Light-sheet Imaging Research Articles

CooperationSplenic CD169+ marginal zone macrophages directly cross-prime CD8+ T cells in vivo using a vacuolar processing pathway

Cross-priming of CD8+ T cells is of critical importance in triggering CD8+ T cell responses against pathogens and tumors. It is commonly thought that conventional type 1 dendritic cells (cDC1) cross-prime with unequalled efficacy, conferred to them by a proteasome and TAP-dependent pathway. Here we present data challenging the unique cross-priming efficacy of both the cDC1 subset and the proteasome/TAP-dependent pathway. Splenic CD169 macrophages are strategically placed in the marginal zone for capture of blood-borne pathogens. However, they are considered unable to directly cross-present and to depend on antigen transfer to cDC1 for cross-priming. We have developed a protocol for purification of CD169 macrophages. Extensive characterization shows that these cells display morphology, phenotype and gene expression distinguishing them clearly from cDC1, cDC2, plasmacytoid DC and red pulp macrophages. In vitro, CD169 cells cross-present soluble, receptor-targeted and phagocytosed antigen with equal or better efficiency than cDC1. Remarkably, this is achieved through a vacuolar, BFA and epoxomicin-independent pathway. Using intravital biphoton microscopy, 3D light sheet imaging and antigen targeting to CD169, we show that CD169 macrophages establish long-lasting antigen-dependent contacts with cognate CD8+ T cells that result in T cell activation in situ and generation of triple-positive effector as well as memory cells. Therefore, splenic CD169 macrophages represent a second set of myeloid cells equipped for highly efficient cross-priming. The biological role of cross-priming by these cells as well as their cooperation with cDC1 cells are under investigation.

JAG1-NOTCH4 mechanosensing drives atherosclerosis.

Endothelial cell (EC) sensing of disturbed blood flow triggers atherosclerosis, a disease of arteries that causes heart attack and stroke, through poorly defined mechanisms. The Notch pathway plays a central role in blood vessel growth and homeostasis, but its potential role in sensing of disturbed flow has not been previously studied. Here, we show using porcine and murine arteries and cultured human coronary artery EC that disturbed flow activates the JAG1-NOTCH4 signaling pathway. Light-sheet imaging revealed enrichment of JAG1 and NOTCH4 in EC of atherosclerotic plaques, and EC-specific genetic deletion of Jag1 (Jag1ECKO) demonstrated that Jag1 promotes atherosclerosis at sites of disturbed flow. Mechanistically, single-cell RNA sequencing in Jag1ECKO mice demonstrated that Jag1 suppresses subsets of ECs that proliferate and migrate. We conclude that JAG1-NOTCH4 sensing of disturbed flow enhances atherosclerosis susceptibility by regulating EC heterogeneity and that therapeutic targeting of this pathway may treat atherosclerosis.

Ablating Lgr5-expressing prostatic stromal cells activates the ERK-mediated mechanosensory signaling and disrupts prostate tissue homeostasis.

SUMMARYFunctional implication of stromal heterogeneity in the prostate remains incompletely understood. Using lineage tracing and light-sheet imaging, we show that some fibroblast cells at the mouse proximal prostatic ducts and prostatic urethra highly express Lgr5. Genetic ablation of these anatomically restricted stromal cells, but not nonselective ablation of prostatic stromal cells, rapidly induces prostate epithelial turnover and dedifferentiation that are reversed following spontaneous restoration of the Lgr5+ stromal cells. RNA sequencing (RNA-seq) analysis indicates that ablating the Lgr5+ stromal cells activates a mechanosensory response. Ablating the Lgr5+ stromal cells impairs the control of prostatic ductal outlet, increases prostate tissue stiffness, and activates the mitogen-activated protein kinase (MAPK). Suppressing MAPK overrides the elevated epithelial proliferation. In summary, the Lgr5+ stromal cells regulate prostate tissue homeostasis and maintain its functional integrity in a long-distance manner. Our study implies that the cells at organ junctions most likely control organ homeostasis by sustaining a balanced mechanoforce.

