Optical sectioning deep inside live embryos by selective plane illumination microscopy

3D image stack reconstruction in live cell microscopy of Drosophila muscles and its validation

Rapid movements of live tissues during the acquisition of 3D image stacks can result in misalignments between successive image slices. The remodeling of the muscles in Drosophila metamorphosis is an example where sporadic motion during image acquisition impede image analysis and volume visualization. Most of the image stack registration algorithms applied in microscopy are aimed at the linear alignment of fixed histological sections. However, live muscles are nonrigid objects and their contractions and relaxations represent nonlinear transformations that cannot be properly rectified by applying purely linear registration methods. We developed a fully automated area-based nonrigid stack registration (NSR) method that minimizes the mean square error of intensities between successive image slices. The mapping function is formulated using the thin plate spline (TPS). A hierarchical linear to nonlinear, coarse to fine matching strategy is applied to ensure stability and fast convergence. Topological structure is preserved by constraining the step size of the nonlinear transformation. To assess the accuracy of 3D reconstruction, we propose a new benchmarking method that measures geometrical features of restored nuclei. We tested our algorithm on image stacks generated by laser scanning confocal microscopy that show live muscles during the prepupal stage of Drosophila metamorphosis. Our registration algorithm is able to restore image stacks that are distorted by periodic contraction of muscles. Quantitative assessment of registration performance agrees well with qualitative visual inspection. Our NSR method is able to restore image stacks for the purpose of visualization and quantitative analysis of Drosophila metamorphosis and, potentially, various other processes in developmental biology studied by 3D live cell microscopy.

Resolution of ultramicroscopy and field of view analysis

In a recent publication we described a microscopical technique called Ultramicroscopy, combined with a histological procedure that makes biological samples transparent. With this combination we can gather three-dimensional image data of large biological samples. Here we present the theoretical analysis of the z-resolution. By analyzing the cross-section of the illuminating sheet of light we derive resolution values according to the Rayleigh-criterion. Next we investigate the resolution adjacent to the focal point of the illumination beam, analyze throughout what extend the illumination beam is of acceptable sharpness and investigate the resolution improvements caused by the objective lens. Finally we conclude with a useful rule for the sampling rates. These findings are of practical importance for researchers working with Ultramicroscopy to decide on adequate sampling rates. They are also necessary to modify deconvolution techniques to gain further image improvements.

The Gal4/UAS toolbox in zebrafish: new approaches for defining behavioral circuits

Over recent years, several groundbreaking techniques have been developed that allow for the anatomical description of neurons, and the observation and manipulation of their activity. Combined, these approaches should provide a great leap forward in our understanding of the structure and connectivity of the nervous system and how, as a network of individual neurons, it generates behavior. Zebrafish, given their external development and optical transparency, are an appealing system in which to employ these methods. These traits allow for direct observation of fluorescence in describing anatomy and observing neural activity, and for the manipulation of neurons using a host of light-triggered proteins. Gal4/Upstream Activating Sequence techniques, as they are based on a binary system, allow for the flexible deployment of a range of transgenes in expression patterns of interest. As such, they provide a promising approach for viewing neurons in a variety of ways, each of which can reveal something different about their structure, connectivity, or function. In this study, the author will review recent progress in the development of the Gal4/Upstream Activating Sequence system in zebrafish, feature examples of promising studies to date, and examine how various new technologies can be used in the future to untangle the complex mechanisms by which behavior is generated.

Genetic evidence for a noncanonical function of seryl-tRNA synthetase in vascular development

In a recent genetic screen, we identified mutations in genes important for vascular development and maintenance in zebrafish (Jin et al. Dev Biol. 2007;307:29-42). Mutations [corrected] at the adrasteia (adr) locus cause a pronounced dilatation of the aortic arch vessels as well as aberrant patterning of the hindbrain capillaries and, to a lesser extent, intersomitic vessels. This dilatation of the aortic arch vessels does not appear to be caused by increased cell proliferation but is dependent on vascular endothelial growth factor (Vegf) signaling. By positional cloning, we isolated seryl-tRNA synthetase (sars) as the gene affected by the adr mutations. Small interfering RNA knockdown experiments in human umbilical vein endothelial cell cultures indicate that SARS also regulates endothelial sprouting. These analyses of zebrafish and human endothelial cells reveal a new noncanonical function of Sars in endothelial development.

