Abstract: An apparatus and method to compensate for under-corrected aberrations computationally is disclosed. The system includes an excitation radiation source that emits an excitation beam that is focused on a flow cell surface. More specifically, the excitation beam is focused on either an upper surface, a lower surface, or in a channel between the upper and lower surfaces of the flow cell. As imaging both the upper and lower surfaces simultaneously will result in aberration in at least one of the upper and lower surfaces, aberration correction is useful for dual surface imaging. A processor is configured to determine base calls of irradiated sites that fluoresce within the flow cell. An aberration compensation model is trained to compensate for aberrations in at least one image or image data corresponding to the upper surface, the lower surface, or the channel between the upper and lower surfaces.

Abstract: AI-driven enhancement of low-resolution images enables sequencing of a nucleic acid material under low-resolution conditions with requisite accuracy and improved cost and operational efficiency. A training set of images obtained under actual or simulated high-resolution and low-resolution conditions is used to train a model to recover enhanced images, as if taken under high resolution conditions, from unenhanced images taken under low resolution conditions.

Abstract: A method for extending a depth of field of a nucleic acid sequencer may comprise optimization steps which are repeated one or more times, in which a result of passing light through an objective lens and a mask is compared with an ideal result, and any discrepancy is used to update the mask. Such a mask may be incorporated into a nucleic acid sequencer which adds fluorescent tags to nucleic acid sites and then detect light emitted from the fluorescent tags, thereby extending the sequencer's depth of field.

Abstract: Some implementations of the disclosure describe an imaging instrument, including: an image sensor to image a sample; and one or more processors configured to cause the imaging instrument to: obtain surface profile data of a swath of the sample, the swath divided into multiple regions, and the surface profile data including surface profile data for each region; calculate, based at least on a threshold residual and the surface profile data of the swath, one or more zones of the swath that include the multiple regions, each zone including a respective one or more of the regions that are adjacent; and associate, based on the surface profile data of the one or more regions of each zone, a detilt or detip value with each zone, the detilt or detip value indicating an amount to adjust, before imaging the zone, a relative tilt or tip between the sample and image sensor.

Abstract: Artificial intelligence driven enhancement of motion blurred sequencing images enables enhanced sequencing that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken after unreduced and reduced movement settling times during sequencing is used to train a neural network to enable the neural network to recover enhanced images, as if taken after the unreduced movement settling time, from unenhanced images taken after the reduced movement settling time.

Abstract: Some implementations of the disclosure relate to a method including: obtaining surface profile data of a swath of a sample, the swath divided into multiple tiles, and the surface profile data including surface profile data for each tile; calculating, based at least on a threshold residual and the surface profile data of the swath, one or more zones of the swath that include the multiple tiles, each zone including a respective one or more of the tiles that are adjacent; and associating, based on the surface profile data associated with the one or more tiles of each zone, a detilt value or detip value with each zone, the detilt value or detip value indicating an amount to adjust, before capturing one or more images of the zone, a relative tilt or tip between the sample and an image sensor of an imaging system capturing the one or more images.

Abstract: A method for extending a depth of field of a nucleic acid sequencer may comprise optimization steps which are repeated one or more times, in which a result of passing light through an objective lens and a mask is compared with an ideal result, and any discrepancy is used to update the mask. Such a mask may be incorporated into a nucleic acid sequencer which adds fluorescent tags to nucleic acid sites and then detect light emitted from the fluorescent tags, thereby extending the sequencer's depth of field.

Abstract: Some implementations of the disclosure relate to a method including: obtaining surface profile data of a swath of a sample, the swath divided into multiple tiles, and the surface profile data including surface profile data for each tile; calculating, based at least on a threshold residual and the surface profile data of the swath, one or more zones of the swath that include the multiple tiles, each zone including a respective one or more of the tiles that are adjacent; and associating, based on the surface profile data associated with the one or more tiles of each zone, a detilt value or detip value with each zone, the detilt value or detip value indicating an amount to adjust, before capturing one or more images of the zone, a relative tilt or tip between the sample and an image sensor of an imaging system capturing the one or more images.

