Abstract: An autofocus apparatus is capable of detecting the position of a sample on a microscope. The sample may consist of a specimen mounted between a microscope slide and coverslip or specimens within a well plate. The device tracks the position of a sample by identifying refractive index boundaries through Fresnel reflections. A change in refractive index can correspond to the top and bottom of a coverslip, the top of a slide, the bottom of a well plate or the bottom of a well within a well plate. Using optical coherence tomography (OCT) these reflections are used to form a depth scan of the sample which gives the positions of these surfaces relative to the objective. The device functions as an autofocus system by compensating for any variation of the position of the sample from the focal plane of the objective.

Abstract: A tunable source includes a short-cavity laser optimized for performance and reliability in SSOCT imaging systems, spectroscopic detection systems, and other types of detection and sensing systems. The short cavity laser has a large free spectral range cavity, fast tuning response and single transverse, longitudinal and polarization mode operation, and includes embodiments for fast and wide tuning, and optimized spectral shaping. Disclosed are both electrical and optical pumping in a MEMS-VCSEL geometry with mirror and gain regions optimized for wide tuning, high output power, and a variety of preferred wavelength ranges; and a semiconductor optical amplifier, combined with the short-cavity laser to produce high-power, spectrally shaped operation. Several preferred imaging and detection systems make use of this tunable source for optimized operation are also disclosed.

Abstract: A method for correcting images acquired via an asynchronous triggered acquisition, wherein image acquisition is triggered by a trigger signal based on the motion and/or position of the sample to be imaged by an image sensor, the method including: measurement of the motion and/or position of the sample; determination of an exposure time based on the aforementioned measurement; and correction of an acquired image based on the determined exposure time and a desired exposure time.

Abstract: An amplified tunable source includes a short-cavity laser coupled to an optical amplifier for high power, spectrally shaped operation. The short-cavity laser is coupled to a quantum well semiconductor optical amplifier with two quantum states for broadened gain. Two preferred wavelength ranges of the amplified tunable source include 1200-1400 nm and 800-1100 nm. Also disclosed is the short cavity tunable laser coupled to a fiber amplifier. Various combinations of tunable optical filters with the amplified tunable source to reduce noise or improve spectral purity are presented.

Abstract: A method for operating a focal plane array in a Time Delay Integration (TDI) mode, the method including: shifting a number of rows during TDI integration, wherein the number of rows shifted is less than a total number of rows of the focal plane array; and reading out a number of rows equal to the total number of rows of the focal plane array minus the number of rows shifted, leaving behind the partially-integrated rows.

Abstract: Optical systems employ a tunable source which includes a short cavity laser with a large free spectral range cavity, fast tuning response, and single transverse and longitudinal mode operation. Systems for optical spectroscopy with optimized scanning, a system for optical beam steering and a system for a tunable local oscillator are disclosed.

Abstract: A tunable source includes a short-cavity laser optimized for performance and reliability in SSOCT imaging systems, spectroscopic detection systems, and other types of detection and sensing systems. A short cavity laser with a large free spectral range cavity, fast tuning response and single transverse, longitudinal and polarization mode operation is disclosed. Methods for obtaining polarization stable operation of the tunable source are presented.

Abstract: A method for matching one or more channels to a reference channel in a multiple-channel detector having a digital output, the method including: receiving an analog-to-digital unit (ADU) input value from the multiple-channel detector for each channel; and replacing the ADU input value by an output value corresponding to each channel from a look up table (LUT); wherein the LUT is created by taking a relative intensity ratio of signals from each channel compared to the reference channel over a range of voltage values; calculating a signal value on the detector that generates a specific ADU value across the entire ADU range of the detector; interpolating the relative intensity ratios to obtain ratios corresponding to the calculated signal values for each channel; and dividing the each of the specific ADU value by the corresponding interpolated ratio to obtain the corresponding output value for each channel.

Abstract: Apparatus and methods are described herein for cleaving an optical element at a defined distance from a splice (or other reference point/feature) of the optical element within a desired precision and/or accuracy. In some embodiments, a method includes receiving an indication of a location of a feature in an intermediate optical assembly visible within an image of the intermediate optical assembly. The feature can be for example, a splice. A position of the intermediate optical assembly is translated relative to a cleave unit based on the indication. After translating, the intermediate optical assembly, the intermediate optical assembly is cleaved to form an optical assembly that has an end face at a location disposed at a non-zero distance from the location of the feature. In some embodiments, the location of the feature can be determined with an image recognition system.

Abstract: An adaptive optics scanning system using a beam projection module with four or more axes of motion that can project and control the position and angle of a beam of light to or from an adaptive optics element. The adaptive optics scanning system is compact in size, overcoming the challenges of a traditional lens and mirror based pupil relay design. The adaptive optics scanning system has little to no dispersion, chromatic aberration, and off-axis aberration for improved optical performance. The system and methods for calibrating and optimizing the system are described. A modular adaptive optics unit that scans and interfaces an adaptive optics element is described.