Ultramicroscopy reveals axonal transport impairments in cortical motor neurons at prion disease

The functional imaging of neuronal circuits of the central nervous system is crucial for phenotype screenings or investigations of defects in neurodegenerative disorders. Current techniques yield either low penetration depth, yield poor resolution, or are restricted by the age of the animals. Here, we present a novel ultramicroscopy protocol for fluorescence imaging and three-dimensional reconstruction in the central nervous system of adult mice. In combination with tracing as a functional assay for axonal transport, retrogradely labeled descending motor neurons were visualized with >4 mm penetration depth. The analysis of the motor cortex shortly before the onset of clinical prion disease revealed that >80% neurons have functional impairments in axonal transport. Our study provides evidence that prion disease is associated with severe axonal transport defects in the cortical motor neurons and suggests a novel mechanism for prion-mediated neurodegeneration.

Advances in the speed and resolution of light microscopy

Neurobiological processes occur on spatiotemporal scales spanning many orders of magnitude. Greater understanding of these processes therefore demands improvements in the tools used in their study. Here we review recent efforts to enhance the speed and resolution of one such tool, fluorescence microscopy, with an eye toward its application to neurobiological problems. On the speed front, improvements in beam scanning technology, signal generation rates, and photodamage mediation are bringing us closer to the goal of real-time functional imaging of extended neural networks. With regard to resolution, emerging methods of adaptive optics may lead to diffraction-limited imaging or much deeper imaging in optically inhomogeneous tissues, and super-resolution techniques may prove a powerful adjunct to electron microscopic methods for nanometric neural circuit reconstruction.

Live cell fluorescence microscopy to study microbial pathogenesis

Advances in microscopy and fluorescent probes provide new insight into the nanometer-scale biochemistry governing the interactions between eukaryotic cells and pathogens. When combined with mathematical modelling, these new technologies hold the promise of qualitative, quantitative and predictive descriptions of these pathways. Using the light microscope to study the spatial and temporal relationships between pathogens, host cells and their respective biochemical machinery requires an appreciation for how fluorescent probes and imaging devices function. This review summarizes how live cell fluorescence microscopy with common instruments can provide quantitative insight into the cellular and molecular functions of hosts and pathogens.

Live-imaging fluorescent proteins in mouse embryos: multi-dimensional, multi-spectral perspectives

Microscopy has always been an obligate tool in the field of developmental biology, a goal of which is to elucidate the essential cellular and molecular interactions that coordinate the specification of different cell types and the establishment of body plans. The 2008 Nobel Prize in chemistry was awarded 'for the discovery and development of the green fluorescent protein, GFP' in recognition that the discovery of genetically encoded fluorescent proteins (FPs) has spearheaded a revolution in applications for imaging of live cells. With the development of more-sophisticated imaging technology and availability of FPs with different spectral characteristics, dynamic processes can now be live-imaged at high resolution in situ in embryos. Here, we review some recent advances in this rapidly evolving field as applied to live-imaging capabilities in the mouse, the most genetically tractable mammalian model organism for embryologists.

Three-dimensional coherent transfer function for a confocal microscope with two D-shaped pupils

The three-dimensional coherent transfer function for D-shaped pupils in reflection-mode confocal scanning microscopy is analytically derived under the paraxial approximation. Three-dimensional numerical plots are presented, showing the dependence of the transfer functions on the width of a central divider. The applications in fiber-optical confocal scanning microscopy are also discussed.

Tomographic imaging of macroscopic biomedical objects in high resolution and three dimensions using orthogonal-plane fluorescence optical sectioning

A new optical-fluorescence microscopy technique, called HR-OPFOS, is discussed and situated among similar OPFOS-implementations. OPFOS stands for orthogonal-plane fluorescence optical sectioning and thus is categorized as a laser light sheet based fluorescence microscopy method. HR-OPFOS is used to make tomographic recordings of macroscopic biomedical specimens in high resolution. It delivers cross sections through the object under study with semi-histological detail, which can be used to create three-dimensional computer models for finite-element modeling or anatomical studies. The general innovation of this class of microscopy setup consists of the separation of the illumination and observation axes, but now in our setup combined with focal line scanning to improve sectioning resolution. HR-OPFOS is demonstrated on gerbil hearing organs and on mouse and bird brains. The necessary specimen preparation is discussed.

