In some embodiments, a non-transitory processor-readable medium stores code representing instructions to be executed by a processor. The code includes code to cause the processor to receive a plurality of sets of images associated with a sample treated with fluorescence in situ hybridization (FISH) probes. Each image from that set of images is associated with a different focal length using a fluorescence microscope. Each FISH probe can selectively bind to a unique location on chromosomal DNA in the sample. The code further causes the processor to identify cell nuclei in the images. The code further causes the processor to apply a convolutional neural network (CNN) to each set of images. The CNN is configured to identify a probe indication from a plurality of probe indications for that set of images. The code further causes the processor to identify the sample as containing circulating tumor cells.

Described herein are methods and systems for the optical imaging of a physical specimen of interest that is in contact with, or in close proximity to, the backplane of a high refractive index solid-immersion lens (SIL), wherein the specimen comprises features of interest that act as a local high-refractive index regions. The SIL lens preferably comprises fiducial markers.

A microscope system is provided with a microscope that acquires images at least at a first magnification and a second magnification higher than the first magnification, and a processor. The processor is configured to specify a type of a container in which a specimen is placed, and when starting observation of the specimen placed in the container at the second magnification, the processor is configured to specify an observation start position by performing object detection according to the type of container on a first image that includes the container acquired by the microscope at the first magnification, and control a relative position of the microscope with respect to the specimen such that the observation start position is contained in a field of view at the second magnification of the microscope.

Example embodiments relate to methods and devices for generating (quasi-) periodic interference patterns. One embodiment includes a method for generating an interference pattern using multi-beam interference of electromagnetic radiation. The method includes computing a set of grid points in a complex plane representing a grid with a desired symmetry. The method also includes selecting a radius of a virtual circle. Additionally, the method includes selecting a set of grid points in the complex plane that lies on the virtual circle centered around a virtual center point. Further, the method includes associating an argument of each grid point of the selected set of grid points in the complex plane with a propagation direction of plane waves or quasi plane waves or parallel wave fronts. In addition, the method includes obtaining the interference pattern that is a superposition of the plane waves or quasi plane waves or parallel wave fronts.

A laser scanning microscope includes a light source configured to emit an illumination light beam. The illumination light beam has a transverse light intensity profile comprising an intensity minimum. The laser scanning microscope further includes a scanning device configured to scan the illumination light beam along a closed trajectory in a target area of a specimen, and a detector configured to detect fluorescence light emitted by a fluorophore within the target area of the specimen. The fluorophore is excited by the illumination light beam. The laser scanning microscope further includes a processor configured to determine an intensity distribution of the fluorescence light as a function of time and to determine a position of the fluorophore within the target area based on the intensity distribution of the fluorescence light.

The present invention discloses a photon enhancement apparatus comprising a reflective component and 4f coherent imaging system, which increases a photon collection efficiency. The present invention also provides a microscope comprising said photon enhancement apparatus and methods of improving photon collection efficiency, signal-to-noise ratio, and/or optical resolution using the said photon enhancement apparatus.

A system, including an optical imaging assembly configured to image a sample at an object plane to an image plane; an image sensor arranged at the image plane and configured to capture images of the sample for a field of view of the system; a light source configured to emit light having a wavelength, λ; a spatial light modulator (SLM) arranged to receive the light emitted from the light source and to provide a spatially modulated light pattern; one or more optical elements arranged to receive the spatially modulated light pattern from the SLM and to direct the spatially modulated light pattern to the image plane; and an electronic controller in communication with the image sensor and the spatial light modulator, the electronic controller being programmed to identify one or more targets in the field of view of the optical imaging assembly and to control the spatial light modulator to selectively direct light from the light source to the one or more targets identified by the electronic controller.

Improved resolution of a time-varying optical image is provided with a wide field optical intensity modulator having a bandwidth greater than that of the detector array(s). The modulator configuration can have high photon collection efficiency, e.g. by using polarization modulation to split the incident light into several timegated channels.

A light sheet fluorescence microscope includes a light source configured to emit excitation light suitable for inducing fluorescent light emitted from a specimen, a detector configured to detect the fluorescent light from the specimen, and an optical system configured to illuminate the specimen with a light sheet formed from the excitation light, and to guide the fluorescent light from the illuminated specimen to the detector. The optical system includes an objective facing the specimen, the objective being configured to collect the fluorescent light emitted from the specimen. The light source is further configured to emit manipulation light suitable for photomanipulating the specimen. The optical system is further configured to direct the manipulation light through a spatially limited sub-area of an entrance pupil of the objective onto the specimen along a light propagation direction which is different from a light propagation direction of the light sheet.

A sample observation device includes: an emission optical system that emits planar light to a sample on an XZ plane; a scanning unit that scans the sample in a Y-axis direction so as to pass through an emission surface of the planar light; an imaging optical system that has an observation axis inclined with respect to the emission surface and forms an image of observation light generated in the sample; an image acquisition unit that acquires a plurality of pieces of XZ image data corresponding to an optical image of the observation light; and an image generation unit 8 that generates XY image data based on the plurality of pieces of XZ image data. The image generation unit extracts an analysis region of the plurality of pieces of XZ image data acquired in the Y-axis direction, integrates brightness values of at least the analysis region in a Z-axis direction to generate X image data, and combines the X image data in the Y-axis direction to generate the XY image data.