Multiscale light-sheet organoid imaging framework

Organoids provide an accessible in vitro system to mimic the dynamics of tissue regeneration and development. However, long-term live-imaging of organoids remains challenging. Here we present an experimental and image-processing framework capable of turning long-term light-sheet imaging of intestinal organoids into digital organoids. The framework combines specific imaging optimization combined with data processing via deep learning techniques to segment single organoids, their lumen, cells and nuclei in 3D over long periods of time. By linking lineage trees with corresponding 3D segmentation meshes for each organoid, the extracted information is visualized using a web-based “Digital Organoid Viewer” tool allowing combined understanding of the multivariate and multiscale data. We also show backtracking of cells of interest, providing detailed information about their history within entire organoid contexts. Furthermore, we show cytokinesis failure of regenerative cells and that these cells never reside in the intestinal crypt, hinting at a tissue scale control on cellular fidelity.

Computational single-objective scanning light sheet (cSOLS)

Single-objective scanning light sheet (SOLS) imaging has fueled major advances in volumetric bioimaging because it supports low phototoxic, high-resolution imaging over an extended period. The remote imaging unit in the SOLS does not use a conventional epifluorescence image detection scheme (a single tube lens). In this paper, we propose a technique called the computational SOLS (cSOLS) that achieves light sheet imaging without the remote imaging unit. Using a single microlens array after the tube lens (lightfield imaging), the cSOLS is immediately compatible with conventional epifluorescence detection. The core of cSOLS is a Fast Optical Ray (FOR) model. FOR generates 3D imaging volume (40 × 40 × 14 µm3) using 2D lightfield images taken under SOLS illumination within 0.5 s on a standard central processing unit (CPU) without multicore parallel processing. In comparison with traditional lightfield retrieval approaches, FOR reassigns fluorescence photons and removes out-of-focus light to improve optical sectioning by a factor of 2, thereby achieving a spatial resolution of 1.59 × 1.92 × 1.39 µm3. cSOLS with FOR can be tuned over a range of oblique illumination angles and directions and, therefore, paves the way for next-generation SOLS imaging. cSOLS marks an important and exciting development of SOLS imaging with computational imaging capabilities.

High-Resolution Ex Vivo Tissue Clearing, Lightsheet Imaging, and Data Analysis to Support Macromolecular Drug and Biomarker Distribution in Whole Organs and Tumors

High-Resolution Ex Vivo Tissue Clearing, Lightsheet Imaging, and Data Analysis to Support Macromolecular Drug and Biomarker Distribution in Whole Organs and Tumors

Open-top light-sheet imaging of CLEAR emulsion for high-throughput loss-free analysis of massive fluorescent droplets

Digital droplet PCR (ddPCR) is classified as the third-generation PCR technology that enables absolute quantitative detection of nucleic acid molecules and has become an increasingly powerful tool for clinic diagnosis. We previously established a CLEAR-dPCR technique based on the combination of CLEAR droplets generated by micro-centrifuge-based microtubule arrays (MiCA) and insitu 3D readout by light-sheet fluorescence imaging. This CLEAR-dPCR technique attains very high readout speed and dynamic range. Meanwhile, it is free from sample loss and contamination, showing its advantages over commercial d-PCR technologies. However, a conventional orthogonal light-sheet imaging setup in CLEAR d-PCR cannot image multiple centrifuge tubes, thereby limiting its widespread application to large-scale, high-speed dd-PCR assays. Herein, we propose an in-parallel 3D dd-PCR readout technique based on an open-top light-sheet microscopy setup. This approach can continuously scan multiple centrifuge tubes which contain CLEAR emulsions with highly diverse concentrations, and thus further boost the scale and throughput of our 3D dd-PCR technique.

Depth random-access two-photon Bessel light-sheet imaging in brain tissue.

Two-photon light-sheet fluorescence microscopy enables high-resolution imaging of neural activity in brain tissue at a high frame rate. Traditionally, light-sheet microscopy builds up a 3D stack by multiple depth scans with uniform spatial intervals, which substantially limits the volumetric imaging speed. Here, we introduce the depth random-access light-sheet microscopy, allowing rapid switching scanning depth for light-sheet imaging. With a low-cost electrically tunable lens and minimum modification of an existing two-photon light-sheet imaging instrument, we demonstrated fast random depth hopping light-sheet imaging at 100 frames per second in the live brain slice. Through depth random-access, calcium activities for an astrocyte were recorded on four user-selected detection planes at a refreshing rate of 25 Hz.