Recent advances in three-dimensional multicellular spheroid culture for biomedical research

Many types of mammalian cells can aggregate and differentiate into 3-D multicellular spheroids when cultured in suspension or a nonadhesive environment. Compared to conventional monolayer cultures, multicellular spheroids resemble real tissues better in terms of structural and functional properties. Multicellular spheroids formed by transformed cells are widely used as avascular tumor models for metastasis and invasion research and for therapeutic screening. Many primary or progenitor cells on the other hand, show significantly enhanced viability and functional performance when grown as spheroids. Multicellular spheroids in this aspect are ideal building units for tissue reconstruction. Here we review the current understanding of multicellular spheroid formation mechanisms, their biomedical applications, and recent advances in spheroid culture, manipulation, and analysis techniques.

Cardio-respiratory control during early development in the model animal zebrafish

Independent of species, the cardiovascular system is the first functioning component of developing vertebrate embryos. One of the main hypotheses is the assumption that larval and juvenile stages of fish and amphibians are not just smaller versions of an adult phenotype. In this review, the cardiovascular and respiratory responses to environmental, genetic and epigenetic perturbations are discussed in detail to understand the relationships between cardiac and respiratory performance, haematopoiesis for embryonic or larval stages with special focus on the popular model animal, the zebrafish. Zebrafish are tiny animals which have many advantages as a model organism in analysis of the cardio-respiratory system. It obtains sufficient amounts of oxygen via bulk diffusion, in contrast to convection-dependent mammals. It is possible to study genetic mutants even with extreme defective phenotypes of the cardio-respiratory system in order to understand its developmental and physiological mechanisms. It has become apparent that the cardio-respiratory system and its control starts functioning very early during development, long before oxygen uptake becomes diffusion limited in zebrafish. Finally, recent improvements in imaging techniques for the use of fish models relevant for developmental physiology and biomedical research are discussed.

Detection of deformable objects in 3D images using Markov-Chain Monte Carlo and spherical harmonics

We address the problem of segmenting 3D microscopic volumetric intensity images of a collection of spatially correlated objects (such as fluorescently labeled nuclei in a tissue). This problem arises in the study of tissue morphogenesis where cells and cellular components are organized in accord with biological role and fate. We formulate the image model as stochastically generated based on biological priors and physics of image formation. We express the segmentation problem in terms of Bayesian inference and use data-driven Markov Chain Monte Carlo to fit the image model to data. We perform an initial step in which the intensity volume is approximated as an expansion in 4D spherical harmonics, the coefficients of which capture the general organization of objects. Since cell nuclei are membrane-bound their shapes are subject to membrane lipid bilayer bending energy, which we use to constrain individual contours. Moreover, we parameterize the nuclear contours using spherical harmonic functions, which provide a shape description with no restriction to particular symmetries. We demonstrate the utility of our approach using synthetic and real fluorescence microscopy data.

Multilayer three-dimensional super resolution imaging of thick biological samples

Recent advances in optical microscopy have enabled biological imaging beyond the diffraction limit at nanometer resolution. A general feature of most of the techniques based on photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM) has been the use of thin biological samples in combination with total internal reflection, thus limiting the imaging depth to a fraction of an optical wavelength. However, to study whole cells or organelles that are typically up to 15 microm deep into the cell, the extension of these methods to a three-dimensional (3D) super resolution technique is required. Here, we report an advance in optical microscopy that enables imaging of protein distributions in cells with a lateral localization precision better than 50 nm at multiple imaging planes deep in biological samples. The approach is based on combining the lateral super resolution provided by PALM with two-photon temporal focusing that provides optical sectioning. We have generated super-resolution images over an axial range of approximately 10 microm in both mitochondrially labeled fixed cells, and in the membranes of living S2 Drosophila cells.

Optically sectioned imaging by oblique plane microscopy

This paper describes a new optically sectioning microscopy technique based on oblique selective plane illumination combined with oblique imaging. This method differs from previous selective plane illumination techniques as the same high numerical aperture lens is used to both illuminate and image the specimen. Initial results obtained using fluorescent pollen grains are presented, together with a measurement of the resolution of the system and an analysis of the potential performance of future systems. Since only the plane of the specimen that is being imaged is illuminated, this technique is particularly suited to time-lapse 3-D imaging of sensitive biological systems where photobleaching and phototoxicity must be kept to a minimum, and it could also be applied to image microfluidic technology for lab-on-a-chip, cytometry and other applications.

