of second-level multiplexers are organized into multiplexer groups. Each of a plurality of lookup tables is associated with one of the multiplexer groups and has a plurality of lookup table inputs. Each lookup table input is coupled to the output of a different one of the second-level multiplexers in the one of the multiplexer groups with which it is associated. The data inputs of the second-level multiplexers are connected to the outputs of the first-level multiplexers such that each output of each first-level multiplexer is connected to an input of only one second-level multiplexer in each multiplexer group.

Abstract: The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.

Abstract: An interconnect architecture for a programmable logic device comprises a plurality of interconnect routing lines. The data inputs of a plurality of first-level multiplexers are connected to the plurality of interconnect routing lines such that each interconnect routing line is connected to only one multiplexer. A plurality of second-level multiplexers are organized into multiplexer groups. Each of a plurality of lookup tables is associated with one of the multiplexer groups and has a plurality of lookup table inputs. Each lookup table input is coupled to the output of a different one of the second-level multiplexers in the one of the multiplexer groups with which it is associated. The data inputs of the second-level multiplexers are connected to the outputs of the first-level multiplexers such that each output of each first-level multiplexer is connected to an input of only one second-level multiplexer in each multiplexer group.

Abstract: A line scanning arrangement for imaging microarrays includes a line illuminator that converts output from one or more lasers to a radiation line. The laser output passes through a single mode fiber and a module that converts the laser light to the radiation line. The line is confocally directed to sites on the microarray, and retrobeams returned from the sites are collected on an imaging detector. The microarray is moved in the imaging apparatus so as to progressively illuminate an array or matrix of sites for imaging.

Abstract: The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.

Abstract: The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.