Light-sheet Fluorescence Microscopy Imaging Research Articles

An MR-based brain template and atlas for optical projection tomography and light sheet fluorescence microscopy in neuroscience.

Optical Projection Tomography (OPT) and light sheet fluorescence microscopy (LSFM) are high resolution optical imaging techniques, ideally suited for ex vivo 3D whole mouse brain imaging. Although they exhibit high specificity for their targets, the anatomical detail provided by tissue autofluorescence remains limited. T1-weighted images were acquired from 19 BABB or DBE cleared brains to create an MR template using serial longitudinal registration. Afterwards, fluorescent OPT and LSFM images were coregistered/normalized to the MR template to create fusion images. Volumetric calculations revealed a significant difference between BABB and DBE cleared brains, leading to develop two optimized templates, with associated tissue priors and brain atlas, for BABB (OCUM) and DBE (iOCUM). By creating fusion images, we identified virus infected brain regions, mapped dopamine transporter and translocator protein expression, and traced innervation from the eye along the optic tract to the thalamus and superior colliculus using cholera toxin B. Fusion images allowed for precise anatomical identification of fluorescent signal in the detailed anatomical context provided by MR. The possibility to anatomically map fluorescent signals on magnetic resonance (MR) images, widely used in clinical and preclinical neuroscience, would greatly benefit applications of optical imaging of mouse brain. These specific MR templates for cleared brains enable a broad range of neuroscientific applications integrating 3D optical brain imaging.

Distortion Correction and Denoising of Light Sheet Fluorescence Images.

Light Sheet Fluorescence Microscopy (LSFM) has emerged as a valuable tool for neurobiologists, enabling the rapid and high-quality volumetric imaging of mice brains. However, inherent artifacts and distortions introduced during the imaging process necessitate careful enhancement of LSFM images for optimal 3D reconstructions. This work aims to correct images slice by slice before reconstructing 3D volumes. Our approach involves a three-step process: firstly, the implementation of a deblurring algorithm using the work of K. Becker; secondly, an automatic contrast enhancement; and thirdly, the development of a convolutional denoising auto-encoder featuring skip connections to effectively address noise introduced by contrast enhancement, particularly excelling in handling mixed Poisson-Gaussian noise. Additionally, we tackle the challenge of axial distortion in LSFM by introducing an approach based on an auto-encoder trained on bead calibration images. The proposed pipeline demonstrates a complete solution, presenting promising results that surpass existing methods in denoising LSFM images. These advancements hold potential to significantly improve the interpretation of biological data.

Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy.

The pathogenesis of cancer and cardiovascular diseases is subjected to spatiotemporal regulation by the tissue microenvironment. Multiplex visualization of the microenvironmental components, including immune cells, vasculature and tissue hypoxia, provides critical information underlying the disease progression and therapy resistance, which is often limited by imaging depth and resolution in large-volume tissues. To this end, light sheet fluorescence microscopy, following tissue clarification and immunostaining, may generate three-dimensional high-resolution images at a whole-organ level. Here we provide a detailed description of light sheet fluorescence microscopy imaging analysis of immune cell composition, vascularization, tissue perfusion and hypoxia in mouse normal brains and hearts, as well as brain tumors. We describe a procedure for visualizing tissue vascularization, perfusion and hypoxia with a transgenic vascular labeling system. We provide the procedures for tissue collection, tissue semi-clearing and immunostaining. We further describe standard methods for analyzing tissue immunity and vascularity. We anticipate that this method will facilitate the spatial illustration of structure and function of the tissue microenvironmental components in cancer and cardiovascular diseases. The procedure requires 1-2 weeks and can be performed by users with expertise in general molecular biology.

Reduction of the trans-cortical vessel was associated with bone loss, another underlying mechanism of osteoporosis

RationaleNumerous studies have established a robust association between bone morrow microvascular diseases and osteoporosis. This study sought to investigate the relationship between alterations in trans-cortical vessel (TCVs) and the onset of osteoporosis in various mouse models. MethodsAged mice, ovariectomized mice, and db/db mice, were utilized as osteoporosis models. TCVs in the tibia were detected using tissue clearing and light sheet fluorescence microscopy imaging. Femurs bone mass were analyzed using micro-CT scanning. Correlations between the number of TCVs and bone mass were analyzed using Pearson correlation analysis. ResultsAll osteoporosis mouse models showed a significant reduction in the number of TCVs compared to the control group. Correlation analysis revealed a positive association between the number of TCVs and bone mass. TCVs were also expressed high levels of CD31 and EMCN proteins as type H vessels. ConclusionsThis study underscores a consistent correlation between the number of TCVs and bone mass. Moreover, TCVs may serve as a potential biomarker for bone mass evaluation.