In vivo assessment of cold adaptation in insect larvae by magnetic resonance imaging and magnetic resonance spectroscopy

BACKGROUND

Temperatures below the freezing point of water and the ensuing ice crystal formation pose serious challenges to cell structure and function. Consequently, species living in seasonally cold environments have evolved a multitude of strategies to reorganize their cellular architecture and metabolism, and the underlying mechanisms are crucial to our understanding of life. In multicellular organisms, and poikilotherm animals in particular, our knowledge about these processes is almost exclusively due to invasive studies, thereby limiting the range of conclusions that can be drawn about intact living systems.

METHODOLOGY

Given that non-destructive techniques like (1)H Magnetic Resonance (MR) imaging and spectroscopy have proven useful for in vivo investigations of a wide range of biological systems, we aimed at evaluating their potential to observe cold adaptations in living insect larvae. Specifically, we chose two cold-hardy insect species that frequently serve as cryobiological model systems--the freeze-avoiding gall moth Epiblema scudderiana and the freeze-tolerant gall fly Eurosta solidaginis.

RESULTS

In vivo MR images were acquired from autumn-collected larvae at temperatures between 0 degrees C and about -70 degrees C and at spatial resolutions down to 27 microm. These images revealed three-dimensional (3D) larval anatomy at a level of detail currently not in reach of other in vivo techniques. Furthermore, they allowed visualization of the 3D distribution of the remaining liquid water and of the endogenous cryoprotectants at subzero temperatures, and temperature-weighted images of these distributions could be derived. Finally, individual fat body cells and their nuclei could be identified in intact frozen Eurosta larvae.

CONCLUSIONS

These findings suggest that high resolution MR techniques provide for interesting methodological options in comparative cryobiological investigations, especially in vivo.

Miniaturization and defocus correction for objective-coupled planar illumination microscopy

Recently, a light sheet-based technique called objective-coupled planar illumination (OCPI) microscopy [Holekamp et al., Neuron 57, 661 (2008)] was shown to permit low-phototoxicity, high-speed, three-dimensional fluorescence imaging of extended tissue samples. Here, we introduce two major improvements in OCPI microscopy. First, we miniaturize the objective coupler by using a uniaxial gradient-index lens to produce the light sheet. Second, we demonstrate theoretically and experimentally that refractive index mismatch at the fluid/tissue interface causes a significant defocus aberration. By introducing the ability to tune the angle of the light sheet, we show that defocus correction in a miniaturized OCPI microscope leads to a significant improvement in image sharpness deeper into tissue.

The divided aperture technique for microscopy through scattering media

A diffraction analysis is presented for image formation in confocal microscopy using the divided aperture technique, which uses two D-shaped apertures (also called specular microscopy). The effects of increasing the width of a divider, that separates the two D shapes, are investigated. As the width is increased, the resolution degrades. The efficiency of singly-scattered light rejection is not improved with increased width.

Fluorescence lifetime optical projection tomography

We describe a quantitative fluorescence projection tomography technique which measures the 3-D fluorescence lifetime distribution in optically cleared specimens up 1 cm in diameter. This is achieved by acquiring a series of wide-field time-gated images at different relative time delays with respect to a train of excitation pulses, at a number of projection angles. For each time delay, the 3-D time-gated intensity distribution is reconstructed using a filtered back projection algorithm and the fluorescence lifetime subsequently determined for each reconstructed horizontal plane by iterative fitting to a mono-exponential decay. Due to its inherently ratiometric nature, fluorescence lifetime is robust against intensity based artefacts as well as producing a quantitative measure of the fluorescence signal. We present a 3-D fluorescence lifetime reconstruction of a mouse embryo labelled with an alexa-488 conjugated antibody targeted to the neurofilament, which clearly differentiates between the extrinsic label and the autofluorescence, particularly from the heart and dorsal aorta.

Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage

Light-sheet-based fluorescence microscopy (LSFM) is a fluorescence technique that combines optical sectioning, the key capability of confocal and two-photon fluorescence microscopes with multiple-view imaging, which is used in optical tomography. In contrast to conventional wide-field and confocal fluorescence microscopes, a light sheet illuminates only the focal plane of the detection objective lens from the side. Excitation is, thus, restricted to the fluorophores in the volume near the focal plane. This provides optical sectioning and allows the use of regular cameras in the detection process. Compared to confocal fluorescence microscopy, LSFM reduces photo bleaching and photo toxicity by up to three orders of magnitude. In LSFM, the specimen is embedded in a transparent block of hydrogel and positioned relative to the stationary light sheet using precise motorized translation and rotation stages. This feature is used to image any plane in a specimen. Additionally, multiple views obtained along different angles can be combined into a single data set with an improved resolution. LSFMs are very well suited for imaging large live specimens over long periods of time. However, they also perform well with very small specimens such as single yeast cells. This perspective introduces the principles of LSFM, explains the challenges of specimen preparation, and introduces the basics of a microscopy that takes advantage of multiple views.

