Quantum dots (QDots) are nanometer-sized crystals, typically of semiconductor material and ranging from 2–10 nanometers in diameter, which exhibit fluorescence: a physical phenomenon in which a substance is excited by photons of a shorter wavelength and subsequently releases photons of a longer wavelength as it relaxes back into its ground state1. The small size of quantum dots leads to a discretization of the energy levels within the semiconductor material and gives rise to the size-dependent fluorescence spectra of quantum dots: a decrease in the crystal size results in a larger energy bandgap and thus blue-shifts the excitation and emission spectra of the quantum dot2. Apart from the size tunability of their fluorescence spectra, other key features of quantum dots that make them highly attractive fluorophores include high photoluminescence quantum yield3, broad excitation coupled with narrow and symmetrical emission spectra4, high resistance to photobleaching5, and ease of surface modification6.
Since their discovery, quantum dots have been utilized in various bioimaging applications7; such as cellular labeling8–10, in vivo tissue imaging11–13, bioassays14–17, and as Förster Resonance Energy Transfer (FRET) donors18–20; where their high quantum efficiency and high photostability afford good detection sensitivity and allow for imaging to be performed over extended periods of time. Owing to their well-studied surface chemistries21, quantum dots have been conjugated to a variety of biomolecules, including antibodies16, 22, proteins23–25, and oligonucleotides14, 15, 26; to achieve specific targeting of various biomarkers of interest. Additionally, given the narrow and symmetrical emission spectra of quantum dots which minimize their spectral overlap with other fluorophores, as well as their broad excitation spectra which allows for multiple quantum dots to be excited from a single UV light source; quantum dots possess great potential towards multiplexed imaging and have seen repeated use in such applications14, 16, 17, 27, 28. Xu et al. utilized multiple quantum dot-antibody conjugates to perform simultaneous immuno-histo-fluorescence (IHF) staining of different targets in formalin-fixed, paraffin-embedded (FFPE) tissue slides of human head and neck cancer17. Peng et al. studied the patterns of tumor invasion in human gastric and breast cancer FFPE tissue slides via multiplexed IHF28. Chan et al. utilized multiple quantum dot-labeled oligonucleotide probes for fluorescence in situ hybridization (FISH) imaging of mRNA biomarkers in mouse brain sections14.
The technique of utilizing fluorophores such as quantum dots to label and image particular features in a sample is known as fluorescence imaging29, on the basis that fluorophores can provide better visual contrast and localization information for the features of interest as compared to an unlabeled sample. Currently, there are two broad types of microscopes used in fluorescence imaging. A widefield fluorescence microscope typically uses a broadband incoherent light source such as a light emitting diode (LED), and a pair of excitation and emission filters which serve the purpose of selecting the desired excitation wavelength and filtering out wavelengths other than the fluorescence emission, respectively30. On the other hand, a confocal laser-scanning fluorescence microscope utilizes a high-intensity monochromatic light source, such as a laser, which determines the excitation wavelength, while the emission wavelengths are selected by emission filters31. The high spatial resolution and contrast in the acquired images, due to the optical sectioning capability which confocal microscopes are well known for, is achieved by the use of a spatial pinhole to block out-of-focus light from other focal planes in the sample.
While fluorescence imaging can acquire spatial information regarding the localization of fluorophores across a sample, it cannot identify each fluorophore according to its unique spectral fingerprint; for this to be accomplished, fluorescence spectroscopy has to be performed instead. Conversely, while it is able to acquire spectral information to deduce the type of a particular fluorophore and its intensity, the technique of fluorescence spectroscopy is only able to do so for a single point within a sample and lacks the ability to visualize the localization of fluorophores across the sample. Currently, emission filters are used to isolate the spectral band corresponding to the fluorescence emission of each fluorophore, thus allowing for one fluorophore to be imaged at a time; as such it is not strictly necessary for fluorophores to be identified by their spectral fingerprint. However, imaging multiple fluorophores with different spectral characteristics remains a tedious process, requiring the use of separate excitation and emission filters that are specifically optimized for each fluorophore, which has to be swapped out before imaging each fluorophore; as such the sample has to be imaged sequentially for each fluorophore used. Unconventional fluorophores thus pose an added challenge when they do not match well with the spectral bandwidth of commonly used emission filters. Furthermore, it is especially challenging to identify fluorophores with highly similar emission spectra and large spectral overlap. This may impose limitations on the experimental design when multiple fluorophores are intended to be used simultaneously or when imaging targets in the sample are located close to each other spatially.
Several solutions have been proposed to solve this problem, for example, fluorescent imaging with switchable photochromic naphthopyrans and fluorescent lifetime imaging microscopy (FLIM) 32, 33. Hyperspectral fluorescent imaging is another promising solution because the spectral channel selection is very precise which allows the detection of hundreds of different fluorophores simultaneously and rapidly. Hyperspectral imaging (HSI) is an imaging technique that combines the principles of optical imaging with spectroscopy, capturing three-dimensional images comprised of information from the spatial dimensions (x, y) and the spectral dimension (λ)34. As such, each pixel in a hyperspectral image contains the complete spectrum of the sample imaged by that pixel, and conversely, each wavelength on the spectrum contains its corresponding single-channel image. This technique is useful in multiplexed fluorescence imaging where each fluorophore within the sample can be identified by its spectral characteristics and at the same time, the spatial localization of each type of fluorophore can be elucidated. Recent review articles from Fakhrullin’s team and Rivera Gil’s team discussed the use of hyperspectral imaging combined with darkfield imaging modality for detecting nanoscale particles such as quantum dots for environmental and biological research35, 36.
In this paper, we present a customized wide-field hyperspectral fluorescence microscopy system based on a liquid crystal tunable filter as well as detailed characterization methods that aim to address the challenge of multiplexed detection. Compared to angle-tuned filters or filter wheels, the liquid crystal tunable filter contains no moving parts, thus the optical pathway through the system is not affected during operation and the captured images are not subject to any undesirable pixel shift effect. The liquid crystal tunable filter also features a high wavelength switching speed of less than 200 ms which is important in live imaging. We demonstrate the capabilities of our microscope for multiplexed fluorescence imaging and present a systematic way of studying the optical properties of fluorophores in a mixture environment. We characterized the fluorescence spectra of a series of six types of quantum dots with different emission peaks and discovered their spectral differences in wet and dry conditions. We also studied a homogenous mixture and a heterogeneous mixture of quantum dots. We showed how to use the spectral unmixing technique to identify each quantum dot type, quantify its relative proportion, and elucidate its spatial localization within the mixture sample. Lastly, we proposed a multiplexed sensing framework for quantum dot-labeled biomolecules using hyperspectral fluorescence microscopy. The results here provide valuable information for real-time simultaneous multi-channel fluorescence imaging in the future.