Deep learning-based spectroscopic single-molecule localization microscopy.

Significance: Spectroscopic single-molecule localization microscopy (sSMLM) takes advantage of nanoscopy and spectroscopy, enabling sub-10 nm resolution as well as simultaneous multicolor imaging of multi-labeled samples. Reconstruction of raw sSMLM data using deep learning is a promising approach for visualizing the subcellular structures at the nanoscale. Aim: Develop a novel computational approach leveraging deep learning to reconstruct both label-free and fluorescence-labeled sSMLM imaging data. Approach: We developed a two-network-model based deep learning algorithm, termed DsSMLM, to reconstruct sSMLM data. The effectiveness of DsSMLM was assessed by conducting imaging experiments on diverse samples, including label-free single-stranded DNA (ssDNA) fiber, fluorescence-labeled histone markers on COS-7 and U2OS cells, and simultaneous multicolor imaging of synthetic DNA origami nanoruler. Results: For label-free imaging, a spatial resolution of 6.22 nm was achieved on ssDNA fiber; for fluorescence-labeled imaging, DsSMLM revealed the distribution of chromatin-rich and chromatin-poor regions defined by histone markers on the cell nucleus and also offered simultaneous multicolor imaging of nanoruler samples, distinguishing two dyes labeled in three emitting points with a separation distance of 40 nm. With DsSMLM, we observed enhanced spectral profiles with 8.8% higher localization detection for single-color imaging and up to 5.05% higher localization detection for simultaneous two-color imaging. Conclusions: We demonstrate the feasibility of deep learning-based reconstruction for sSMLM imaging applicable to label-free and fluorescence-labeled sSMLM imaging data. We anticipate our technique will be a valuable tool for high-quality super-resolution imaging for a deeper understanding of DNA molecules' photophysics and will facilitate the investigation of multiple nanoscopic cellular structures and their interactions.

Clinical application of multicolor scanning laser ophthalmology in diagnosis and grading of central retinal artery occlusion.

Purpose: To characterize features of central retinal artery occlusion (CRAO) using multicolor (MC) imaging and to assess the differences in CRAO grading between color fundus photography (CFP) and MC image qualitatively and quantitatively. Methods: We conducted a prospective, cross-sectional study in the Department of Ophthalmology of Renmin Hospital of Wuhan University. In total, 86 acute CRAO patients were included. Spectral-domain optical coherence tomography (SD-OCT), CFP, and MC examinations were taken at baseline. Based on the findings of these three examinations, CRAO was divided into three grades (incomplete, subtotal, and total). Based on OCT grading criteria, we qualitatively compared the ability of grading CRAO by CFP and MC. CRAO patient's visual acuity (VA) was obtained from the initial visit. The retinal thickness was measured by SD-OCT. Superficial capillary plexus (SCP) and deep capillary plexus (DCP) were obtained from optical coherence tomography angiography (OCTA) examinations. Quantitative data were compared across the three acute CRAO subgroups and against three examination findings. Results: MC image had significantly higher power of acute CRAO detection than CFP (P = 0.03). In the same group of CRAO patients, there was no significant difference in VA when comparing OCT with the MC grading system or with the CFP grading system (all P > 0.05). Significant differences in VA were found between the three CRAO subgroups only under MC grading (P = 0.016). In incomplete CRAO patients, significant differences were found in central fovea thickness (CFT) when comparing OCT with the CFP grading system (P = 0.019). In the same group of CRAO patients, there was no significant difference in retinal thickness when comparing OCT with the MC grading system (All P > 0.05). Significance differences in CFT (P < 0.001), innermost retinal layer (IMRL; P < 0.01), middle retinal layer (MRL; P < 0.001), and outer retinal layer (ORL; P = 0.021) were found between the three CRAO subgroups by MC grading. Vessel density of SCP showed a statistically increased as the severity of three CRAO subgroups (P = 0.03), whereas DCP did not have significant differences (P = 0.745). Comparisons were made between the OCT grading method and the MC and CFP grading methods; there is no significant difference in vessel density of SCP and DCP (All P > 0.05). Conclusion: The images obtained by MC are superior to those obtained by CFP in CRAO grading, retinal thickness, and vessel density measurement. MC imaging may be more capable of CRAO grading than OCT. We recommend MC imaging to determine CRAO severity to guide disease treatment and predict visual prognosis.