Abstract: An autofocus apparatus includes, in one embodiment, a light source; a splitter; a fiber optic circulator; an optical collimator; a balance detector; and a microprocessor. The fiber optic circulator couples one of the split light signals at a first port, to the optical collimator at a second port, and to the balance detector at the third port. The optical collimator directs the light beam from the fiber optic circulator onto a sample through a Dichroic mirror and a microscope objective. The balance detector uses another one of the split light signals as an input, and converts a light signal, reflected off of a substrate the sample is placed on, into an analog voltage signal. The microprocessor processes the output of the balance detector and position feedbacks from an adjustable microscopy stage to generate a command for moving the position of the adjustable microscopy stage to achieve a desired focus.

Abstract: An autofocus apparatus includes a light source; an optical coupler having a first port, second port and a third port; wherein the optic coupler couples to the light source at the first port; an optical collimator for directing a light output from the second port of the optical coupler onto a sample through a Dichroic mirror and a microscope objective, wherein the sample is placed on a substrate supported by an adjustable microscopy stage; a scanning device for focusing the light at a plurality of focal points along an axis; a photodiode detector for converting a reflected light signal into an intensity signal; a memory device for storing a signal template; and a microprocessor for detecting a peak in the intensity signal by cross-correlating the intensity signal with the signal template; wherein the microprocessor generates a command for moving the position of the adjustable microscopy stage along the axis.

Abstract: An optical imaging system includes an optical radiation source (410, 510), a frequency clock module outputting frequency clock signals (420), an optical interferometer (430), a data acquisition (DAQ) device (440) triggered by the frequency clock signals, and a computer (450) to perform multi-dimensional optical imaging of the samples. The frequency clock signals are processed by software or hardware to produce a record containing frequency-time relationship of the optical radiation source (410, 510) to externally clock the sampling process of the DAQ device (440). The system may employ over-sampling and various digital signal processing methods to improve image quality. The system further includes multiple stages of routers (1418, 1425) connecting the light source (1410) with a plurality of interferometers (1420a-1420n) and a DAQ system (1450) externally clocked by frequency clock signals to perform high-speed multi-channel optical imaging of samples.

Abstract: A system for swept source optical coherence tomography, the system including a light source emitting multiplexed wavelength-swept radiation over a total wavelength range, the light source including N wavelength-swept vertical cavity lasers (VCL) emitting N tunable VCL outputs having N wavelength trajectories, a combiner for combining the N tunable VCL optical outputs into a common optical path to create the multiplexed wavelength-swept radiation, a splitter for splitting the multiplexed wavelength-swept radiation to a sample and a reference path, an optical detector for detecting an interference signal created by an optical interference between a reflection from the sample and light traversing the reference path, and a signal processing system which uses the interference signal to construct an image of the sample, wherein at least one of the N wavelength trajectories differs from another of the N wavelength trajectories with respect to at least one parameter.

Abstract: A high-speed, single-mode, high power, reliable and manufacturable wavelength-tunable light source operative to emit wavelength tunable radiation over a wavelength range contained in a wavelength span between about 950 nm and about 1150 nm, including a vertical cavity laser (VCL), the VCL having a gain region with at least one compressively strained quantum well containing Indium, Gallium, and Arsenic.

Abstract: An optical mount is disclosed having at least one restraining element for an optic having at least one contact point with a first surface of the optic and at least one force element having at least one contact point with a second surface of the optic, wherein each contact point on the first surface of the optic has a corresponding contact point on the second surface of the optic.

Abstract: A shutter assembly comprises a plurality of shutter blades movable between an open position and a closed position, and a plurality of drive mechanisms arranged circumferentially about the plurality of shutter blades for moving the plurality of shutter blades, wherein each of said drive mechanisms is stable in at least a first position and a second position.

Abstract: An optical imaging system includes an optical radiation source, a frequency clock module outputting frequency clock signals, an optical interferometer, a data acquisition (DAQ) device triggered by the frequency clock signals, and a computer to perform multi-dimensional optical imaging of the samples. The frequency clock signals are processed by software or hardware to produce a record containing frequency-time relationship of the optical radiation source to externally clock the sampling process of the DAQ device. The system may employ over-sampling and various digital signal processing methods to improve image quality. The system further includes multiple stages of routers connecting the light source with a plurality of interferometers and a DAQ system externally clocked by frequency clock signals to perform high-speed multi-channel optical imaging of samples.

Abstract: An adaptive optics scanning system using a beam projection module with four or more axes of motion that can project and control the position and angle of a beam of light to or from an adaptive optics element. The adaptive optics scanning system is compact in size, overcoming the challenges of a traditional lens and mirror based pupil relay design. The adaptive optics scanning system has little to no dispersion, chromatic aberration, and off-axis aberration for improved optical performance. The system and methods for calibrating and optimizing the system are described. A modular adaptive optics unit that scans and interfaces an adaptive optics element is described.

Abstract: A method for operating a focal plane array in a Time Delay Integration (TDI) mode, the method including: shifting a number of rows during TDI integration, wherein the number of rows shifted is less than a total number of rows of the focal plane array; and reading out a number of rows equal to the total number of rows of the focal plane array minus the number of rows shifted, leaving behind the partially-integrated rows.