High‐Throughput Parallel Optofluidic 3D‐Imaging Flow Cytometry

High-Throughput 3D Imaging Flow Cytometry In article number 2100126, Masashi Ugawa and Sadao Ota develop a high-throughput 3D imaging flow cytometry technology based on light-sheet imaging and acoustofluidic particle focusing. With a maximum detection throughput of over 2 000 cells/s, 3D image analysis of 4 × 105 cells is achieved to demonstrate practical 3D imaging flow cytometry. Cover illustration by Shinichiro Kinoshita.

Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification.

Current imaging approaches limit the ability to perform multi-scale characterization of three-dimensional (3D) organotypic cultures (organoids) in large numbers. Here, we present an automated multi-scale 3D imaging platform synergizing high-density organoid cultures with rapid and live 3D single-objective light-sheet imaging. It is composed of disposable microfabricated organoid culture chips, termed JeWells, with embedded optical components and a laser beam-steering unit coupled to a commercial inverted microscope. It permits streamlining organoid culture and high-content 3D imaging on a single user-friendly instrument with minimal manipulations and a throughput of 300 organoids per hour. We demonstrate that the large number of 3D stacks that can be collected via our platform allows training deep learning-based algorithms to quantify morphogenetic organizations of organoids at multi-scales, ranging from the subcellular scale to the whole organoid level. We validated the versatility and robustness of our approach on intestine, hepatic, neuroectoderm organoids and oncospheres.

Single-Lens Light-Sheet Fluorescence Microscopy Based on Micro-Mirror Array.

Conventional light sheet fluorescence microscopy (LSFM) utilizes two perpendicularly arranged objective lenses for optical excitation and detection, respectively. Such a configuration often limits the use of high-numerical-aperture (NA) objectives or requires specially designed long-working-distance objectives. Here, a LSFM based on a micro-mirror array (MMA) to enable light sheet imaging with a single objective lens is reported. The planar fluorescent emission excited by the light sheet illumination is collected by the same objective, relayed onto an MMA and detected by a side-view camera. The proposed scheme makes LSFM compatible to single objective imaging system and shows promising candidacy for high spatiotemporal imaging.

GIANI - open-source software for automated analysis of 3D microscopy images.

ABSTRACTThe study of cellular and developmental processes in physiologically relevant three-dimensional (3D) systems facilitates an understanding of mechanisms underlying cell fate, disease and injury. While cutting-edge microscopy technologies permit the routine acquisition of 3D datasets, there is currently a limited number of open-source software packages to analyse such images. Here, we describe General Image Analysis of Nuclei-based Images (GIANI; https://djpbarry.github.io/Giani), new software for the analysis of 3D images. The design primarily facilitates segmentation of nuclei and cells, followed by quantification of morphology and protein expression. GIANI enables routine and reproducible batch-processing of large numbers of images, and comes with scripting and command line tools. We demonstrate the utility of GIANI by quantifying cell morphology and protein expression in confocal images of mouse early embryos and by segmenting nuclei from light-sheet microscopy images of the flour beetle embryo. We also validate the performance of the software using simulated data. More generally, we anticipate that GIANI will be a useful tool for researchers in a variety of biomedical fields.

Mapping Brain‐wide Pathologies in Mouse Models of Neurodegeneration

Neurodegenerative diseases are characterized by deposition of abnormal protein aggregates in the brain in predictable spatial and temporal patterns. This selective vulnerability to pathology, which encompasses vulnerabilities of cell types, regions, and brain networks, is a fundamental feature of disease that is not yet understood. Mouse models of human disease are required for preclinical investigations into molecular and cellular mechanisms underlying vulnerability and resilience. Yet, little data exists on how well aligned commonly used models are with the brain‐wide human spatiotemporal vulnerability maps. To address this gap and more deeply characterize existing models, we built a high‐throughput whole brain imaging and informatics pipeline to systematically quantify spatiotemporal patterns of disease‐relevant pathologies in mice. Using whole brain clearing, antibody labeling, and lightsheet imaging, we have quantified tyrosine hydroxylase levels in a mouse model of Parkinson’s Disease with nigrostriatal degeneration and show the utility of 3D imaging to identify disease‐relevant regional vulnerabilities.