Multicolor Long-Term Single-Particle Tracking Using 10 nm Upconverting Nanoparticles.

Single-particle tracking (SPT) is a powerful technique to unveil molecular behaviors crucial to the understanding of many biological processes, but it is limited by factors such as probe photostability and spectral orthogonality. To overcome these limitations, we develop upconverting nanoparticles (UCNPs), which are photostable over several hours at the single-particle level, enabling long-term multicolor SPT. We investigate the brightness of core-shell UCNPs as a function of inert shell thickness to minimize particle size while maintaining sufficient signal for SPT. We explore different rare-earth dopants to optimize for the brightest probes and find that UCNPs doped with 2% Tm3+/30% Yb3+, 10% Er3+/90% Yb3+, and 15% Tm3+/85% Yb3+ represent the optimal probes for blue, green, and near-infrared emission, respectively. The multiplexed 10 nm probes enable three-color single-particle tracking on live HeLa cells for tens of minutes using a single, near-infrared excitation source. These photostable and multiplexed probes open new avenues for numerous biological applications.

Colorimetric Barcoding to Track, Isolate, and Analyze Hematopoietic Stem Cell Clones.

In zebrafish, hematopoietic stem cells (HSCs) are born in the developing aorta during embryogenesis. From the definitive wave of hematopoiesis onward, blood homeostasis relies on self-renewal and differentiation of progeny of existing HSCs, or clones, rather than de novo generation. Here, we describe an approach to quantify the number and size of HSC clones at various times throughout the lifespan of the animal using a fluorescent, multicolor labeling strategy. The system is based on combining the multicolor Zebrabow system with an inducible, early lateral plate mesoderm and hematopoietic lineage specific cre driver (draculin (drl)). The cre driver can be temporally controlled and activated in early hematopoiesis to introduce a color barcoding unique to each HSC and subsequently inherited by their daughter cells. Clonal diversity and dominance can be investigated in normal development and blood disease progression, such as blood cancers. This adoptable method allows researchers to obtain quantitative insight into clonality-defining events and their contribution to adult hematopoiesis.

Enhanced synaptic protein visualization by multicolor super-resolution expansion microscopy.

Significance: Understanding the organization of biomolecules into complexes and their dynamics is crucial for comprehending cellular functions and dysfunctions, particularly in neuronal networks connected by synapses. In the last two decades, various powerful super-resolution (SR) microscopy techniques have been developed that produced stunning images of synapses and their molecular organization. However, current SR microscopy methods do not permit multicolor fluorescence imaging with 20 to 30 nm spatial resolution. Aim: We developed a method that enables 4-color fluorescence imaging of synaptic proteins in neurons with 20 to 30 nm lateral resolution. Approach: We used post-expansion immunolabeling of eightfold expanded hippocampal neurons in combination with Airyscan and structured illumination microscopy (SIM). Results: We demonstrate that post-expansion immunolabeling of approximately eightfold expanded hippocampal neurons enables efficient labeling of synaptic proteins in crowded compartments with minimal linkage error and enables in combination with Airyscan and SIM four-color three-dimensional fluorescence imaging with 20 to 30 nm lateral resolution. Using immunolabeling of Synaptobrevin 2 as an efficient marker of the vesicle pool allowed us to identify individual synaptic vesicles colocalized with Rab3-interacting molecule 1 and 2 (RIM1/2), a marker of pre-synaptic fusion sites. Conclusions: Our optimized expansion microscopy approach improves the visualization and location of pre- and post-synaptic proteins and can thus provide invaluable insights into the spatial organization of proteins at synapses.

