Systems, methods, and devices for fluorescence imaging with a minimal area image sensor are disclosed. A system includes an emitter for emitting pulses of electromagnetic radiation and an image sensor comprising a pixel array for sensing reflected electromagnetic radiation, wherein the pixel array comprises active pixels and optical black pixels. The system includes a black clamp providing offset control for data generated by the pixel array and a controller comprising a processor in electrical communication with the image sensor and the emitter. The system is such that at least a portion of the pulses of electromagnetic radiation emitted by the emitter comprises electromagnetic radiation having a wavelength from about 770 nm to about 790 nm.

Aspects of the present disclosure include methods for spectrally resolving light from fluorophores having overlapping fluorescence spectra in a sample. Methods according to certain embodiments include detecting light with a light detection system from a sample having a plurality of fluorophores having overlapping fluorescence spectra and spectrally resolving light from each fluorophore in the sample. In some embodiments, methods include estimating the abundance of one or more of the fluorophores in the sample, such as on a particle. In certain instances, methods include identifying the particle in the sample based on the abundance of each fluorophore and sorting the particle. Methods according to some embodiments includes spectrally resolving the light from each fluorophore by calculating a spectral unmixing matrix for the fluorescence spectra of each fluorophore. Systems and integrated circuit devices (e.g., a field programmable gate array) for practicing the subject methods are also provided.

Provided herein are devices, systems, and methods for characterizing a biological sample in vivo or ex vivo in real-time using time-resolved spectroscopy. A light source generates a light pulse or continuous light wave and excites the biological sample, inducing a responsive fluorescent signal. A demultiplexer splits the signal into spectral bands and a time delay is applied to the spectral bands so as to capture data with a detector from multiple spectral bands from a single excitation pulse. The biological sample is characterized by analyzing the fluorescence intensity magnitude and/or decay of the spectral bands. The sample may comprise one or more exogenous or endogenous fluorophore. The device may be a two-piece probe with a detachable, disposable distal end. The systems may combine fluorescence spectroscopy with other optical spectroscopy or imaging modalities. The light pulse may be focused at a single focal point or scanned or patterned across an area.

Methods and systems for analysing products comprising marked materials and marking and tracking such materials are provided. A method of quantifying the proportion of a marked material comprising luminescent markers in a product comprises (i) obtaining a composite signal associated with the product, the composite signal including spectroscopic data and imaging data collected from the product, the spectroscopic and imaging data associated with a luminescent signal of the one or more luminescent markers in the marked material; (ii) identifying the marked material based on spectroscopic data associated with the one or more luminescent markers; (iii) quantifying the proportion of the marked material that is present in the product based at least in part on said imaging data of the composite signal, wherein said quantifying is based at least in part on the relative positions of and/or the number of luminescent markers detected in each image of the product.

Aspects of the present disclosure may include a method and/or a system for applying, to one or more ions in an ion chain, a first light beam having a first polarization and a second light beam having a second polarization to transfer the one or more ions from a first state of a first manifold to a second state of the first manifold, applying, to the one or more ions, the first light beam and the second light beam to transfer the one or more ions from the second state back to the first state, and applying, to the one or more ions, a third light beam to transition the one or more ions from the first state to a third state in a second manifold.

An LED spectrofluorometer (100) for analysis of an object (101) includes a light excitation element (11, 112, 113) suitable for illuminating a study zone (101B) of the object with an excitation light beam (1), and an optical routing element (121, 122, 123, 124) suitable for collecting a fluorescent light flux (2) emitted by the study zone excited by the excitation light beam and for routing the fluorescent light flux to an optical spectrometer (131) for analysis of the light spectrum thereof. The light excitation element includes a first light-emitting diode (111) and a second-light emitting diode (112), the first light-emitting diode emitting at a first wavelength (λ1) between 250 and 300 nm and the excitation light beam being formed from one or other of the light beams generated by each light-emitting diode.

An optical detector (1) on an application specific integrated circuit (ASIC) comprises at least one photodiode (5) for receiving incident light and configured to provide at least one diode signal, a modulator (2) configured to provide an AC drive signal and to provide a reference signal associated with the AC drive signal; and a lock-in amplifier (6) configured to receive said at least one diode signal from said at least one photodiode (5) and to receive the reference signal from the modulator (2), and to determine at least one of a phase and an amplitude of said at least one diode signal using the reference signal.

A method of fluorescence spectroscopy includes providing a high-performance sensor that combines imaging with high intrinsic time resolution and high-rate capability, and resolving fluorescence data in four dimensions.

Pulsed fluorescence imaging in a light deficient environment is disclosed. A system includes an emitter for emitting pulses of electromagnetic radiation and an image sensor comprising a pixel array for sensing reflected electromagnetic radiation. The system includes a controller configured to synchronize timing of the emitter and the image sensor. The system is such that at least a portion of the pulses of electromagnetic radiation emitted by the emitter comprises electromagnetic radiation having a wavelength from about 795 nm to about 815 nm.

Apparatuses for collection of upstream and downstream transmission electron microscopy (TEM) cathodoluminescence (CL) emitted from a sample exposed to an electron beam are described. A first fiber optic cable carries first CL light emitted from a first TEM sample surface, into a spectrograph. A second fiber optic cable carries second CL light emitted from a second TEM sample surface into the spectrograph. The first and second fiber optic cables are positioned such that the spectrograph produces a first light spectrum for the first fiber optic cable and a separate light spectrum for the second fiber optic cable. The described embodiments allow collection of TEM CL data in a manner that allows analyzing upstream and downstream TEM CL signals separately and simultaneously with an imaging spectrograph.