Double-layer focal plane microscopy for high throughput DNA sequencing.

Throughput is one of the most important properties in DNA sequencing. We propose a novel double-layer focal plane microscopy that doubles the DNA sequencing throughput. Each fluorescence channel is divided into two tube lens channels by energy splitting, and the camera is adjusted to take images corresponding to different defocus positions of the objective, thus doubling the information capacity of the microscopy. The microscopy is applied to gene chip, which has high spatial frequency and good uniformity, so the simultaneous imaging of the two tubes has little influence on each other due to the spatial averaging effect. Experimental results show that the image signal to noise ratio (SNR) is reduced by 1%, while the sequencing throughput is doubled.

Improvement in focusing accuracy of DNA sequencing microscope with multi-position laser differential confocal autofocus method.

High focusing accuracy in microscopes could improve the imaging quality to reduce the error rate in DNA sequencing. We propose a new feedback method to improve the focusing condition to a very high accuracy. A reference laser reflected by the sample is detected by two or more sensors around the confocal point. After acquiring the signals from the out-of-focus positions, online data processing is implemented to provide feedbacks for real-time focus-plane locking on the sample surface. This method provides an accuracy better than 1/10 of the objective depth-of-focus. To balance optical aberrations, a specific optical feedback system should be designed, with athermal design considerations to adapt DNA sequencing work to temperature fluctuations.

Experimental investigation in nodal aberration theory (NAT) with a customized Ritchey-Chrétien system: third-order coma.

Nodal aberration theory (NAT) describes the aberration properties of optical systems without symmetry. NAT was fully described mathematically and investigated through real-ray tracing software, but an experimental investigation is yet to be realized. In this study, a two-mirror Ritchey-Chrétien telescope was designed and built, including testing of the mirrors in null configurations, for experimental investigation of NAT. A feature of this custom telescope is a high-precision hexapod that controls the secondary mirror of the telescope to purposely introduce system misalignments and quantify the introduced aberrations interferometrically. A method was developed to capture interferograms for multiple points across the field of view without moving the interferometer. A simulation result of Fringe Zernike coma was generated and analyzed to provide a direct comparison with the experimental results. A statistical analysis of the measurements was conducted to assess residual differences between simulations and experimental results. The interferograms were consistent with the simulations, thus experimentally validating NAT for third-order coma.

High-accuracy measurement of the focal length and distortion of optical systems based on interferometry.

A figure measuring interferometer (FMI) method is proposed for high-accuracy measurement of the focal length and distortion of optical systems simultaneously. FMI uses the Zernike coefficients of interference fringe to identify the image point position precisely, and then measures the distance between the image points under the different fields to determine the image height. The field of view can also be accurately obtained by a precise rotating platform. Linear fitting between the field of view and the image height is used to calculate the focal length and distortion. The experimental results indicate that FMI has a relative expanded standard uncertainty of less than 0.01% for focal length and 0.02% for distortion. In brief, the proposed method is feasible for measurement of the focal length and distortion with high accuracy, promising further industrial applications.

Active lens for thermal aberration compensation in lithography lens.

High laser absorption and strong resolution enhancement technology make thermal aberration control of lithography lenses more challenging. We present an active lens that uses four bellows actuators to generate astigmatism (Z5) on the lens surface. The apparatus utilizes optical path difference to compensate the system wavefront. In order to assess the specifications of the compensator, the finite element method and experimental analyses are carried out to obtain and validate the general properties of the apparatus. The results show that the Z5 deformation quantity of lens's upper surface exceeds 600 nm; further, Z5 coefficient accuracy is better than ±1 nm. The apparatus can be an efficient compensator for thermal aberration compensation, especially aberration caused by the dipole illumination.

Internal stray radiation measurement for cryogenic infrared imaging systems using a spherical mirror.

