Intelligent Image-Activated Cell Sorting.

A fundamental challenge of biology is to understand the vast heterogeneity of cells, particularly how cellular composition, structure, and morphology are linked to cellular physiology. Unfortunately, conventional technologies are limited in uncovering these relations. We present a machine-intelligence technology based on a radically different architecture that realizes real-time image-based intelligent cell sorting at an unprecedented rate. This technology, which we refer to as intelligent image-activated cell sorting, integrates high-throughput cell microscopy, focusing, and sorting on a hybrid software-hardware data-management infrastructure, enabling real-time automated operation for data acquisition, data processing, decision-making, and actuation. We use it to demonstrate real-time sorting of microalgal and blood cells based on intracellular protein localization and cell-cell interaction from large heterogeneous populations for studying photosynthesis and atherothrombosis, respectively. The technology is highly versatile and expected to enable machine-based scientific discovery in biological, pharmaceutical, and medical sciences.

Visualization of Modified Bisarylbutadiyne-Tagged Small Molecules in Live-Cell Nuclei by Stimulated Raman Scattering Microscopy.

Visualizing the distribution of small-molecule drugs in living cells is an important strategy for developing specific, effective, and minimally toxic drugs. As an alternative to fluorescence imaging using bulky fluorophores or cell fixation, stimulated Raman scattering (SRS) imaging combined with bisarylbutadiyne (BADY) tagging enables the observation of small molecules closer to their native intracellular state. However, there is evidence that the physicochemical properties of BADY-tagged analogues of small-molecule drugs differ significantly from those of their parent drugs, potentially affecting their intracellular distribution. Herein, we developed a modified BADY to reduce deviations in physicochemical properties (in particular, lipophilicity and membrane permeability) between tagged and parent drugs, while maintaining high Raman activity in live-cell SRS imaging. We highlight the practical application of this approach by revealing the nuclear distribution of a modified BADY-tagged analogue of JQ1, a bromodomain and extra-terminal motif inhibitor with applications in targeted cancer therapy, in living HeLa cells. The modified BADY, methoxypyridazyl pyrimidyl butadiyne (MPDY), revealed intranuclear JQ1, while BADY-tagged JQ1 did not show a clear nuclear signal. We anticipate that the present approach combining MPDY tagging with live-cell SRS imaging provides important insight into the behavior of intracellular drugs and represents a promising avenue for improving drug development.

Cyano-Hydrol green derivatives: Expanding the 9-cyanopyronin-based resonance Raman vibrational palette.

9-cyanopyronin is a promising scaffold that exploits resonance Raman enhancement to enable sensitive, highly multiplexed biological imaging. Here, we developed cyano-Hydrol Green (CN-HG) derivatives as resonance Raman scaffolds to expand the color palette of 9-cyanopyronins. CN-HG derivatives exhibit sufficiently long wavelength absorption to produce strong resonance Raman enhancement for near-infrared (NIR) excitation, and their nitrile peaks are shifted to a lower frequency than those of 9-cyanopyronins. The fluorescence of CN-HG derivatives is strongly quenched due to the lack of the 10th atom, unlike pyronin derivatives, and this enabled us to detect spontaneous Raman spectra with high signal-to-noise ratios. CN-HG derivatives are powerful candidates for high performance vibrational imaging.

Activatable Raman Probes Utilizing Enzyme-Induced Aggregate Formation for Selective Ex Vivo Imaging.

Detecting multiple enzyme activities simultaneously with high spatial specificity is a promising strategy to investigate complex biological phenomena, and Raman imaging would be an excellent tool for this purpose due to its high multiplexing capabilities. We previously developed activatable Raman probes based on 9CN-pyronins, but specific visualization of cells with target enzyme activities proved difficult due to leakage of the hydrolysis products from the target cells after activation. Here, focusing on rhodol bearing a nitrile group at the position of 9 (9CN-rhodol), we established a novel mechanism for Raman signal activation based on a combination of aggregate formation (to increase local dye concentration) and the resonant Raman effect along with the bathochromic shift of the absorption, and utilized it to develop Raman probes. We selected the 9CN-rhodol derivative 9CN-JCR as offering a suitable combination of increased stimulated Raman scattering (SRS) signal intensity and high aggregate-forming ability, resulting in good retention in target cells after probe activation. By using isotope-edited 9CN-JCR-based probes, we could simultaneously detect ß-galactosidase, γ-glutamyl transpeptidase, and dipeptidyl peptidase-4 activities in live cultured cells and distinguish cell regions expressing target enzyme activity in Drosophila wing disc and fat body ex vivo.

