Various embodiments for a multi-focal selective illumination microscopy (SIM) system for generating multi-focal patterns of a sample are disclosed. The multi-focal SIM system performs a focusing, scaling and summing operation on each generated multi-focal pattern in a sequence of multi-focal patterns that completely scan the sample to produce a high resolution composite image.

The present invention provides a light-field microscope including: an illumination optical system that radiates excitation light onto a sample; and a detection optical system including an objective lens that collects fluorescence generated in the sample as a result of the sample being irradiated with the excitation light by the illumination optical system, an image-acquisition element that acquires an image of the fluorescence collected by the objective lens, and a microlens array disposed between the image-acquisition element and the objective lens. The illumination optical system radiates a beam of the excitation light having a predetermined width in the optical-axis direction of the objective lens so as to include the focal plane of the objective lens onto the sample in a direction substantially perpendicular to the optical axis.

An optical system including a first light source, a first lens, and a light splitting module, wherein the light splitting module has a first splitter, a second lens, a first camera and a second camera, the first lens is configured for receiving a first light beam from the first light source and collimating the first light beam onto a sample, and for receiving and collimating a light beam from the sample, the second lens is configured for focusing the collimated light beam from the first lens to the first camera and the second camera, the first splitter is configured for splitting the focused light beam from the second lens into a second light beam and a third light beam, the first camera is configured for receiving the second light beam, and the second camera is configured for receiving the third light beam.

A biological analysis system can include an excitation module and an emission module. The excitation module can include a collimator element for receiving excitation light from the excitation light source and transmitting collimated excitation light in a first direction, and a plurality of excitation mirrors arrayed along the excitation light path, each excitation mirror disposed at an acute angle relative to the first direction and configured to reflect collimated excitation light along a second direction. The emission module can be positioned to receive excitation light transmitted along the second direction and can include a sample block comprising a plurality of sample receptacles positioned to receive a beam of collimated excitation light, and a plurality of photodetectors configured to receive emission light transmitted from a respective sample receptacle in a direction transverse to the second direction of the excitation light path.

A method and associated apparatus for generating instantaneous and uniform total internal reflection fluorescence (TIRF) excitation. An annular fiber bundle and is used with spatially incoherent light to provide appropriate illumination matched to parameters of the back focal plane of an oil-immersion or in-air imaging objective lens, enabling quantitative shadowless TIRF imaging.

The sample imaging apparatus includes: an imaging unit that images a sample by using an achromatic lens in which longitudinal chromatic aberration is corrected in a wavelength range of chemiluminescent light of the sample; an excitation light source (the first epi-illumination light source and/or the second epi-illumination light source) that irradiates the sample with excitation light for causing the sample to emit fluorescent light; and an imaging control unit that adjusts a focal length of the achromatic lens in each imaging in a case of imaging the single sample a plurality of times by changing a wavelength range of the fluorescent light emitted by the sample, and performs imaging in a wavelength order of the fluorescent light used for the imaging.

Standardizing MERFISH imaging system provides a method to standardize a fluorescence microscope for a MERFISH analysis, the fluorescence microscope includes an excitation focus lens assembly and a light source. The method includes determining a roll-off value for the fluorescence microscope and adjusting the roll-off value of the fluorescence microscope to be 65% or lower by controlling a distance between the excitation focus lens assembly and the light source.

Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.

A target may be tagged, and its position tracked to maintain the position of the target at the center (e.g., zero region) of a suppression beam, where suppression is minimal, so the signal from the target is not suppressed relative to signal from background molecules. Point scanning is not needed, as a pixelated detector of a camera can be used to acquire the position of the target in one shot. Images of the object from the pixelated detector can be analyzed to acquire the position of the target. To maintain the target in the zero, the beams may be steered onto the target. Alternatively or additionally, the sample may be moved to place the sample in the center. A correction signal may be sent to cause the sample and/or beams to be moved to maintain the target in position.

A fluorescence image analyzer, analyzing method, and pretreatment evaluation method capable of determining with high accuracy whether a sample is positive or negative are provided. A pretreatment part performs pretreatment including a step of labeling a target site with a fluorescent dye to prepare a sample. A fluorescence image analyzer measures and analyzes the sample. The fluorescent image analyzer includes light sources to irradiate light on the sample, imaging part to capture the fluorescent light given off from the sample irradiated by light, and processing part for processing the fluorescence image captured by the imaging part. The processing part extracts the bright spot of fluorescence generated from the fluorescent dye that labels the target site from the fluorescence image for each of a plurality of cells included in the sample, and generates information used for determining whether the sample is positive or negative based on the bright spots extracted for each of the plurality of cells.