Regulation of neurocoel morphogenesis by Pard6 gamma b

The Par3/Par6/aPKC protein complex plays a key role in the establishment and maintenance of apicobasal polarity, a cellular characteristic essential for tissue and organ morphogenesis, differentiation and homeostasis. During a forward genetic screen for liver and pancreas mutants, we identified a pard6gammab mutant, representing the first known pard6 mutant in a vertebrate organism. pard6gammab mutants exhibit defects in epithelial tissue development as well as multiple lumens in the neural tube. Analyses of the cells lining the neural tube cavity, or neurocoel, in wildtype and pard6gammab mutant embryos show that lack of Pard6gammab function leads to defects in mitotic spindle orientation during neurulation. We also found that the PB1 (aPKC-binding) and CRIB (Cdc-42-binding) domains and the KPLG amino acid sequence within the PDZ domain (Pals1-and Crumbs binding) are not required for Pard6gammab localization but are essential for its function in neurocoel morphogenesis. Apical membranes are reduced, but not completely absent, in mutants lacking the zygotic, or both the maternal and zygotic, function of pard6gammab, leading us to examine the localization and function of the three additional zebrafish Pard6 proteins. We found that Pard6alpha, but not Pard6beta or Pard6gammaa, could partially rescue the pard6gammab(s441) mutant phenotypes. Altogether, these data indicate a previously unappreciated functional diversity and complexity within the vertebrate pard6 gene family.

In vivo imaging of the inflammatory receptor CD40 after cerebral ischemia using a fluorescent antibody

BACKGROUND AND PURPOSE

Brain inflammation is a hallmark of stroke, where it has been implicated in tissue damage as well as in repair. Imaging technologies that specifically visualize these processes are highly desirable. In this study, we explored whether the inflammatory receptor CD40 can be noninvasively and specifically visualized in mice after cerebral ischemia using a fluorescent monoclonal antibody, which we labeled with the near-infrared fluorescence dye Cy5.5 (Cy5.5-CD40MAb).

METHODS

Wild-type and CD40-deficient mice were subjected to transient middle cerebral artery occlusion. Mice were either intravenously injected with Cy5.5-CD40MAb or control Cy5.5-IgGMAb. Noninvasive and ex vivo near-infrared fluorescence imaging was performed after injection of the compounds. Probe distribution and specificity was further assessed with single-plane illumination microscopy, immunohistochemistry, and confocal microscopy.

RESULTS

Significantly higher fluorescence intensities over the stroke-affected hemisphere, compared to the contralateral side, were only detected noninvasively in wild-type mice that received Cy5.5-CD40MAb, but not in CD40-deficient mice injected with Cy5.5-CD40MAb or in wild-type mice that were injected with Cy5.5-IgGMAb. Ex vivo near-infrared fluorescence showed an intense fluorescence within the ischemic territory only in wild-type mice injected with Cy5.5-CD40MAb. In the brains of these mice, single-plane illumination microscopy demonstrated vascular and parenchymal distribution, and confocal microscopy revealed a partial colocalization of parenchymal fluorescence from the injected Cy5.5-CD40MAb with activated microglia and blood-derived cells in the ischemic region.

CONCLUSIONS

The study demonstrates that a CD40-targeted fluorescent antibody enables specific noninvasive detection of the inflammatory receptor CD40 after cerebral ischemia using optical techniques.

Cylindrical illumination confocal spectroscopy: rectifying the limitations of confocal single molecule spectroscopy through one-dimensional beam shaping

Cylindrical illumination confocal spectroscopy (CICS) is a new implementation of single molecule detection that can be generically incorporated into any microfluidic system and allows highly quantitative and accurate analysis of single fluorescent molecules. Through theoretical modeling of confocal optics and Monte Carlo simulations, one-dimensional beam shaping is used to create a highly uniform sheet-like observation volume that enables the detection of digital fluorescence bursts while retaining single fluorophore sensitivity. First, we theoretically show that when used to detect single molecules in a microchannel, CICS can be optimized to obtain near 100% mass detection efficiency, <10% relative SD in burst heights, and a high signal/noise ratio. As a result, CICS is far less sensitive to thresholding artifacts than traditional single molecule detection and significantly more accurate at determining both burst rate and burst parameters. CICS is then experimentally implemented, optically characterized, and integrated into separate two microfluidic devices for the analysis of fluorescently stained plasmid DNA and single Cy5 labeled oligonucleotides. CICS rectifies the limitations of traditional confocal spectroscopy-based single molecule detection without the significant operational complications of competing technologies.