Phase locking of squeezed vacuum generated by a single-pass optical parametric amplifier.

In high-precision optical measurements, squeezed vacuum states are a promising resource for reducing the shot noise. To utilize a squeezed vacuum, it is important to lock the phase of the local oscillator (LO) to the squeezed light. The coherent control sideband (CCSB) scheme has been established for the precise phase locking, while the previous CCSB scheme was designed for the squeezed vacuum generated with an optical parametric oscillator (OPO). Thus the previous CCSB scheme is not applicable to squeezing by a single-pass optical parametric amplifier (OPA), which is attractive for generating broadband squeezed vacuum states. In this study, we propose a variant of CCSB scheme, which is applicable to the squeezing by single-pass OPA. In this scheme, we inject pump light and frequency-shifted signal light into an OPA crystal in the same way as the previous CCSB scheme. The parametric process in the OPA crystal generates a squeezed vacuum, amplifies the signal light, generates an idler light, and causes the pump depletion reflecting the interference of the amplified signal light and the idler light. Through the lock-in detection of the pump depletion, we can phase-lock the injected signal light to the pump light. Then, after the heterodyne detection of the signal and the idler light, we get the error signal of LO and realize the precise phase locking of LO to the squeezed quadrature. We show the feasibility of the proposed scheme by deriving the signal-to-noise ratio (SNR) of the modulated pump signal. We experimentally demonstrate the proposed scheme on pulsed squeezing by a single-pass OPA.

Stimulated Raman scattering spectroscopy with quantum-enhanced balanced detection.

Quantum-enhanced stimulated Raman scattering (QE-SRS) is a promising technique for highly sensitive molecular vibrational imaging and spectroscopy surpassing the shot noise limit. However, the previous demonstrations of QE-SRS utilized rather weak optical power which hinders from competing with the sensitivity of state-of-the-art SRS microscopy and spectroscopy using relatively high-power optical pulses. Here, we demonstrate SRS spectroscopy with quantum-enhanced balanced detection (QE-BD) scheme, which works even when using high-power optical pulses. We used 4-ps pulses to generate pulsed squeezed vacuum at a wavelength of 844 nm with a squeezing level of -3.28 ± 0.12 dB generated from a periodically-poled stoichiometric LiTaO3 waveguide. The squeezed vacuum was introduced to an SRS spectrometer employing a high-speed spectral scanner to acquire QE-SRS spectrum in the wavenumber range of 2000-2280 cm-1 within 50 ms. Using SRS pump pulses with an average power of 11.3 mW, we successfully obtained QE-SRS spectrum whose SNR was better than classical SRS with balanced-detection by 2.27 dB.

Complete characterization of picosecond optical pulses by the offset frequency intensity modulation.

We present a method for characterizing the intensity waveform, spectrum, frequency chirp, and spectral phase of picosecond pulses at a moderate repetition rate of ∼100 MHz. The proposed method exploits the intensity modulation at ∼10 GHz, which is slightly offset from the integer multiple of the repetition rate of the pulses. The modulated pulses are split into two, and one is measured by an optical spectrum analyzer, whose output is detected by a lock-in amplifier, while the other is directly detected by a photodiode and its output is used as a reference signal of the lock-in amplifier. In the experiment, we demonstrate the measurement of picosecond Ti:sapphire laser pulses to investigate frequency chirp induced by self-phase modulation. We anticipate that the proposed method will be useful for the characterization of various types of picosecond pulses.