Internal stray radiation is a key factor that influences infrared imaging systems, and its suppression level is an important criterion to evaluate system performance, especially for cryogenic infrared imaging systems, which are highly sensitive to thermal sources. In order to achieve accurate measurement for internal stray radiation, an approach is proposed, which is based on radiometric calibration using a spherical mirror. First of all, the theory of spherical mirror design is introduced. Then, the calibration formula considering the integration time is presented. Following this, the details regarding the measurement method are presented. By placing a spherical mirror in front of the infrared detector, the influence of internal factors of the detector on system output can be obtained. According to the calibration results of the infrared imaging system, the output caused by internal stray radiation can be acquired. Finally, several experiments are performed in a chamber with controllable inside temperatures to validate the theory proposed in this paper. Experimental results show that the measurement results are in good accordance with the theoretical analysis, and demonstrate that the proposed theories are valid and can be employed in practical applications. The proposed method can achieve accurate measurement for internal stray radiation at arbitrary integration time and ambient temperatures. The measurement result can be used to evaluate whether the suppression level meets the system requirement.

Generation of coherent and incoherent Airy beam arrays and experimental comparisons of their scintillation characteristics in atmospheric turbulence.

We investigate, through numerical calculation and experiments, the incoherent combination of a 2D Airy beam array (ICCAB) and the coherent combination of a 2D Airy beam array (CCAB), respectively. Excellent experimental results are obtained for both ICCAB and CCAB. The on-axis scintillation indices of ICCAB and CCAB at the receiver plane in atmospheric turbulence are also compared experimentally. It is shown that ICCAB has a smaller scintillation index than that of CCAB in the same turbulent condition due to the coherence reduction of the constituent beamlets. The results obtained in this paper are useful for the development of beam propagation through atmosphere turbulence.

Design, fabrication, and verification of a three-dimensional autocollimator.

The autocollimator is an optical instrument for noncontact angle measurement with high resolution and a long detection range. It measures two-dimensional angles, i.e., pitch and yaw, but not roll. In this paper, we present a novelly structured autocollimator capable of measuring three-dimensional (3D) angles simultaneously. In this setup, two collimated beams of different wavelengths are projected onto a right-angle prism. One beam is reflected by the hypotenuse of the prism and received by an autocollimation unit for detecting pitch and yaw. The other is reflected by the two legs of the right-angle prism and received by a moiré fringe imaging unit for detecting roll. Furthermore, a prototype is designed and fabricated. Experiments are carried out to evaluate its basic performance. Calibration results show that this prototype has angular RMS errors of less than 5 arcsec in all 3Ds over a range of 1000 arcsec at a working distance of 2 m.

Improved method to fully compensate the spatial phase nonuniformity of LCoS devices with a Fizeau interferometer.

Liquid crystal on silicon (LCoS) devices usually show spatial phase nonuniformity (SPNU) in applications of phase modulation, which comprises the phase retardance nonuniformity (PRNU) as a function of the applied voltage and inherent wavefront distortion (WFD) introduced by the device itself. We propose a multipoint calibration method utilizing a Fizeau interferometer to compensate SPNU of the device. Calibration of PRNU is realized by defining a grid of 3×6 cells onto the aperture and then calculating phase retardance of each cell versus a gradient gray pattern. With designing an adjusted gray pattern calculated by the calibrated multipoint phase retardance function, compensation of inherent WFD is achieved. The peak-to-valley (PV) value of the residual WFD compensated by the multipoint calibration method is significantly reduced from 2.5λ to 0.140λ, while the PV value of the residual WFD after global calibration is reduced to 0.364λ. Experimental results of the generated finite-energy 2D Airy beams in Fourier space demonstrate the effectiveness of this multipoint calibration method.

High-precision compliant mechanism for lens XY micro-adjustment.

The high resolution of lithography lenses has led to a requirement for high-precision lens-adjusting compensators. This paper presents the design, analysis, and testing of a high-precision two-degrees-of-freedom compliant mechanism to be used for lens XY micro-adjustment. The monolithic mechanism, which is based on a 1RR-2RRR configuration, uses flexure hinges to connect the movable inner ring with the fixed outer ring. The apparatus is driven using two piezoelectric actuators, and the lens terminal displacement is fed back in real time using two capacitive sensors. This paper describes the principle of the mechanism. Simulations and experiments are then performed to evaluate the system. The results show that the strokes along both the x-axis and the y-axis exceed ±25 µm. The accuracy of the proposed mechanism is better than ±7 nm. The root-mean-square induced figure error is better than 0.051 nm. The coupling z and tip/tilt rigid motions are less than 50 nm and 220 mas, respectively. The first natural frequency of the mechanism is 212 Hz. These results indicate that the mechanism has advantages that include high accuracy, low coupling errors, high rigidity, and compactness and that it will act as an efficient compensator for lithography lenses.