Abstract 12907: Aging Drives Cerebrovascular Network Remodeling and Functional Changes in the Mouse Brain

Introduction: Cerebrovascular dysfunction has been implicated in age-related cognitive decline and dementia, but the underlying vascular mechanisms are not well understood. An improved understanding of the nature of normal cerebrovascular aging is needed to help to establish the role that vascular dysfunction might play in cognitive decline and dementia. Methods: Here, we asked how normal aging differentially impacts the vascular structure and function in different brain areas in mice. We investigated structural changes in aged cerebrovascular networks and pericytes utilizing serial two-photon tomography (STPT). To further investigate potential remodeling of different vascular compartments and pericyte subtypes, we utilized tissue clearing, 3D immunolabeling, and light sheet fluorescence microscopy (LSFM) imaging. We also assessed how healthy aging impacts brain hemodynamics in response to voluntary locomotion and whisker stimulation in awake, head-fixed mice using wide field optical signal imaging and two-photon imaging. We tested mice of both sexes at 2-month, 18-month (early aging), and 24-month (late aging) of age. Results: Whole-brain vascular tracing using STPT showed an overall ~10% decrease in vascular length and branching density, and LSFM imaging with 3D immunolabeling further revealed increased arteriole tortuosity in aged brains. We also uncovered a selective vascular and pericyte loss in deep cortical layers, basal forebrain regions, and the hippocampal network. This may contribute to their regional vulnerabilities in neurodegenerative disorders. Moreover, our in vivo imaging in awake, head-fixed mice identified delayed neurovascular coupling response and inefficient oxygen delivery in aged brains. Conclusions: Our study reveals aging-related brain-wide changes in vascular and mural cell types that can explain vulnerability and resilience of different brain areas in normal aging. Moreover, we identified an age-related decrease in brain oxygenation and delayed neurovascular coupling responses which can be linked with cognitive impairment in aged brains. These aging-related changes will serve as a common factor to understand many neurodegenerative disorders and cognition decline in the elderly population.

Image-based modeling of vascular organization to evaluate anti-angiogenic therapy

In tumor therapy anti-angiogenic approaches have the potential to increase the efficacy of a wide variety of subsequently or co-administered agents, possibly by improving or normalizing the defective tumor vasculature. Successful implementation of the concept of vascular normalization under anti-angiogenic therapy, however, mandates a detailed understanding of key characteristics and a respective scoring metric that defines an improved vasculature and thus a successful attempt. Here, we show that beyond commonly used parameters such as vessel patency and maturation, anti-angiogenic approaches largely benefit if the complex vascular network with its vessel interconnections is both qualitatively and quantitatively assessed. To gain such deeper insight the organization of vascular networks, we introduce a multi-parametric evaluation of high-resolution angiographic images based on light-sheet fluorescence microscopy images of tumors. We first could pinpoint key correlations between vessel length, straightness and diameter to describe the regular, functional and organized structure observed under physiological conditions. We found that vascular networks from experimental tumors diverted from those in healthy organs, demonstrating the dysfunctionality of the tumor vasculature not only on the level of the individual vessel but also in terms of inadequate organization into larger structures. These parameters proofed effective in scoring the degree of disorganization in different tumor entities, and more importantly in grading a potential reversal under treatment with therapeutic agents. The presented vascular network analysis will support vascular normalization assessment and future optimization of anti-angiogenic therapy.

Optical sectioning of label-free samples using standard bright-field microscopy.

The three-dimensional (3D) images produced by the traditional bright-field (BF) light microscope are ill-defined and therefore require reconstruction. Current alternatives to perform 3D BF imaging require dedicated instrumentation or extensive computer modeling. We report optical sectioning in bright-field microscopy (OSBM), a direct method for 3D imaging of label-free samples, where the BF inverse-imaging problem is solved in real space by using an elemental combination of hardware and software. Our method consists in acquiring z-stack images of minimally treated samples under Köhler illumination in the coherent regime, followed by a digital image processing pipeline designed to localize the source of axial intensity gradients that correspond to the z-locations of scatterers within the sample. We validate OSBM by visualizing fungal, animal tissue, and plant samples and comparing with light sheet fluorescence microscopy imaging, finding excellent match for sparse spatial distributions. Our work demonstrates how the standard microscope can be used as an effective 3D imaging device.