Genetic and physiologic dissection of the vertebrate cardiac conduction system

Vertebrate hearts depend on highly specialized cardiomyocytes that form the cardiac conduction system (CCS) to coordinate chamber contraction and drive blood efficiently and unidirectionally throughout the organism. Defects in this specialized wiring system can lead to syncope and sudden cardiac death. Thus, a greater understanding of cardiac conduction development may help to prevent these devastating clinical outcomes. Utilizing a cardiac-specific fluorescent calcium indicator zebrafish transgenic line, Tg(cmlc2:gCaMP)(s878), that allows for in vivo optical mapping analysis in intact animals, we identified and analyzed four distinct stages of cardiac conduction development that correspond to cellular and anatomical changes of the developing heart. Additionally, we observed that epigenetic factors, such as hemodynamic flow and contraction, regulate the fast conduction network of this specialized electrical system. To identify novel regulators of the CCS, we designed and performed a new, physiology-based, forward genetic screen and identified for the first time, to our knowledge, 17 conduction-specific mutations. Positional cloning of hobgoblin(s634) revealed that tcf2, a homeobox transcription factor gene involved in mature onset diabetes of the young and familial glomerulocystic kidney disease, also regulates conduction between the atrium and the ventricle. The combination of the Tg(cmlc2:gCaMP)(s878) line/in vivo optical mapping technique and characterization of cardiac conduction mutants provides a novel multidisciplinary approach to further understand the molecular determinants of the vertebrate CCS.

Fast fluorescence microscopy for imaging the dynamics of embryonic development

Live imaging has gained a pivotal role in developmental biology since it increasingly allows real-time observation of cell behavior in intact organisms. Microscopes that can capture the dynamics of ever-faster biological events, fluorescent markers optimal for in vivo imaging, and, finally, adapted reconstruction and analysis programs to complete data flow all contribute to this success. Focusing on temporal resolution, we discuss how fast imaging can be achieved with minimal prejudice to spatial resolution, photon count, or to reliably and automatically analyze images. In particular, we show how integrated approaches to imaging that combine bright fluorescent probes, fast microscopes, and custom post-processing techniques can address the kinetics of biological systems at multiple scales. Finally, we discuss remaining challenges and opportunities for further advances in this field.

High-contrast single-particle tracking by selective focal plane illumination microscopy

Wide-field single molecule microscopy is a versatile tool for analyzing dynamics and molecular interactions in biological systems. In extended three-dimensional systems, however, the method suffers from intrinsic out-of-focus fluorescence. We constructed a high-resolution selective plane illumination microscope (SPIM) to efficiently solve this problem. The instrument is an optical sectioning microscope featuring the high speed and high sensitivity of a video microscope. We present theoretical calculations and quantitative measurements of the illumination light sheet thickness yielding 1.7 microm (FWHM) at 543 nm, 2.0 microm at 633 nm, and a FWHM of the axial point spread function of 1.13 microm. A direct comparison of selective plane and epi-illumination of model samples with intrinsic background fluorescence illustrated the clear advantage of SPIM for such samples. Single fluorescent quantum dots in aqueous solution are readily visualized and tracked proving the suitability of our setup for the study of fast and dynamic processes in spatially extended biological specimens.

Three-dimensional microtubule behavior in Xenopus egg extracts reveals four dynamic states and state-dependent elastic properties

Although microtubules are key players in many cellular processes, very little is known about their dynamic and mechanical properties in physiological three-dimensional environments. The conventional model of microtubule dynamic instability postulates two dynamic microtubule states, growth and shrinkage. However, several studies have indicated that such a model does not provide a comprehensive quantitative and qualitative description of microtubule behavior. Using three-dimensional laser light-sheet fluorescence microscopy and a three-dimensional sample preparation in spacious Teflon cylinders, we measured microtubule dynamic instability and elasticity in interphase Xenopus laevis egg extracts. Our data are inconsistent with a two-state model of microtubule dynamic instability and favor an extended four-state model with two independent metastable pause states over a three-state model with a single pause state. Moreover, our data on kinetic state transitions rule out a simple GTP cap model as the driving force of microtubule stabilization in egg extracts on timescales of a few seconds or longer. We determined the three-dimensional elastic properties of microtubules as a function of both the contour length and the dynamic state. Our results indicate that pausing microtubules are less flexible than growing microtubules and suggest a growth-speed-dependent persistence length. These data might hint toward mechanisms that enable microtubules to efficiently perform multiple different tasks in the cell and suggest the development of a unified model of microtubule dynamics and microtubule mechanics.

