Abstract: Apparatus and methods for controlling heating of an objective in a linescanning sequencing system to improve resolution are disclosed. In accordance with a first implementation, an apparatus includes or comprises a beam source for providing input radiation and a beam shaping group including or comprising one or more optical elements positioned to receive the input radiation from the beam source, and to perform beam shaping on the input radiation to form a shaped beam. The apparatus further including or comprising an objective positioned to receive the shaped beam and to transform the shaped beam into a probe beam and configured to provide the probe beam to a focal plane of the objective for optically probing a sample. The beam shaping group is configured to adjust one or more properties of the shaped beam over time to generally uniformly heat the objective over a region of incidence for the shaped beam.

Abstract: Apparatus and methods for transmitting light are disclosed. In an implementation, an apparatus includes a collimator at an input end positioned to receive an input beam from a fiber beam source and to produce a collimated beam. The apparatus further includes a beam shaping group having one or more optical elements and positioned to receive the collimated beam from the collimator and format the collimated beam into a shaped propagation beam having a substantially rectangular cross-section in a far field. The apparatus further includes an objective stage for optically probing a sample, such as a flow cell, using substantially rectangular cross-section sampling beam, where fluorescence from the sample is captured by a line sensor for detecting properties of the sample, such as chemical reactions therein.

Abstract: An apparatus includes a sample stage region, an optical assembly, and a camera assembly. The optical assembly includes an objective element, a tube lens, a first dichroic element, and a compensating element. The objective element provides a field of view including the object plane. The tube lens is configured to receive light transmitted through the objective element. The optical assembly is configured to transmit light in at least a first color channel, a second color channel, a third color channel, and a fourth color channel from the tube lens toward the first dichroic element. The first dichroic element is configured to transmit light of the first and third color channels while reflecting light of the second and fourth color channels. The compensating element is configured to induce an astigmatism in the first and third color channels offsetting an astigmatism induced by the dichroic element.

Abstract: Imaging systems and related methods are disclosed. In accordance with an implementation, a system includes a flow cell receptacle to receive a flow cell that receives a sample and an imaging system having a light source assembly, and an imaging device. The light source assembly to form a substantially collimated beam. The optical assembly including an asymmetric beam expander group that includes one or more asymmetric elements or anamorphic elements disposed along an optical axis. The optical assembly to receive the substantially collimated beam from the light source assembly, and transform the substantially collimated beam into a shaped sampling beam having an elongated cross section in a far field at or near a focal plane of the optical assembly to optically probe the sample. The imaging device to obtain image data associated with the sample in response to the optical probing of the sample with the sampling beam.

Abstract: An apparatus and method for imaging includes an imaging system formed of a movable objective stage proximal to a sample and positioned for providing an excitation beam onto and for capturing an emission from the sample. The movable objective stage includes an optical lens apparatus and a turn reflector optically coupled to the imaging optics, where at least one of the optical lens apparatus and the turn reflector are movable relative to one another for scanning the sample, and wherein the movement is achieved while maintaining a substantially fixed optical path length between the optical lens apparatus and a fixed plane in a fixed imaging optics stage.

Abstract: An apparatus and method for imaging includes an imaging system formed of a movable objective stage proximal to a sample and positioned for providing an excitation beam onto and for capturing an emission from the sample. The movable objective stage includes an optical lens apparatus and a turn reflector optically coupled to the imaging optics, where at least one of the optical lens apparatus and the turn reflector are movable relative to one another for scanning the sample, and wherein the movement is achieved while maintaining a substantially fixed optical path length between the optical lens apparatus and a fixed plane in a fixed imaging optics stage.

Abstract: Apparatus and methods for controlling heating of an objective in a linescanning sequencing system to improve resolution are disclosed. In accordance with a first implementation, an apparatus includes or comprises a beam source for providing input radiation and a beam shaping group including or comprising one or more optical elements positioned to receive the input radiation from the beam source, and to perform beam shaping on the input radiation to form a shaped beam. The apparatus further including or comprising an objective positioned to receive the shaped beam and to transform the shaped beam into a probe beam and configured to provide the probe beam to a focal plane of the objective for optically probing a sample. The beam shaping group is configured to adjust one or more properties of the shaped beam over time to generally uniformly heat the objective over a region of incidence for the shaped beam.

Abstract: An apparatus and method for imaging includes an imaging system formed of a movable objective stage proximal to a sample and positioned for providing an excitation beam onto and for capturing an emission from the sample. The movable objective stage includes an optical lens apparatus and a turn reflector optically coupled to the imaging optics, where at least one of the optical lens apparatus and the turn reflector are movable relative to one another for scanning the sample, and wherein the movement is achieved while maintaining a substantially fixed optical path length between the optical lens apparatus and a fixed plane in a fixed imaging optics stage.

Abstract: Apparatus and methods for transmitting light are disclosed. In an implementation, an apparatus includes a collimator at an input end positioned to receive an input beam from a fiber beam source and to produce a collimated beam. The apparatus further includes a beam shaping group having one or more optical elements and positioned to receive the collimated beam from the collimator and format the collimated beam into a shaped propagation beam having a substantially rectangular cross-section in a far field. The apparatus further includes an objective stage for optically probing a sample, such as a flow cell, using substantially rectangular cross-section sampling beam, where fluorescence from the sample is captured by a line sensor for detecting properties of the sample, such as chemical reactions therein.