Abstract: A method for extending a depth of field of a nucleic acid sequencer may comprise optimization steps which are repeated one or more times, in which a result of passing light through an objective lens and a mask is compared with an ideal result, and any discrepancy is used to update the mask. Such a mask may be incorporated into a nucleic acid sequencer which adds fluorescent tags to nucleic acid sites and then detect light emitted from the fluorescent tags, thereby extending the sequencer's depth of field.

Abstract: Defocus is introduced during sequencing by synthesis by tilt of a flow cell and by variations in flatness of the flow cell. Effects of the defocus are reduced, and base calling quality is improved using techniques relating to dependence of base calling on flow cell tilt. For example, the flow cell surface height is measured throughout the flow cell. A focal height of an imager having a sensor for the sequencing is set, optionally adaptively, one or more times during the sequencing. Each image captured by the sensor is partitioned, e.g., based on differences between focal height and the measured flow cell surface height across areas of the sensor. Filters, e.g., related to defocus correction, are selected based at least in part on the difference between the focal height and the measured flow cell surface height at a particular area of the image being corrected for defocus.

Abstract: Artificial intelligence driven signal enhancement of sequencing images enables enhanced sequencing by synthesis that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken at unreduced and reduced power levels used to excite fluorescence during sequencing by synthesis is used to train a neural network to enable the neural network to recover enhanced images, as if taken at the unreduced power level, from unenhanced images taken at the reduced power level.

Abstract: Artificial intelligence driven enhancement of motion blurred sequencing images enables enhanced sequencing that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken after unreduced and reduced movement settling times during sequencing is used to train a neural network to enable the neural network to recover enhanced images, as if taken after the unreduced movement settling time, from unenhanced images taken after the reduced movement settling time.

Abstract: A rotation apparatus for a dish antenna provides a system for easily adjusting the dish antenna to a precise receiving position. The rotation apparatus includes a dish bracket which is fixed to the back of the dish antenna. The dish bracket includes a plurality of circular grooves and a concentric axle center. An elevation bracket includes a pair of wings and a bottom. The wings are parallel, and the bottom is perpendicular to the wings. Each wing pivots about an axle which passes through a first portion of each wing. A second portion of each wing includes a guide groove to adjust a elevation angle of the dish. The bottom includes a central axle hole and a plurality of holes. The central axle hole is coupled to the concentric axle center. After the dish is rotated to a selected position, the plurality of holes are secured to the circular grooves using a plurality of screws.

Abstract: A rotation apparatus for a dish antenna provides a system for easily adjusting the dish antenna to a precise receiving position. The rotation apparatus includes a dish bracket which is fixed to the back of the dish antenna. The dish bracket includes a plurality of circular grooves and a concentric axle center. An elevation bracket includes a pair of wings and a bottom. The wings are parallel, and the bottom is perpendicular to the wings. Each wing pivots about an axle which passes through a first portion of each wing. A second portion of each wing includes a guide groove to adjust a elevation angle of the dish. The bottom includes a central axle hole and a plurality of holes. The central axle hole is coupled to the concentric axle center. After the dish is rotated to a selected position, the plurality of holes are secured to the circular grooves using a plurality of screws.

Abstract: A rotation apparatus for a dish antenna provides a system for easily adjusting the dish antenna to a precise receiving position. The rotation apparatus includes a dish bracket which is fixed to the back of the dish antenna. The dish bracket includes a plurality of circular grooves and a concentric axle center. An elevation bracket includes a pair of wings and a bottom. The wings are parallel, and the bottom is perpendicular to the wings. Each wing pivots about an axle which passes through a first portion of each wing. A second portion of each wing includes a guide groove to adjust a elevation angle of the dish. The bottom includes a central axle hole and a plurality of holes. The central axle hole is coupled to the concentric axle center. After the dish is rotated to a selected position, the plurality of holes are secured to the circular grooves using a plurality of screws.