Trifunctional Linkers Enable Improved Visualization of Actin by Expansion Microscopy.

Expansion microscopy (ExM) revolutionized the field of super-resolution microscopy by allowing for subdiffraction resolution fluorescence imaging on standard fluorescence microscopes. However, it has been found that it is hard to visualize actin filaments efficiently using ExM. To improve actin imaging, multifunctional molecules have been designed with moderate success. Here, we present optimized methods for phalloidin conjugate grafting that have a high efficiency for both cellular and tissue samples. Our optimized strategy improves anchoring and signal retention by ∼10 times. We demonstrate the potential of optimized trifunctional linkers (TRITON) for actin imaging in combination with immunolabeling using different ExM protocols. 10X ExM of actin labeled with optimized TRITON enabled us to visualize the periodicity of actin rings in cultured hippocampal neurons and brain slices by Airyscan confocal microscopy. Thus, TRITON linkers provide an efficient grafting method, especially in cases in which the concentration of target-bound monomers is insufficient for high-quality ExM.

[Horseshoe retinal tear: factors that determine the risk of developing rhegmatogenous retinal detachment]. / Klapannyi razryv setchatki: faktory, opredelyayushchie risk razvitiya regmatogennoi otsloiki setchatki.

Horseshoe (flap) retinal tears are the leading cause of rhegmatogenous retinal detachment (RRD). Identification of the most significant predictors of RRD in patients with a horseshoe tear will enable the development of an optimal treatment strategy. PURPOSE: This study aimed to determine the main risk factors for RRD development based on the analysis of the condition of vitreoretinal interface in the area of horseshoe tears, both isolated and those that resulted in retinal detachment. MATERIAL AND METHODS: A total of 88 patients with horseshoe retinal tears (43 patients with RRD due to the horseshoe tear and 45 with isolated horseshoe tears) were included in the study. All patients underwent wide-field multispectral laser scanning and optical coherence tomography to determine the shape of the horseshoe tear and the extent of vitreoretinal adhesion (VRA). Cluster analysis was used to differentiate horseshoe tears by shape. Spearman's correlation analysis was used to identify the relationship between the shape of the horseshoe tear and localization of VRA. RESULTS: Spearman's correlation analysis revealed a strong negative correlation between the length-to-width ratio of the horseshoe tear and the extent of VRA. Cluster analysis helped determine four shapes of horseshoe tears, each corresponding to a certain localization of VRA. Analysis of RRD risk, depending on the characteristics of the horseshoe tear, showed that the most significant risk factor for the development of RRD is the presence of a horseshoe tear with width greater than its length, which is characterized by a larger VRA area. CONCLUSION: The study established that the larger the horseshoe tear width and the smaller its length, the larger the VRA area and, consequently, the higher the risk of RRD development. Horseshoe retinal tears with a length-to-width ratio of less than 1/1 are the most dangerous in terms of RRD risk, which is important to consider when selecting the treatment tactics.

Multimodal imaging in a case of bilateral astrocytic hamartoma with retinitis pigmentosa.

Astrocytic hamartoma is a benign glial tumor. It may be associated with tuberous sclerosis and can also be found incidentally on retinal examination as an isolated presentation. Here, we describe multimodal imaging characteristics of astrocytic hamartoma in a patient with retinitis pigmentosa. Spectral domain optical coherence tomography of both eyes showed moth-eaten optically empty spaces and hyperreflective dots along with foveal thinning. Multicolor image highlighted mulberry appearance of the lesion with green shift signifying elevated lesion. In infrared reflectance, lesion was hyporeflective with its margins well delineated. Green reflectance and blue reflectance highlighted calcification as multiple hyperreflective dots. Autofluorescence showed typical hyperautofluorescence.

Water Soluble PMPC-Derived Bright Fluorescent Nitrogen/Phosphorous-Doped Carbon Dots for Fluorescent Ink (Anti-Counterfeiting) and Cellular Multicolor Imaging.