Quantum-enhanced stimulated Raman scattering microscopy in a high-power regime.

Quantum-enhanced stimulated Raman scattering (QESRS) microscopy is expected to realize molecular vibrational imaging with sub-shot-noise sensitivity, so that weak signals buried in the laser shot noise can be uncovered. Nevertheless, the sensitivity of previous QESRS did not exceed that of state-of-the-art stimulated Raman scattering (SOA-SRS) microscopes mainly because of the low optical power (3 mW) of amplitude squeezed light [Nature594, 201 (2021)10.1038/s41586-021-03528-w]. Here, we present QESRS based on quantum-enhanced balanced detection (QE-BD). This method allows us to operate QESRS in a high-power regime (>30 mW) that is comparable to SOA-SRS microscopes, at the expense of 3 dB sensitivity drawback due to balanced detection. We demonstrate QESRS imaging with 2.89 dB noise reduction compared with classical balanced detection scheme. The present demonstration confirms that QESRS with QE-BD can work in the high-power regime, and paves the way for breaking the sensitivity of SOA-SRS microscopes.

Label-free chemical imaging flow cytometry by high-speed multicolor stimulated Raman scattering.

Combining the strength of flow cytometry with fluorescence imaging and digital image analysis, imaging flow cytometry is a powerful tool in diverse fields including cancer biology, immunology, drug discovery, microbiology, and metabolic engineering. It enables measurements and statistical analyses of chemical, structural, and morphological phenotypes of numerous living cells to provide systematic insights into biological processes. However, its utility is constrained by its requirement of fluorescent labeling for phenotyping. Here we present label-free chemical imaging flow cytometry to overcome the issue. It builds on a pulse pair-resolved wavelength-switchable Stokes laser for the fastest-to-date multicolor stimulated Raman scattering (SRS) microscopy of fast-flowing cells on a 3D acoustic focusing microfluidic chip, enabling an unprecedented throughput of up to ∼140 cells/s. To show its broad utility, we use the SRS imaging flow cytometry with the aid of deep learning to study the metabolic heterogeneity of microalgal cells and perform marker-free cancer detection in blood.

Probing the Biogenesis of Polysaccharide Granules in Algal Cells at Sub-Organellar Resolution via Raman Microscopy with Stable Isotope Labeling.

Phototrophs assimilate CO2 into organic compounds that accumulate in storage organelles. Elucidation of the carbon dynamics of storage organelles could enhance the production efficiency of valuable compounds and facilitate the screening of strains with high photosynthetic activity. To comprehensively elucidate the carbon dynamics of these organelles, the intraorganellar distribution of the carbon atoms that accumulate at specific time periods should be probed. In this study, the biosynthesis of polysaccharides in storage organelles was spatiotemporally probed via stimulated Raman scattering (SRS) microscopy using a stable isotope (13C) as the tracking probe. Paramylon granules (a storage organelle of ß-1,3-glucan) accumulated in a unicellular photosynthetic alga, Euglena gracilis, were investigated as a model organelle. The carbon source of the culture medium was switched from NaH12CO3 to NaH13CO3 during the production of the paramylon granules; this resulted in the distribution of the 12C and 13C constituents in the granules, so that the biosynthetic process could be tracked. Taking advantage of high-resolution SRS imaging and label switching, the localization of the 12C and 13C constituents inside a single paramylon granule could be visualized in three dimensions, thus revealing the growth process of paramylon granules. We propose that this method can be used for comprehensive elucidation of the dynamic activities of storage organelles.

Alkyne-Tagged Dopamines as Versatile Analogue Probes for Dopaminergic System Analysis.