Three-dimensional Imaging Reveals Immune-driven Tumor-associated High Endothelial Venules as a Key Correlate of Tumor Rejection Following Depletion of Regulatory T Cells.

High endothelial venules (HEV) are specialized post capillary venules that recruit naïve T cells and B cells into secondary lymphoid organs (SLO) such as lymph nodes (LN). Expansion of HEV networks in SLOs occurs following immune activation to support development of an effective immune response. In this study, we used a carcinogen-induced model of fibrosarcoma to examine HEV remodeling after depletion of regulatory T cells (Treg). We used light sheet fluorescence microscopy imaging to visualize entire HEV networks, subsequently applying computational tools to enable topological mapping and extraction of numerical descriptors of the networks. While these analyses revealed profound cancer- and immune-driven alterations to HEV networks within LNs, these changes did not identify successful responses to treatment. The presence of HEV networks within tumors did however clearly distinguish responders from nonresponders. Finally, we show that a successful treatment response is dependent on coupling tumor-associated HEV (TA-HEV) development to T-cell activation implying that T-cell activation acts as the trigger for development of TA-HEVs which subsequently serve to amplify the immune response by facilitating extravasation of T cells into the tumor mass.

Abstract 1876: ROCKETS Science: A novel processing toolbox for light sheet microscopy reveals unknown binding sites for EpCAM-targeted antibodies

Abstract Summary: We present a novel light sheet fluorescence microscopy (LSFM)-based imaging platform and corresponding set of procedures for greatly improved preclinical investigation of the biodistribution of novel drug candidates by the example of an EpCAM-targeting antibody. Methods: An anti-EpCAM antibody (G.8.8R) was applied intravenously to mice. Whole mice or individual organs were optically cleared following novel protocols, which we termed Rapid Optical Clearing Kit for Enhanced Tissue Scanning (ROCKETS). The procedures enabled processing of mouse organs and entire bodies for LSFM. For the GI tract, we developed 3D-Swiss rolls, a method that enables fixation, clearing and imaging of intestines in a compact form as a whole. The new procedures allowed us to investigate the biodistribution of G.8.8R in the entire mouse body and highly detailed in individual organs. Results: The ROCKETS concept achieved full transparency of any mouse organ, the entire GI tract and whole mouse bodies. All positive organs were easily identified in scans of whole mice, thereby providing excellent guidance for scanning of positive individual organs at higher magnifications. We detected G8.8R bound to all normal cuboidal and columnar epithelia, as well as in lymphoid organs and were able to reproducibly score binding levels. All reported EpCAM+ tissues in mice were accessed by G8.8R after intravenous application and binding was restricted to basolateral membranes of epithelia, as expected from published expression analyses. Moreover, we detected G8.8R in tissues that were reported EpCAM- or were not investigated, e.g. gustatory papillae of the tongue, choroid plexi in the brain or lingual mucous salivary glands. 3D-Swiss rolls of the GI tract revealed a highly heterogeneous binding pattern in the stomach, while the pattern along the small intestine was overall homogeneous. All binding was restricted to basolateral membranes of epithelial cells. We detected a general gradient of signals, decreasing from the bottom of the crypts to differentiated cells in all tissues, corresponding to described EpCAM downregulation with progressing differentiation. Furthermore, we first describe significantly increased signals at the common bile duct, major and minor duodenal papillae, as well as the mucosa in proximity of Peyer's patches (PP). Conclusions: The developed ROCKETS toolbox allowed for simple preparation of mouse organs and bodies for high-quality LSFM imaging. Our investigations of the highly heterogeneous biodistribution of G8.8R revealed previously unknown EpCAM binding locations, which may have far-reaching implications for EpCAM-targeting therapeutics in general, many of which failed in clinical studies due to dose limiting toxicities. In the future, the developed LSFM-imaging platform may contribute valuable data to preclinical drug development studies of any targeted therapeutic. Citation Format: Joerg P. Mueller, Nils O'Brien, Franz Osl, Frank Herting, Christian Klein, Pablo Umana, Sara Colombetti, Thomas Poeschinger, Andreas Beilhack. ROCKETS Science: A novel processing toolbox for light sheet microscopy reveals unknown binding sites for EpCAM-targeted antibodies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1876.