Here, a simple one-step hydrothermal-assisted carbonization process was adopted for the preparation of nitrogen/phosphorous-doped carbon dots from a water-soluble polymer, poly 2-(methacryloyloxy)ethyl phosphorylcholine (PMPC). By the free-radical polymerization method, PMPC was synthesized using 2-(methacryloyloxy)ethyl phosphorylcholine (MPC) and 4,4'-azobis (4-cyanovaleric acid). The water-soluble polymers, PMPC, that have nitrogen/phosphorus moieties are used to prepare carbon dots (P-CDs). The resulting P-CDs were thoroughly characterized by various analytical techniques such as field emission-scanning electron microscopy (FESEM) with energy-dispersive X-ray spectroscopy (EDS), high-resolution transmittance electron microscopy (HRTEM), X-ray diffraction (XRD), Raman spectroscopy, attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), Ultraviolet-visible (UV-vis) spectroscopy and fluorescence spectroscopy to determine their structural and optical properties. The synthesized P-CDs displayed bright/durable fluorescence, were stable for long periods, and confirmed the enrichment of functionalities including oxygen, phosphorus, and nitrogen heteroatoms in the carbon matrix. Since the synthesized P-CDs showed bright fluorescence with excellent photostability, excitation-dependent fluorescence emission, and excellent quantum yield (23%), it has been explored as a fluorescent (security) ink for drawing and writing (anti-counterfeiting). Further, cytotoxicity study results advised for biocompatibility and thus were used for cellular multicolor imaging in nematodes. This work not only demonstrated the preparation of CDs from polymers that can be used as advanced fluorescence ink, a bioimaging agent for anti-counterfeiting, and cellular multicolor imaging candidate, but additionally prominently opened a new perspective on the bulk preparation of CDs simply and efficiently for various applications.

Multicolor imaging compared with red-free fundus photography in the detection of glaucomatous retinal nerve fiber layer thinning.

BACKGROUND: To compare the ability of multicolor imaging (MCI) with red-free fundus photography (RFP) to detect glaucomatous retinal nerve fiber layer (RNFL) thinning. METHODS: A total of 127 eyes of 79 patients with glaucoma underwent MCI using blue light, RFP, and circumpapillary optical coherence tomography (OCT) scanning on the same day. Angular location and width of the RNFL defects (RNFLDs) identified on the MCI and RFP were independently measured, and compared with those of RNFL thinning indicated by abnormal color codes on OCT. RESULTS: The angular location and width of the RNFLDs determined by both MCI and RFP were well correlated with those of RNFL thinning determined by OCT (all P ≤ 0.013). The correlation of angular width with OCT was significantly stronger for MCI than for RFP (R = 0.708 vs. R = 0.616, P = 0.009). The superiority of MCI to RFP in the detection of OCT-determined RNFL thinning was significant in the inferior (P = 0.025) and marginally significant in the superior (P = 0.084) hemisectors. Thinner RNFL and longer axial length were significantly associated with better visualization of RNFLD by MCI than by RFP, respectively in the superior (OR = 0.948, P = 0.048) and inferior (OR = 1.490, P = 0.012) hemisectors. CONCLUSIONS: RNFLD on MCI correlated well with OCT measurement of RNFL thinning in eyes with glaucoma. MCI performed better than conventional RFP in the detection of OCT-determined RNFL thinning, specifically in eyes with thinner RNFL and those with myopia. MCI may be more useful than conventional RFP in evaluating glaucomatous RNFL thinning.

Simultaneous labeling and multicolor fluorescence imaging of multiple immune cells on liver frozen section by polychromatic quantum dots below freezing points.