The dopaminergic system is essential for the function of the brain in health and disease. Therefore, detailed studies focused on unraveling the mechanisms involved in dopaminergic signaling are required. However, the lack of probes that mimic dopamine in living tissues, owing to the neurotransmitter's small size, has hampered analysis of the dopaminergic system. The current study aimed to overcome this limitation by developing alkyne-tagged dopamine compounds (ATDAs) that have a minimally invasive and uniquely identifiable alkyne group as a tag. ATDAs were established as chemically and functionally similar to dopamine and readily detectable by methods such as specific click chemistry and Raman scattering. The ATDAs developed here were verified as analogue probes that mimic dopamine in neurons and brain tissues, allowing the detailed characterization of dopamine dynamics. Therefore, ATDAs can act as safe and versatile tools with wide applicability in detailed studies of the dopaminergic system. Furthermore, our results suggest that the alkyne-tagging approach can also be applied to other small-sized neurotransmitters to facilitate characterization of their dynamics in the brain.

Reduction of excess intensity noise of picosecond Yb soliton fiber lasers in a >10-mW power regime.

We demonstrate that excess intensity noise of soliton fiber lasers in the average power regime exceeding 10 mW can be reduced by increasing the intracavity dispersion and reducing the pump power. Based on this strategy, we present a polarization-maintaining picosecond Yb fiber laser mode-locked by a nonlinear amplifying loop mirror whose excess noise is equal to the shot noise at an optical power of >10 mW.

Photoswitchable stimulated Raman scattering spectroscopy and microscopy.

Photoswitchable fluorescence is a powerful technique to realize super-resolution imaging, highlighting, and optical storage, while its multiplexing capability is limited. Raman scattering is attracting attention because it generates narrowband vibrational signatures, which are potentially useful for highly multiplexed detection of different constituents. Here, we demonstrate photoswitchable stimulated Raman scattering (SRS) spectroscopy and microscopy where narrowband vibrational signatures are switched with full reversibility at high speed. The demonstration of live-cell photoswitchable SRS imaging shows good sensitivity and compatibility with biological living systems.

Multicolour chemical imaging of plant tissues with hyperspectral stimulated Raman scattering microscopy.

Recent development of stimulated Raman scattering (SRS) microscopy allows for label-free biological imaging with chemical specificity based on molecular-vibrational signatures. In particular, hyperspectral SRS imaging can acquire a molecular-vibrational spectrum at each pixel, allowing us not only to investigate the spectral difference of various biological molecules but also to discriminate different constituents based on their spectral difference. However, the number of constituents discriminated in previous label-free SRS imaging was limited to four because of the subtleness of spectral difference. Here, we report hyperspectral SRS imaging of plant tissues including leaves of Camellia japonica, roots of Arabidopsis thaliana, and thalli of a liverwort Marchantia polymorpha L. We show that SRS can discriminate as many as six components in Marchantia polymorpha L. without labeling. Our results demonstrate the effectiveness of hyperspectral SRS imaging as a tool for label-free multicolour imaging analysis of various biomolecules in plant tissues.

Low-loss microscope optics with an axicon-based beam shaper.

We present low-loss microscope optics using an axicon-based beam shaper, which can convert a Gaussian beam to a ring beam to minimize the optical loss from blocking by the back aperture of the objective lens while maintaining spatial resolution. To design the beam shaper, we characterize the position-dependent transmittance of high-transmittance objective lenses and numerically calculate the beam propagation in the beam shaper. We also clarify the effect of misalignments of the beam shaper and wavefront distortion of the input beam. Furthermore, we experimentally demonstrate a low-loss microscope optical system with a high transmittance of 86.6% and high spatial resolution using the full numerical aperture of the objective lenses.

Multicolor Activatable Raman Probes for Simultaneous Detection of Plural Enzyme Activities.

Raman probes based on alkyne or nitrile tags hold promise for highly multiplexed imaging. However, sensing of enzyme activities with Raman probes is difficult because few mechanisms are available to modulate the vibrational response. Here we present a general strategy to prepare activatable Raman probes that show enhanced Raman signals due to electronic preresonance (EPR) upon reaction with enzymes under physiological conditions. We identified a xanthene derivative bearing a nitrile group at position 9 (9CN-JCP) as a suitable scaffold dye, and synthesized four types of activatable Raman probes, which are targeted to different enzymes (three aminopeptidases and a glycosidase) and tuned to different vibrational frequencies by isotope editing of the nitrile group. We validated the activation of the Raman signals of these probes by the target enzymes and succeeded in simultaneous imaging of the four enzyme activities in live cells. Different cell lines showed different patterns of these enzyme activities.