Optimized U-Net model for 3D light-sheet image segmentation of zebrafish trunk vessels.

The growth of zebrafish's vessels can be used as an indicator of the vascular development process and to study the biological mechanisms. The three-dimensional (3D) structures of zebrafish's trunk vessels could be imaged by state-of-art light-sheet fluorescent microscopy with high efficiency. A large amount of data was then produced. Accurate segmentation of these 3D images becomes a new bottleneck for automatic and quantitative analysis. Here, we propose a Multi-scale 3D U-Net model to perform the segmentation of trunk vessels. The segmentation accuracies of 82.3% and 83.0%, as evaluated by the IoU (Intersection over Union) parameter, were achieved for intersegmental vessels and the dorsal longitudinal anastomotic vessels respectively. The growth of zebrafish vasculature from 42-62 hours was then analyzed quantitatively.

Edinger-Westphal peptidergic neurons enable maternal preparatory nesting.

SummaryOptimizing reproductive fitness in mammalians requires behavioral adaptations during pregnancy. Maternal preparatory nesting is an essential behavior for the survival of the upcoming litter. Brain-wide immediate early gene mapping in mice evoked by nesting sequences revealed that phases of nest construction strongly activate peptidergic neurons of the Edinger-Westphal nucleus in pregnant mice. Genetic ablation, bidirectional neuromodulation, and in vitro and in vivo activity recordings demonstrated that these neurons are essential to modulate arousal before sleep to promote nesting specifically. We show that these neurons enable the behavioral effects of progesterone on preparatory nesting by modulating a broad network of downstream targets. Our study deciphers the role of midbrain CART+ neurons in behavioral adaptations during pregnancy vital for reproductive fitness.

High Spatial and Temporal Resolution NIR-IIb Gastrointestinal Imaging in Mice.

Conventional biomedical imaging modalities, including endoscopy, X-rays, and magnetic resonance, are invasive and insufficient in spatial and temporal resolutions for gastrointestinal (GI) tract imaging to guide prognosis and therapy. Here we report a noninvasive method based on lanthanide-doped nanocrystals with ∼1530 nm fluorescence in the near-infrared-IIb window (NIR-IIb, 1500-1700 nm). The rational design of nanocrystals have led to an absolute quantum yield (QY) up to 48.6%. Further benefiting from the minimized scattering through the NIR-IIb window, we enhanced the spatial resolution to ∼1 mm in GI tract imaging, which is ∼3 times higher compared with the near-infrared-IIa (NIR-IIa, 1000-1500 nm) method. The approach also realized a high temporal resolution of 8 frames per second; thus the moment of mice intestinal peristalsis can be captured. Furthermore, with a light-sheet imaging system, we demonstrated a three-dimensional (3D) imaging on the GI tract. Moreover, we successfully translated these advances to diagnose inflammatory bowel disease.

Distinct spatial arrangements of ACE2 and TMPRSS2 expression in Syrian hamster lung lobes dictates SARS-CoV-2 infection patterns.

SARS-CoV-2 attaches to angiotensin-converting enzyme 2 (ACE2) to gain entry into cells after which the spike protein is cleaved by the transmembrane serine protease 2 (TMPRSS2) to facilitate viral-host membrane fusion. ACE2 and TMPRSS2 expression profiles have been analyzed at the genomic, transcriptomic, and single-cell RNAseq levels. However, transcriptomic data and actual protein validation convey conflicting information regarding the distribution of the biologically relevant protein receptor in whole tissues. To describe the organ-level architecture of receptor expression, related to the ability of ACE2 and TMPRSS2 to mediate infectivity, we performed a volumetric analysis of whole Syrian hamster lung lobes. Lung tissue of infected and control animals was stained using antibodies against ACE2 and TMPRSS2, combined with SARS-CoV-2 nucleoprotein staining. This was followed by light-sheet microscopy imaging to visualize their expression and related infection patterns. The data demonstrate that infection is restricted to sites containing both ACE2 and TMPRSS2, the latter is expressed in the primary and secondary bronchi whereas ACE2 is predominantly observed in the bronchioles and alveoli. Conversely, infection completely overlaps where ACE2 and TMPRSS2 co-localize in the tertiary bronchi, bronchioles, and alveoli.