Abstract 3650: Trace'n'Seq: Assessing neuronal infiltration and its impact in pancreatic ductal carcinoma

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive tumor entity with dismal prognosis. PDAC is characterized by an extensive desmoplastic stroma and the tumor microenvironment (TME) has been recognized to play crucial roles in tumor development, therapy resistance, progression and metastasis. Although different cell types of the TME have been molecularly analyzed, tumor-infiltrating neurons could not be considered so far, because their cell bodies are located in adjacent ganglia of the peripheral nervous system and thus they are not part of the tumor mass (Demir, Thiel et al, Nature Cancer 2020; Demir, Thiel et al. Cancer Cell 2020). One of the unique features of PDAC is the strong infiltration by nerve fibers which correlates directly with tumor malignancy. In recent years it has been shown that either neurotransmitters secreted by neurons, or modulators of neuronal infiltration secreted by cancer cells can influence tumor growth. Here we use 3D light sheet fluorescence microscopy imaging (LSFM) of full tissue cleared PDAC specimen of tumors growing in genetically engineered mouse models or patient-derived xenograft models. Our data showthat these PDACs are innervated by a complex array of sensory and sympathetic neurons. To molecularly analyse neurons innervating the tumor mass, we have developed a novel approach we termed Trace’n’seq. This combines retrograde axonal tracing and FACS analysis with single cell RNA sequencing with the aim to identify, isolate and analyse hundreds of traced neurons infiltrating tumors or their respective healthy organs. Thereby, we have identified previously undescribed neuronal cell types and provide a landscape of sympathetic and sensory nerves innervating the healthy pancreas as well as PDAC. Our single cell transcriptomic analysis revealed signs of reprogramming of neuronal behaviour orchestrated by the tumor cells. These datasets combined with single cell profiling of PDAC cells and its associated stroma provide a first complete, unbiased insight into neurons infiltrating both healthy pancreas and PDAC. Based on a comprehensive interactome analysis of the interplay between tumor cells, stroma and the neurons, we have identified various candidate genes involved in tumor-nerve signalling. We are currently performing gain-and loss- of function approaches to dissect the role of individual factors. In summary, with Trace'n'seq, we have developed a novel technology pipeline to isolate tissue innervating neurons to investigate the role of neuronal infiltration in the development and progression of PDAC. Citation Format: Vera Thiel, Simon Renders, Jasper Panten, Julian Mochayedi, Rienk Offringa, Martin Sprick, Andreas Trumpp. Trace'n'Seq: Assessing neuronal infiltration and its impact in pancreatic ductal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3650.

Quantitative analysis of illumination and detection corrections in adaptive light sheet fluorescence microscopy.

Light-sheet fluorescence microscopy (LSFM) is a high-speed, high-resolution and minimally phototoxic technique for 3D imaging of in vivo and in vitro specimens. LSFM exhibits optical sectioning and when combined with tissue clearing techniques, it facilitates imaging of centimeter scale specimens with micrometer resolution. Although LSFM is ubiquitous, it still faces two main challenges that effect image quality especially when imaging large volumes with high-resolution. First, the light-sheet illumination plane and detection lens focal plane need to be coplanar, however sample-induced aberrations can violate this requirement and degrade image quality. Second, introduction of sample-induced optical aberrations in the detection path. These challenges intensify when imaging whole organisms or structurally complex specimens like cochleae and bones that exhibit many transitions from soft to hard tissue or when imaging deep (> 2 mm). To resolve these challenges, various illumination and aberration correction methods have been developed, yet no adaptive correction in both the illumination and the detection path have been applied to improve LSFM imaging. Here, we bridge this gap, by implementing the two correction techniques on a custom built adaptive LSFM. The illumination beam angular properties are controlled by two galvanometer scanners, while a deformable mirror is positioned in the detection path to correct for aberrations. By imaging whole porcine cochlea, we compare and contrast these correction methods and their influence on the image quality. This knowledge will greatly contribute to the field of adaptive LSFM, and imaging of large volumes of tissue cleared specimens.

Elimination of stripe artifacts in light sheet fluorescence microscopy using an attention-based residual neural network.

Stripe artifacts can deteriorate the quality of light sheet fluorescence microscopy (LSFM) images. Owing to the inhomogeneous, high-absorption, or scattering objects located in the excitation light path, stripe artifacts are generated in LSFM images in various directions and types, such as horizontal, anisotropic, or multidirectional anisotropic. These artifacts severely degrade the quality of LSFM images. To address this issue, we proposed a new deep-learning-based approach for the elimination of stripe artifacts. This method utilizes an encoder-decoder structure of UNet integrated with residual blocks and attention modules between successive convolutional layers. Our attention module was implemented in the residual blocks to learn useful features and suppress the residual features. The proposed network was trained and validated by generating three different degradation datasets with different types of stripe artifacts in LSFM images. Our method can effectively remove different stripes in generated and actual LSFM images distorted by stripe artifacts. Besides, quantitative analysis and extensive comparison results demonstrated that our method performs the best compared with classical image-based processing algorithms and other powerful deep-learning-based destriping methods for all three generated datasets. Thus, our method has tremendous application prospects to LSFM, and its use can be easily extended to images reconstructed by other modalities affected by the presence of stripe artifacts.