A method for simultaneous labeling and multicolor fluorescence imaging of different hepatic immune cells below freezing point is established based on quantum dots. In the experiment, carbon quantum dots with emission wavelength of 435 nm, CdTe@CdS quantum dots at 542 nm and CdSe@ZnS quantum dots at 604 nm are synthesized respectively, it is found that when the mass fractions of KCl (as antifreeze) are 12 %, 14 %, and 12 %, respectively, the three quantum dot dispersion systems remain liquid state at -20 °C. After they are conjugated with the corresponding secondary antibodies, agarose gel electrophoresis, circular dichroism and capillary electrophoresis confirm the effectiveness of conjugation. By indirect immunofluorescence method, the above three quantum dot fluorescent probes are used to simultaneously and specifically target a variety of liver immune cells, and the multi-color simultaneous imaging of different liver immune cells is realized under the same excitation wavelength, it is found that hepatic macrophages are arranged radially in the liver, hepatic stellate cells present punctate distribution, and hepatic sinusoidal endothelial cells present circular distribution, which is consistent with the results of H&E staining and ultrathin section TEM. This study provides an important technical means for elucidating the structure and function of the liver.

Acidic pH-Triggered Live-Cell Lysosome Specific Tracking, Ratiometric pH Sensing, and Multicolor Imaging by Visible to NIR Switchable Cy-7 Dyes.

We have demonstrated an efficient synthetic route with crystal structures for the construction of acidic pH-triggered visible-to-NIR interchangeable ratiometric fluorescent pH sensors. This bioresponsive probe exhibits pH-sensitive reversible absorption/emission features, low cytotoxicity, a huge 322 nm bathochromic spectral shift with augmented quantum yield from neutral to acidic pH, high sensitivity and selective targeting ability of live-cell lysosomes with ideal pKa , off-to-on narrow NIR absorption/fluorescence signals with high molar absorption coefficient at acidic lysosomal lumen, and in-situ live-cell pH-activated ratiometric imaging of lysosomal pH. Selective staining and ratiometric pH imaging in human carcinoma live-cell lysosomes were monitored by dual-channel confocal laser scanning microscope using a pH-activatable organic fluorescent dye comprising a morpholine moiety for lysosome targeting and an acidic pH openable oxazolidine ring. Moreover, real-time tracking of lysosomes, 3D, and multicolor live-cell imaging have been achieved using the synthesized pH-activatable probe.

Translational rapid ultraviolet-excited sectioning tomography for whole-organ multicolor imaging with real-time molecular staining.

Rapid multicolor three-dimensional (3D) imaging for centimeter-scale specimens with subcellular resolution remains a challenging but captivating scientific pursuit. Here, we present a fast, cost-effective, and robust multicolor whole-organ 3D imaging method assisted with ultraviolet (UV) surface excitation and vibratomy-assisted sectioning, termed translational rapid ultraviolet-excited sectioning tomography (TRUST). With an inexpensive UV light-emitting diode (UV-LED) and a color camera, TRUST achieves widefield exogenous molecular-specific fluorescence and endogenous content-rich autofluorescence imaging simultaneously while preserving low system complexity and system cost. Formalin-fixed specimens are stained layer by layer along with serial mechanical sectioning to achieve automated 3D imaging with high staining uniformity and time efficiency. 3D models of all vital organs in wild-type C57BL/6 mice with the 3D structure of their internal components (e.g., vessel network, glomeruli, and nerve tracts) can be reconstructed after imaging with TRUST to demonstrate its fast, robust, and high-content multicolor 3D imaging capability. Moreover, its potential for developmental biology has also been validated by imaging entire mouse embryos (~2 days for the embryo at the embryonic day of 15). TRUST offers a fast and cost-effective approach for high-resolution whole-organ multicolor 3D imaging while relieving researchers from the heavy sample preparation workload.

Clinical application of multicolor imaging in Leber hereditary optic neuropathy.