200 Unbiased Interrogation of Whole Brain Circuits Identifies Neurons That Restore Walking After Spinal Cord Injury

INTRODUCTION: Currently, there is no cure for locomotor deficits after spinal cord injury (SCI). Despite advances in spinal cord modulation with epidural electrical stimulation, there remains a paucity of therapies targeting the brain due to a poor understanding of the brain’s role post-SCI. Recently developed tissue clearing and light sheet imaging techniques have permitted unbiased three-dimensional interrogation of whole brain circuits, which has opened unexplored avenues for SCI-related brain interrogation. METHODS: We established a novel brain interrogation pipeline for SCI by optimizing mouse whole brain clearing, imaging, and atlas registration after a spontaneous recovery lateral hemisection model. We examined both whole brain cell activity and connectivity with the lumbar cord using cFos immunolabelling and virus-mediated projection tracing, respectively, to identify a functionally and anatomically dynamic region correlating with recovery. We interrogated the locomotor role of this region with optogenetics and chemogenetics. In a more clinically relevant rat contusion SCI, we assessed the translatability of deep brain electrical stimulation (DBS) of this region by leveraging an established bipedal robotic interface and rehabilitation paradigm. RESULTS: We unexpectedly uncovered the lateral hypothalamus (LH) to be a functionally and anatomically dynamic region post-SCI correlating with recovery. Optogenetic stimulation of mouse LHVglut2 neurons significantly augmented locomotor function, which required medullary reticular formation (MRF) Vglut2-positive neurons. In line with previously demonstrated sparing of MRF-to-spinal cord projections after contusion SCI, we found that LH DBS in rats post-contusion SCI could acutely robustly augment bipedal rat locomotor function. CONCLUSION: This is the first demonstration of the LH's role in locomotion post-SCI. The LH is a novel DBS target that robustly augmented locomotor function, dependent on LH and brainstem glutamatergic cells.

βIII-Tubulin Structural Domains Regulate Mitochondrial Network Architecture in an Isotype-Specific Manner.

βIII-tubulin is a neuronal microtubule protein that is aberrantly expressed in epithelial cancers. The microtubule network is implicated in regulating the architecture and dynamics of the mitochondrial network, although the isotype-specific role for β-tubulin proteins that constitute this microtubule network remains unclear. High-resolution electron microscopy revealed that manipulation of βIII-tubulin expression levels impacts the volume and shape of mitochondria. Analysis of the structural domains of the protein identifies that the C-terminal tail of βIII-tubulin, which distinguishes this protein from other β-tubulin isotypes, significantly contributes to the isotype-specific effects of βIII-tubulin on mitochondrial architecture. Mass spectrometry analysis of protein–protein interactions with β-tubulin isotypes identifies that βIII-tubulin specifically interacts with regulators of mitochondrial dynamics that may mediate these functional effects. Advanced quantitative dynamic lattice light sheet imaging of the mitochondrial network reveals that βIII-tubulin promotes a more dynamic and extended reticular mitochondrial network, and regulates mitochondrial volume. A regulatory role for the βIII-tubulin C-terminal tail in mitochondrial network dynamics and architecture has widespread implications for the maintenance of mitochondrial homeostasis in health and disease.

Microscopic Imaging Methods for Organ-on-a-Chip Platforms.

Microscopic imaging is essential and the most popular method for in situ monitoring and evaluating the outcome of various organ-on-a-chip (OOC) platforms, including the number and morphology of mammalian cells, gene expression, protein secretions, etc. This review presents an overview of how various imaging methods can be used to image organ-on-a-chip platforms, including transillumination imaging (including brightfield, phase-contrast, and holographic optofluidic imaging), fluorescence imaging (including confocal fluorescence and light-sheet fluorescence imaging), and smartphone-based imaging (including microscope attachment-based, quantitative phase, and lens-free imaging). While various microscopic imaging methods have been demonstrated for conventional microfluidic devices, a relatively small number of microscopic imaging methods have been demonstrated for OOC platforms. Some methods have rarely been used to image OOCs. Specific requirements for imaging OOCs will be discussed in comparison to the conventional microfluidic devices and future directions will be introduced in this review.