Abstract: A scanning detection system is provided wherein emissions from locations in a flow cell are detected. In some embodiments, the system can comprise an excitation source, a photocleavage source, and modulating optics configured to cause an excitation beam generated by the excitation source to irradiate a first group of the fixed locations and to cause a photocleavage beam generated by the photocleavage source to irradiate a second group of the fixed locations, which is separate and apart from the first group of fixed locations. Methods of detecting sequencing reactions using such a system are also provided.

Abstract: A scanning detection system is provided wherein emissions from locations in a flow cell are detected. In some embodiments, the system can comprise an excitation source, a photocleavage source, and modulating optics configured to cause an excitation beam generated by the excitation source to irradiate a first group of the fixed locations and to cause a photocleavage beam generated by the photocleavage source to irradiate a second group of the fixed locations, which is separate and apart from the first group of fixed locations. Methods of detecting sequencing reactions using such a system are also provided.

Abstract: A scanning detection system is provided wherein emissions from locations in a flow cell are detected. In some embodiments, the system can comprise an excitation source, a photocleavage source, and modulating optics configured to cause an excitation beam generated by the excitation source to irradiate a first group of the fixed locations and to cause a photocleavage beam generated by the photocleavage source to irradiate a second group of the fixed locations, which is separate and apart from the first group of fixed locations. Methods of detecting sequencing reactions using such a system are also provided.

Abstract: The invention relates to an optical detection system for a thermal cycling device including at least one light source, a light detection device for detecting light received from a plurality of biological samples, and a lens having first and second surfaces formed on the lens, the second surface substantially opposed to the first surface. The first surface may be configured to collimate light and the second surface may be configured to direct light into each of the plurality of biological samples.

Abstract: A system is provided for performing filter-based and monochromator-based measurements. The system includes a light source and a plurality of detectors. An excitation monochromator outputs a selected wavelength component of the excitation light. Emitted light from a sample follows a selected emission optical path. An emission monochromator outputs a selected wavelength component of the emitted light when part of the selected path. An interface cartridge includes emission light ports positioned to direct the emitted light from the sample along a corresponding optical path. The interface cartridge aligns a selected optical path with the main measurement optical axis. A movable sliding switch mechanism provides optical channels corresponding to positions on the sliding switch mechanism to complete a selected emission optical path. The position on the sliding switch mechanism is selected by moving the sliding switch mechanism to align the optical channel for the position with the main measurement optical axis.

Abstract: A cover for a biological sample well tray, comprising a cap for sealing a sample well. The cap comprises a well lens for focusing light into the sample well and collecting light from the sample. In another aspect, the cap comprises an elongate portion configured to permit incoming light to pass into the sample well and out of the sample well. Various other aspects comprise a microcard for biological material, and an apparatus for a plurality of sample well strips. A method for testing a biological sample is also provided.

Abstract: A cover for a biological sample well tray, comprising a cap for sealing a sample well. The cap comprises a well lens for focusing light into the sample well and collecting light from the sample. In another aspect, the cap comprises an elongate portion configured to permit incoming light to pass into the sample well and out of the sample well. Various other aspects comprise a microcard for biological material, and an apparatus for a plurality of sample well strips. A method for testing a biological sample is also provided.

Abstract: A system is provided for performing filter-based and monochromator-based measurements. The system includes a light source and a plurality of detectors. An excitation monochromator outputs a selected wavelength component of the excitation light. Emitted light from a sample follows a selected emission optical path. An emission monochromator outputs a selected wavelength component of the emitted light when part of the selected path. An interface cartridge includes emission light ports positioned to direct the emitted light from the sample along a corresponding optical path. The interface cartridge aligns a selected optical path with the main measurement optical axis. A movable sliding switch mechanism provides optical channels corresponding to positions on the sliding switch mechanism to complete a selected emission optical path. The position on the sliding switch mechanism is selected by moving the sliding switch mechanism to align the optical channel for the position with the main measurement optical axis.

Abstract: The invention relates to an optical detection system for a thermal cycling device including at least one light source, a light detection device for detecting light received from a plurality of biological samples, and a lens having first and second surfaces formed on the lens, the second surface substantially opposed to the first surface. The first surface may be configured to collimate light and the second surface may be configured to direct light into each of the plurality of biological samples.

Abstract: A device for performing biological analysis may include at least one reaction chamber configured to receive at least one sample for biological analysis and a thermal system configured to modulate a temperature of the at least one reaction chamber to cycle a temperature of the at least one biological sample. The thermal system may include a cooling system configured to cool the at least one reaction chamber. The cooling system may include a cooling fluid source positioned distally from the at least one reaction chamber, the cooling fluid source being in flow communication with at least one conduit configured to flow cooling fluid from the cooling fluid source to at least one location in thermal communication with the at least one reaction chamber.

Abstract: Various embodiments described in the application relate to an apparatus, system, and method for fluidically controlling, within a conduit, discrete volumes of one or more fluids that are immiscible with a second fluid. The discrete volumes can be used for biochemical or molecular biology procedures involving small volumes, for example, microliter-sized volumes, nanoliter-sized volumes, or smaller. The system can comprise combinations of detectors, controllers, valves, and fluid supply units to control the spatial size, location and/or fluidic composition of discrete volumes separated from one another by a fluid that is immiscible with the fluid(s) of the discrete volumes, for example, aqueous immiscible-fluid-discrete volumes separated by an oil.