Imaging in vivo: watching the brain in action

The appeal of in vivo cellular imaging to any neuroscientist is not hard to understand: it is almost impossible to isolate individual neurons while keeping them and their complex interactions with surrounding tissue intact. These interactions lead to the complex network dynamics that underlie neural computation which, in turn, forms the basis of cognition, perception and consciousness. In vivo imaging allows the study of both form and function in reasonably intact preparations, often with subcellular spatial resolution, a time resolution of milliseconds and a purview of months. Recently, the limits of what can be achieved in vivo have been pushed into terrain that was previously only accessible in vitro, due to advances in both physical-imaging technology and the design of molecular contrast agents.

Ultramicroscopy: 3D reconstruction of large microscopical specimens

Ultramicroscopy is a microscopical technique that allows optical sectioning and 3D reconstruction of biological and medical specimens. While in confocal microscopy specimen size is limited to several hundred micrometers at best, using ultramicroscopy even centimeter sized objects like whole mouse embryos can be reconstructed with micrometer resolution. This is possible by using a combination of a clearing procedure and the principle of lightsheet illumination. We present ultramicroscopic 3D reconstructions of whole immunohistochemically labelled mouse embryos and adult Drosophila, giving detailed insight into their anatomy. Its speed and simplicity makes ultramicroscopy ideally suited for high-throughput phenotype screening of transgenic mice and thus will benefit the investigation of disease models.

High-speed imaging of developing heart valves reveals interplay of morphogenesis and function

Knowing how mutations disrupt the interplay between atrioventricular valve (AVV) morphogenesis and function is crucial for understanding how congenital valve defects arise. Here, we use high-speed fluorescence microscopy to investigate AVV morphogenesis in zebrafish at cellular resolution. We find that valve leaflets form directly through a process of invagination, rather than first forming endocardial cushions. There are three phases of valve function in embryonic development. First, the atrioventricular canal (AVC) is closed by the mechanical action of the myocardium, rolls together and then relaxes. The growing valve leaflets serve to block the canal during the roll and, depending on the developmental stage, either expand or hang down as a leaflet to block the canal. These steps are disrupted by the subtle morphological changes that result from inhibiting ErbB-, TGFbeta-or Cox2 (Ptgs2)-dependent signaling. Cox2 inhibition affects valve development due to its effect on myocardial cell size and shape, which changes the morphology of the ventricle and alters valve geometry. Thus, different signaling pathways regulate distinct aspects of the behavior of individual cells during valve morphogenesis, thereby influencing specific facets of valve function.

3D representation of Wnt and Frizzled gene expression patterns in the mouse embryo at embryonic day 11.5 (Ts19)

Wnt signalling is one of the fundamental cell communication systems operating in the embryo and the collection of 19 Wnt and 10 Frizzled (Fzd) receptor genes (in mouse and human) represent just part of a complex system to be unravelled. Here we present a spatially comprehensive set of data on the 3D distribution of Wnt and Fzd gene expression patterns at a carefully selected single stage of mouse development. Overviews and selected features of the patterns are presented and the full 3D data set, generated by fully described probes, is available to the research community through the Edinburgh Mouse Atlas of Gene Expression. In addition to being comprehensive, the data set has been generated and recorded in a consistent manner to facilitate comparisons between gene expression patterns with the capacity to generate matching virtual sections from the 3D representations for specific studies. Expression patterns in the left forelimb were selected for more detailed comparative description. In addition to confirming the previously published expression of these genes, our whole embryo and limb bud analyses significantly extend the data in terms of details of the patterns and the addition of previously undetected sites of expression. Our focussed analysis of expression domains in the limb, defined by just two gene families, reveals a surprisingly high degree of spatial complexity and underlines the enormous potential for local cellular interactions that exist within an emerging structure. This work also highlights the use of OPT to generate detailed high-quality, spatially complex expression data that is readily comparable between specimens and can be reviewed and reanalysed as required for specific studies. It represents a core set of data that will be extended with additional stages of development and through addition of potentially interacting genes and ultimately other cross-regulatory communication pathways operating in the embryo.