MRI investigation of vascular remodeling for heterogeneous edema lesions in subacute ischemic stroke rat models: Correspondence between cerebral vessel structure and function

The spatial heterogeneity in the temporal occurrence of pseudo-normalization of MR apparent diffusion coefficient values for ischemic lesions may be related to morphological and functional vascular remodeling. As the area of accelerated pseudo-normalization tends to expand faster and more extensively into the chronic stage, detailed vascular characterization of such areas is necessary. During the subacute stage of transient middle cerebral artery occlusion rat models, the morphological size of the macrovasculature, microvascular vessel size index (VSI), and microvessel density (MVD) were quantified along with functional perfusion measurements of the relative cerebral blood flow (rCBF) and mean transit time (rMTT) of the corresponding areas (33 cases for each parameter). When compared with typical pseudo-normalization lesions, early pseudo-normalization lesions exhibited larger VSI and rCBF (p < 0.001) at reperfusion days 4 and 7, along with reduced MVD and elongated rMTT (p < 0.001) at reperfusion days 1, 4, and 7. The group median VSI and rCBF exhibited a strong positive correlation (r = 0.92), and the corresponding MVD and rMTT showed a negative correlation (r = −0.48). Light sheet fluorescence microscopy images were used to quantitatively validate the corresponding MRI-derived microvascular size, density, and cerebral blood volume.

Amelanotic B16-F10 Melanoma Compatible with Advanced Three-Dimensional Imaging Modalities

Amelanotic B16-F10 Melanoma Compatible with Advanced Three-Dimensional Imaging Modalities

Investigation of the extended focusing capability of the spherical aberration to enlarge the field of view in light-sheet fluorescence microscopy.

In light-sheet fluorescence microscopy (LSFM), using Gaussian beams for light-sheet generation results in a trade-off between the thickness and the field of view (FOV). Here we present a theoretical analysis of using spherical aberration to enlarge the FOV while keeping the light-sheet thickness small. Such spherical aberration can arise when focusing beams through an interface between materials of mismatched refractive indices. The depth-of-focus extension of the Gaussian beam is achieved when using air objectives to focus light into the samples dipped in the immersion medium with a higher refractive index. By scanning this elongated beam, a thin light sheet with a wide FOV can be used for LSFM imaging. Meanwhile, the accompanied sidelobes with the spherical aberrated light sheet, which are mainly distributed in the rear part of the light sheet, are also discussed. Simulation results show that an extended FOV of 64.4µm is possible for an objective lens of NA=0.3, which is about 5 times that of the unaberrated case. For such an extended FOV, a comparatively thin thickness of 1.38µm as well as the first sidelobe about 11.1% of the peak intensity in the center are also demonstrated.

An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO+ and Light Sheet Fluorescence Microscopy

In recent years, the combination of whole-brain immunolabelling, light sheet fluorescence microscopy (LSFM) and subsequent registration of data with a common reference atlas, has enabled 3D visualization and quantification of fluorescent markers or tracers in the adult mouse brain. Today, the common coordinate framework version 3 developed by the Allen’s Institute of Brain Science (AIBS CCFv3), is widely used as the standard brain atlas for registration of LSFM data. However, the AIBS CCFv3 is based on histological processing and imaging modalities different from those used for LSFM imaging and consequently, the data differ in both tissue contrast and morphology. To improve the accuracy and speed by which LSFM-imaged whole-brain data can be registered and quantified, we have created an optimized digital mouse brain atlas based on immunolabelled and solvent-cleared brains. Compared to the AIBS CCFv3 atlas, our atlas resulted in faster and more accurate mapping of neuronal activity as measured by c-Fos expression, especially in the hindbrain. We further demonstrated utility of the LSFM atlas by comparing whole-brain quantitative changes in c-Fos expression following acute administration of semaglutide in lean and diet-induced obese mice. In combination with an improved algorithm for c-Fos detection, the LSFM atlas enables unbiased and computationally efficient characterization of drug effects on whole-brain neuronal activity patterns. In conclusion, we established an optimized reference atlas for more precise mapping of fluorescent markers, including c-Fos, in mouse brains processed for LSFM.