Purpose: To characterize features of retinal never fiber in Leber Hereditary Optic Neuropathy (LHON) using multicolor (MC) imaging and color fundus photography (CFP). Methods: Ninety-two eyes of patients with LHON underwent MC imaging, optic disc spectral domain optical coherence tomography (SD-OCT), and CFP. Two independent observers graded RNFL visibility scores and two other experts determined never fiber bundle defects from four-quadrant readings. CFP, standard MC, infrared reflectance (IR), green reflectance (GR), blue reflectance (BR), and green-blue-enhanced (BG) imaging were compared. Results: Agreement on never fiber bundle defects was substantial for CFP, standard MC, GR, BR, and BG images relative to IR. It was shown that BR (2.71 ± 0.55) had the best mean RNFL visibility score, BG (2.69 ± 0.52), GR (2.69 ± 0.56), standard MC (2.04 ± 0.79), CFP (1.80 ± 0.82), and IR (0.45 ± 0.59) followed. Agreement on temporal area defects was relatively improved. Youden's indices for CFP (78.21%), standard MC (84.48%), GR (90.92%), BR (89.64%), and BG (90.99%) indicated good detection of defects in the papillomacular bundle (PMB)/ high suspicion of patients with LHON, particularly for BG and GR. According to the proportion of never fiber bundle defects, standard MC, GR, BR, and BG can roughly determine the LHON clinical stage, especially in subacute and chronic stages, and standard MC is superior for patients with LHON of all stages. The stage judged by MC was consistent with the course inferred by pRNFL thickness. Conclusion: As an adjunct to SD-OCT, the MC image, particularly the GR and BG can delineate RNFL more effectively than CFP. The MC image may be a useful adjunct to OCT for detecting or monitoring never fiber bundle defects, providing inexpensive and rapid methods that can quickly identify patients with high suspicion of LHON.

Enabling Spectrally Resolved Single-Molecule Localization Microscopy at High Emitter Densities.

Single-molecule localization microscopy (SMLM) is a powerful super-resolution technique for elucidating structure and dynamics in the life- and material sciences. Simultaneously acquiring spectral information (spectrally resolved SMLM, sSMLM) has been hampered by several challenges: an increased complexity of the optical detection pathway, lower accessible emitter densities, and compromised spatio-spectral resolution. Here we present a single-component, low-cost implementation of sSMLM that addresses these challenges. Using a low-dispersion transmission grating positioned close to the image plane, the +1stdiffraction order is minimally elongated and is analyzed using existing single-molecule localization algorithms. The distance between the 0th and 1st order provides accurate information on the spectral properties of individual emitters. This method enables a 5-fold higher emitter density while discriminating between fluorophores whose peak emissions are less than 15 nm apart. Our approach can find widespread use in single-molecule applications that rely on distinguishing spectrally different fluorophores under low photon conditions.

Synergizing Exchangeable Fluorophore Labels for Multitarget STED Microscopy.

Investigating the interplay of cellular proteins with optical microscopy requires multitarget labeling. Spectral multiplexing using high-affinity or covalent labels is limited in the number of fluorophores that can be discriminated in a single imaging experiment. Advanced microscopy methods such as STED microscopy additionally demand balanced excitation, depletion, and emission wavelengths for all fluorophores, further reducing multiplexing capabilities. Noncovalent, weak-affinity labels bypass this "spectral barrier" through label exchange and sequential imaging of different targets. Here, we combine exchangeable HaloTag ligands, weak-affinity DNA hybridization, and hydrophophic and protein-peptide interactions to increase labeling flexibility and demonstrate six-target STED microscopy in single cells. We further show that exchangeable labels reduce photobleaching as well as facilitate long acquisition times and multicolor live-cell and high-fidelity 3D STED microscopy. The synergy of different types of exchangeable labels increases the multiplexing capabilities in fluorescence microscopy, and by that, the information content of microscopy images.

Extending optical chemical tools and technologies to mice by shifting to the shortwave infrared region.

Fluorescence imaging is an indispensable method for studying biological processes non-invasively in cells and transparent organisms. Extension into the shortwave infrared (SWIR, 1000-2000 nm) region of the electromagnetic spectrum has allowed for imaging in mammals with unprecedented depth and resolution for optical imaging. In this review, we summarize recent advances in imaging technologies, dye scaffold modifications, and incorporation of these dyes into probes for SWIR imaging in mice. Finally, we offer an outlook on the future of SWIR detection in the field of chemical biology.