A new and general method for blind shift-variant deconvolution of biomedical images

We present a new method for blind deconvolution of multiple noisy images blurred by a shift-variant point-spread-function (PSF). We focus on a setting in which several images of the same object are available, and a transformation between these images is known. This setting occurs frequently in biomedical imaging, for example in microscopy or in medical ultrasound imaging. By using the information from multiple observations, we are able to improve the quality of images blurred by a shift-variant filter, without prior knowledge of this filter. Also, in contrast to other work on blind and shift-variant deconvolution, in our approach no parametrization of the PSF is required. We evaluate the proposed method quantitatively on synthetically degraded data as well as qualitatively on 3D ultrasound images of liver. The algorithm yields good restoration results and proves to be robust even in presence of high noise levels in the images.

Preparation of cells and tissues for immuno EM

Transmission electron microscopy (TEM) provides a powerful set of methods to investigate cellular and subcellular structures using thin sections. In this article we summarize some of the different approaches available for researchers interested in using these methods. The essential details involved in specimen preparation for immunolabelling are covered. The best sectioning approach for preserving specimens for structural analysis is Cryo EM of Vitrified Sections (CEMOVIS), a method where still frozen sections are examined in the transmission electron microscope. Because the specimens are kept at low temperature during sectioning and examination, this method is not amenable for immunolabelling, where antibodies are applied to sections at ambient temperature. To combine structural analysis with immunocytochemical analysis of antigens, the approach of freeze-substitution without chemical fixative is the method of choice, at least from a theoretical point of view. In practice, however, the vast majority of electron microscopic (EM) immunocytochemical analyses are carried out using chemically-fixed specimens that have been embedded in specialized resins (such as the Lowicryls) using freeze-substitution or ambient temperature methods. Antibody labelling of thawed cryosections through chemically-fixed specimens (the Tokuyasu method) is also a popular method for preparing cells and tissues for TEM analysis. Here, we provide an overview of all these sectioning methods for EM, focusing mostly on the practical details. Given the space limitation, the fine details necessary to apply these methods have been successfully omitted and will have to be obtained from the technical references we provide.

Fluorescence interferometry: principles and applications in biology

The use of fluorescence radiation is of fundamental importance for tackling measurement problems in the life sciences, with recent demonstrations of probing biological systems at the nanoscale. Usually, fluorescent light-based tools and techniques use the intensity of light waves, which is easily measured by detectors. However, the phase of a fluorescence wave contains subtle, but no less important, information about the wave; yet, it has been largely unexplored. Here, we introduce the concept of fluorescence interferometry to allow the measurement of phase information of fluorescent light waves. In principle, fluorescence interferometry can be considered a unique form of optical low-coherence interferometry that uses fluorophores as a light source of low temporal coherence. Fluorescence interferometry opens up new avenues for developing new fluorescent light-based imaging, sensing, ranging, and profiling methods that to some extent resemble interferometric techniques based on white light sources. We propose two experimental realizations of fluorescence interferometry that detect the interference pattern cast by the fluorescence fields. This article discusses their measurement capabilities and limitations and compares them with those offered by optical low-coherence interferometric schemes. We also describe applications of fluorescence interferometry to imaging, ranging, and profiling tasks and present experimental evidences of wide-field cross-sectional imaging with high resolution and large range of depth, as well as quantitative profiling with nanometer-level precision. Finally, we point out future research directions in fluorescence interferometry, such as fluorescence tomography of whole organisms and the extension to molecular interferometry by means of quantum dots and bioluminescence.

The third dimension bridges the gap between cell culture and live tissue

Moving from cell monolayers to three-dimensional (3D) cultures is motivated by the need to work with cellular models that mimic the functions of living tissues. Essential cellular functions that are present in tissues are missed by 'petri dish'-based cell cultures. This limits their potential to predict the cellular responses of real organisms. However, establishing 3D cultures as a mainstream approach requires the development of standard protocols, new cell lines and quantitative analysis methods, which include well-suited three-dimensional imaging techniques. We believe that 3D cultures will have a strong impact on drug screening and will also decrease the use of laboratory animals, for example, in the context of toxicity assays.