Intelligent frequency-shifted optofluidic time-stretch quantitative phase imaging.

Optofluidic time-stretch quantitative phase imaging (OTS-QPI) is a powerful tool as it enables high-throughput (>10,000 cell/s) QPI of single live cells. OTS-QPI is based on decoding temporally stretched spectral interferograms that carry the spatial profiles of cells flowing on a microfluidic chip. However, the utility of OTS-QPI is troubled by difficulties in phase retrieval from the high-frequency region of the temporal interferograms, such as phase-unwrapping errors, high instrumentation cost, and large data volume. To overcome these difficulties, we propose and experimentally demonstrate frequency-shifted OTS-QPI by bringing the phase information to the baseband region. Furthermore, to show its boosted utility, we use it to demonstrate image-based classification of leukemia cells with high accuracy over 96% and evaluation of drug-treated leukemia cells via deep learning.

Double modulation SRS and SREF microscopy: signal contributions under pre-resonance conditions.

Pre-electronic resonance enhancement can increase the sensitivity of non-linear Raman microscopy to the single molecule detection limit. A major problem, however, is the generation of background signal due to unwanted linear and non-linear photophysical processes. In this work, we report the setup of a novel detection scheme for stimulated Raman scattering microspectroscopy based on the simultaneous modulation of pump and Stokes beam. Apart from allowing the parallel detection of stimulated Raman loss and gain (SRL and SRG), the setup gives access to the quantitative analysis of different sources of background signal. We report spectrally and temporally resolved measurements on three exemplary rhodamine dyes and derive the contributions of two-photon absorption and stimulated emission to their SRL, SRG, and stimulated Raman excited fluorescence signals. These results give guidelines for the further improvement of the sensitivity of non-linear Raman micospectroscopy under electronic pre-resonance conditions.

Isolating Single Euglena gracilis Cells by Glass Microfluidics for Raman Analysis of Paramylon Biogenesis.

Time-course analysis of single cells is important to characterize heterogeneous activities of individual cells such as the metabolic response to their environment. Single-cell isolation is an essential step prior to time-course analysis of individual cells by collecting, culturing, and identifying multiple single-cell targets. Although single-cell isolation has been performed by various methods previously, a glass microfluidic device with semiclosed microchannels dramatically improved this process with its simple operation and easy transfer for time-course analysis of identified single cells. This study demonstrates isolating single cells of the highly motile microalgae, Euglena gracilis, by semiclosed microchannels with liquid flow only. The isolated single cells were identified in isolating channels and continuously cultured to track, by Raman microscopy, for the formation of subcellular granules composed of polysaccharide paramylon, a unique metabolite of E. gracilis, generated through photosynthesis. Through low-temperature glass bonding, a thin glass interface was incorporated to the microfluidic device. Thus, the device could perform the direct measurements of cultured single cells at high magnification by Raman microscopy with low background noise. In this study, the first demonstration of sequential monitoring of paramylon biogenesis in a single identified E. gracilis cell is shown.

Synchronized subharmonic modulation in stimulated emission microscopy.

In this work, we have demonstrated a stimulated emission (SE)-based pump-probe microscopy with subharmonic fast gate synchronization, which allows over an order of magnitude improvement in signal-to-noise ratio. Critically, the alternative way of modulation is implemented with the highest possible frequency that follows the lasers' repetition rate. Its working is based on a homemade frequency divider that divides the repetition frequency (76 MHz) of the Ti:sapphire (probe) laser to half of the repetition frequency, 38 MHz, which is used to synchronously drive the pump laser and to provide the reference signal for the ensuing lock-in detection. In this way, SE can be detected with sensitivity reaching the theoretical (shot noise) limits, with a much lower time constant (0.1 ms) for faster image acquisition.