Abstract: Methods and apparatus, including computer program products, implementing and using techniques for collecting optical data pertaining to one or more characteristics of a sample. The apparatus has a light source, one or more illumination optical elements, a scanner, one or more collection optical elements, and a device forming an aperture that limits detection of light from the sample. The illumination optical elements direct a light beam from the light source onto the sample. The scanner scans the light beam across the sample. The collection optical elements collect light from the sample and transmit the collected light to a detector. None of the collection optical elements are included among the illumination optical elements. The device forming an aperture limits detection of light from the sample to light associated with a limited vertical depth within the sample, and is one of the collection optical elements.

Abstract: Methods and apparatus are described for detecting specific binding between first and second chemical entities. The first chemical entity in association with a first fluorophore is immobilized. The second chemical entity is allowed to bind with the immobilized first chemical entity. The second chemical entity is or becomes coupled to a second fluorophore, which forms a FRET pair with the first fluorophore. The bound chemical entities are exposed to radiation at an excitation frequency for either the first or the second fluorophore, and polarization anisotropy of a FRET fluorescent signal from the bound chemical entities is measured to detect specific binding between the first and second chemical entities.

Abstract: Methods and apparatus for performing scatterometry measurements of biological samples as described herein. A substrate having formed therein one or more sample wells is provided. Each sample well is configured to hold a sample solution containing objects that are to be characterized based on their light scattering properties. One or more sample solutions are dispensed into the sample wells. A specular reflection reducing element is applied to at least some of the sample solutions in the sample wells to decrease reflections of light into one or more detectors. A light beam is directed from a light source onto the objects in the sample wells. Light scattered by the objects in the sample wells is collected and transmitted to one or more detectors. The signal from the detectors is analyzed to detect the one or more characteristics of the one or more samples.

Abstract: Methods and apparatus, including computer program products, implementing and using techniques for collecting optical data pertaining to one or more characteristics of a sample. A light beam of a first frequency is scanned onto a sample surface using one or more illumination optical elements. Light of a second frequency is collected from a scan line on the sample surface using one or more collection optical elements. None of the one or more collection optical elements are included among the one or more illumination optical elements. The collected light is transmitted to a detector.

Abstract: Methods, apparatus, and system, implementing and using techniques for detecting a presence of one or more target analytes in particular regions of interest of one or more samples. One or more samples including objects and one or more target analytes are provided. Some of the target analytes are labeled with a fluorophore and are bound to some of the objects in the samples. The samples are illuminated with fluorescence inducing light and fluorescent light is collected from one or more regions of the one or more samples. At least one anisotropy measurement of the samples is performed to identify regions of interest where one or more target analytes are bound to the objects. The collected fluorescent light from the regions of interest is analyzed to determine a presence of target analytes that are bound to the objects in the one or more samples.