Abstract: The disclosure features methods that include exposing a biological sample to illumination light and measuring light emission from the sample to obtain N sample images, where each sample image corresponds to a different combination of a wavelength band of the illumination light and one or more wavelength bands of the light emission, where the one or more wavelength bands of the light emission define a wavelength range, and where N>1, and exposing the sample to illumination light in a background excitation band and measuring light emission from the sample in a background spectral band to obtain a background image of the sample, where the background spectral band corresponds to a wavelength within the wavelength range.

Abstract: The disclosure features methods that include exposing a biological sample to illumination light and measuring light emission from the sample to obtain N sample images, where each sample image corresponds to a different combination of a wavelength band of the illumination light and one or more wavelength bands of the light emission, where the one or more wavelength bands of the light emission define a wavelength range, and where N>1, and exposing the sample to illumination light in a background excitation band and measuring light emission from the sample in a background spectral band to obtain a background image of the sample, where the background spectral band corresponds to a wavelength within the wavelength range.

Abstract: Methods for identifying co-occurrence of nucleic acid segments in a nucleic acid sample from a specimen including obtaining a nucleic acid sample from a specimen, determining sequences of first and second nucleic acid segments in nucleic acid fragments of the sample to generate a first and second sets of sequences, generating a first and second sets of probes from the first and second sets of sequences, exposing a detection sample to a member of the first set of probes and a member of the second set of probes, performing a hybridization analysis to determine whether the members of the first and second sets of probes hybridize to the detection sample, and determining whether the first and second nucleic acid segments co-occur in a common cell of the specimen.

Abstract: The disclosure features methods and systems that include positioning a surface of a coverslip overlying a sample relative to an object plane of a microscope system, projecting a two-dimensional pattern of light onto the surface, where a focal plane of the two-dimensional pattern at a position of the surface is rotated by an angle ? relative to the object plane, obtaining a two-dimensional image of the pattern of light reflected from the surface using a detector that includes an imaging sensor oriented perpendicular to a direction of propagation of the reflected pattern of light at the sensor, analyzing the image to determine a line of best focus of the pattern within the image, determining an offset of the line of best focus from an expected position of the line of best focus within the image, and determining a position adjustment of the surface based on the offset.

Abstract: The disclosure features methods that include exposing a biological sample to illumination light and measuring light emission from the sample to obtain N sample images, where each sample image corresponds to a different combination of a wavelength band of the illumination light and one or more wavelength bands of the light emission, where the one or more wavelength bands of the light emission define a wavelength range, and where N>1, and exposing the sample to illumination light in a background excitation band and measuring light emission from the sample in a background spectral band to obtain a background image of the sample, where the background spectral band corresponds to a wavelength within the wavelength range.

Abstract: The methods and systems disclosed herein include obtaining a first image of a sample, where the first image corresponds to light transmitted through the sample in a first plurality of distinct spectral bands, obtaining a second image of the sample, where the second image corresponds to light transmitted through the sample in a second plurality of distinct spectral bands, and where at least some members of the second plurality of spectral bands are different from the members of the first plurality of spectral bands, and combining the first and second images to form a multispectral image stack, where each pixel in the image stack includes information corresponding to at least four distinct spectral bands, and where the at least four distinct spectral bands include at least one member from the first plurality of spectral bands and at least one member from the second plurality of spectral bands.

Abstract: The methods and systems disclosed herein include obtaining a first plurality of images of a sample, where each image in the first plurality of images corresponds to a different spectral band of illumination light incident on the sample or emission light from the sample, obtaining a second plurality of images of the sample, where each image in the second plurality of images corresponds to a different spectral band of illumination light incident on the sample or emission light from the sample, aligning the first and second pluralities of images based on information from a first image from the first plurality of images and a second image from the second plurality of images, where the first and second images correspond to a shared spectral band, and combining at least some members of the first plurality of images and at least some members of the second plurality of images to form an image stack.