3D imaging of undissected optically cleared Anopheles stephensi mosquitoes and midguts infected with Plasmodium parasites.

Malaria is a life-threatening disease, caused by Apicomplexan parasites of the Plasmodium genus. The Anopheles mosquito is necessary for the sexual replication of these parasites and for their transmission to vertebrate hosts, including humans. Imaging of the parasite within the insect vector has been attempted using multiple microscopy methods, most of which are hampered by the presence of the light scattering opaque cuticle of the mosquito. So far, most imaging of the Plasmodium mosquito stages depended on either sectioning or surgical dissection of important anatomical sites, such as the midgut and the salivary glands. Optical projection tomography (OPT) and light sheet fluorescence microscopy (LSFM) enable imaging fields of view in the centimeter scale whilst providing micrometer resolution. In this paper, we compare different optical clearing protocols and present reconstructions of the whole body of Plasmodium-infected, optically cleared Anopheles stephensi mosquitoes and their midguts. The 3D-reconstructions from OPT imaging show detailed features of the mosquito anatomy and enable overall localization of parasites in midguts. Additionally, LSFM imaging of mosquito midguts shows detailed distribution of oocysts in extracted midguts. This work was submitted as a pre-print to bioRxiv, available at https://www.biorxiv.org/content/10.1101/682054v2.

A practical staging atlas to study embryonic development of Octopus vulgaris under controlled laboratory conditions

BackgroundOctopus vulgaris has been an iconic cephalopod species for neurobiology research as well as for cephalopod aquaculture. It is one of the most intelligent and well-studied invertebrates, possessing both long- and short-term memory and the striking ability to perform complex cognitive tasks. Nevertheless, how the common octopus developed these uncommon features remains enigmatic. O. vulgaris females spawn thousands of small eggs and remain with their clutch during their entire development, cleaning, venting and protecting the eggs. In fact, eggs incubated without females usually do not develop normally, mainly due to biological contamination (fungi, bacteria, etc.). This high level of parental care might have hampered laboratory research on the embryonic development of this intriguing cephalopod.ResultsHere, we present a completely parameter-controlled artificial seawater standalone egg incubation system that replaces maternal care and allows successful embryonic development of a small-egged octopus species until hatching in a laboratory environment. We also provide a practical and detailed staging atlas based on bright-field and light sheet fluorescence microscopy imaging for precise monitoring of embryonic development. The atlas has a comparative section to benchmark stages to the different scales published by Naef (1928), Arnold (1965) and Boletzky (2016). Finally, we provide methods to monitor health and wellbeing of embryos during organogenesis.ConclusionBesides introducing the study of O. vulgaris embryonic development to a wider community, this work can be a high-quality reference for comparative evolutionary developmental biology.

Subtraction method via phase mask enables contrast enhancement in scanned Bessel light-sheet microscopy.

We report on the generation of a hollow Bessel beam with a hole along the direction of propagation by using an easy-to-implement phase mask and investigate its effectiveness to reduce the out-of-focus background in light-sheet fluorescence microscopy (LSFM) with scanned Bessel beams by subtraction imaging. Overlaying ${\pi }$π-phase retardation between the two equal parts of the Bessel beam across the entrance pupil of the objective lens, a hollow Bessel beam with zero intensity at the focal plane can be achieved. By optimizing the numerical aperture of the annular mask applied in the hollow Bessel beam, matched distributions of the ring system between the hollow Bessel beam and the conventional Bessel beam are achieved. By subtraction between the two LSFM images, the out-of-focus blur caused by the ring system of the Bessel beam can be significantly reduced. Comparison with conventional Bessel LSFM images exhibits a better sectioning capability and higher contrast.

Deep learning enables automated volumetric assessments of cardiac function in zebrafish.

ABSTRACTAlthough the zebrafish embryo is a powerful animal model of human heart failure, the methods routinely employed to monitor cardiac function produce rough approximations that are susceptible to bias and inaccuracies. We developed and validated a deep learning-based image-analysis platform for automated extraction of volumetric parameters of cardiac function from dynamic light-sheet fluorescence microscopy (LSFM) images of embryonic zebrafish hearts. This platform, the Cardiac Functional Imaging Network (CFIN), automatically delivers rapid and accurate assessments of cardiac performance with greater sensitivity than current approaches.This article has an associated First Person interview with the first author of the paper.