Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/ß-catenin signaling.

Bcl9 and Pygopus (Pygo) are obligate Wnt/ß-catenin cofactors in Drosophila, yet their contribution to Wnt signaling during vertebrate development remains unresolved. Combining zebrafish and mouse genetics, we document a conserved, ß-catenin-associated function for BCL9 and Pygo proteins during vertebrate heart development. Disrupting the ß-catenin-BCL9-Pygo complex results in a broadly maintained canonical Wnt response yet perturbs heart development and proper expression of key cardiac regulators. Our work highlights BCL9 and Pygo as selective ß-catenin cofactors in a subset of canonical Wnt responses during vertebrate development. Moreover, our results implicate alterations in BCL9 and BCL9L in human congenital heart defects.

Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution.

The CUBIC tissue-clearing protocol has been optimized to produce translucent immunostained whole chicken embryos and embryo brains. When combined with multispectral light-sheet microscopy, the validated protocol presented here provides a rapid, inexpensive and reliable method for acquiring accurate histological images that preserve three-dimensional structural relationships with single-cell resolution in whole early-stage chicken embryos and in the whole brains of late-stage embryos.

Multimodal imaging combining time-domain near-infrared optical tomography and continuous-wave fluorescence molecular tomography.

Fluorescence molecular tomography (FMT) emerges as a powerful non-invasive imaging tool with the ability to resolve fluorescence signals from sources located deep in living tissues. Yet, the accuracy of FMT reconstruction depends on the deviation of the assumed optical properties from the actual values. In this work, we improved the accuracy of the initial optical properties required for FMT using a new-generation time-domain (TD) near-infrared optical tomography (NIROT) system, which effectively decouples scattering and absorption coefficients. We proposed a multimodal paradigm combining TD-NIROT and continuous-wave (CW) FMT. Both numerical simulation and experiments were performed on a heterogeneous phantom containing a fluorescent inclusion. The results demonstrate significant improvement in the FMT reconstruction by taking the NIROT-derived optical properties as prior information. The multimodal method is attractive for preclinical studies and tumor diagnostics since both functional and molecular information can be obtained.

Development of an Inverted Epifluorescence Microscope for Long-Term Monitoring of Bacteria in Multiplexed Microfluidic Devices.

Developing more efficient methods for antibiotic susceptibility testing is a pressing issue in novel drug development as bacterial resistance to antibiotics becomes increasingly common. Microfluidic devices have been demonstrated to be powerful platforms that allow researchers to perform multiplexed antibiotic testing. However, the level of multiplexing within microdevices is limited, evidencing the need of creating simple, low-cost and high-resolution imaging systems that can be integrated in antibiotic development pipelines. This paper describes the design and development of an epifluorescence inverted microscope that enables long-term monitoring of bacteria inside multiplexed microfluidic devices. The goal of this work is to provide a simple microscope powerful enough to allow single-cell analysis of bacteria at a reduced cost. This facilitates increasing the number of microscopes that are simultaneously used for antibiotic testing. We prove that the designed system is able to accurately detect fluorescent beads of 100 nm, demonstrating comparable features to high-end commercial microscopes and effectively achieving the resolution required for single-cell analysis of bacteria. The proposed microscope could thus increase the efficiency in antibiotic testing while reducing cost, size, weight, and power requirements, contributing to the successful development of new antibiotic drugs.

Antigen Availability and DOCK2-Driven Motility Govern CD4+ T Cell Interactions with Dendritic Cells In Vivo.

Parenchymal migration of naive CD4+ T cells in lymph nodes (LNs) is mediated by the Rac activator DOCK2 and PI3Kγ and is widely assumed to facilitate efficient screening of dendritic cells (DCs) presenting peptide-MHCs (pMHCs). Yet how CD4+ T cell motility, DC density, and pMHC levels interdependently regulate such interactions has not been comprehensively examined. Using intravital imaging of reactive LNs in DC-immunized mice, we show that pMHC levels determined the occurrence and timing of stable CD4+ T cell-DC interactions. Despite the variability in interaction parameters, ensuing CD4+ T cell proliferation was comparable over a wide range of pMHC levels. Unexpectedly, decreased intrinsic motility of DOCK2-/- CD4+ T cells did not impair encounters with DCs in dense paracortical networks and, instead, increased interaction stability, whereas PI3Kγ deficiency had no effect on interaction parameters. In contrast, intravital and whole-organ imaging showed that DOCK2-driven T cell motility was required to detach from pMHClow DCs and to find rare pMHChigh DCs. In sum, our data uncover flexible signal integration by scanning CD4+ T cells, suggesting a search strategy evolved to detect low-frequency DCs presenting high cognate pMHC levels.

Optical projection tomography via phase retrieval algorithms.

We describe a computational method for accurate, quantitative tomographic reconstructions in Optical Projection Tomography, based on phase retrieval algorithms. Our method overcomes limitations imposed by light scattering in opaque tissue samples under the memory effect regime, as well as reduces artifacts due to mechanical movements, misalignments or vibrations. We make use of Gerchberg-Saxton algorithms, calculating first the autocorrelation of the object and then retrieving the associated phase under four numerically simulated measurement conditions. By approaching the task in such a way, we avoid the projection alignment procedure, exploiting the fact that the autocorrelation sinogram is always aligned and centered. We thus propose two new, projection-based, tomographic imaging flowcharts that allow registration-free imaging of opaque biological specimens and unlock three-dimensional tomographic imaging of hidden objects. Two main reconstruction approaches are discussed in the text, focusing on their efficiency in the tomographic retrieval and discussing their applicability under four different numerical experiments.

Plenoptic projection fluorescence tomography.

A new method to obtain the three-dimensional localization of fluorochrome distributions in micrometric samples is presented. It uses a microlens array coupled to the image port of a standard microscope to obtain tomographic data by a filtered back-projection algorithm. Scanning of the microlens array is proposed to obtain a dense data set for reconstruction. Simulation and experimental results are shown and the implications of this approach in fast 3D imaging are discussed.

Steady-state total diffuse reflectance with an exponential decaying source.

The increasing preclinical and clinical utilization of digital cameras for photographic measurements of tissue conditions motivates the study of reflectance measurements obtained with planar illumination. We examine herein a formula that models the total diffuse reflectance measured from a semi-infinite medium using an exponentially decaying source, assuming continuous plane wave epi-illumination. The model is validated with experimental reflectance measurements from tissue mimicking phantoms. The need for adjusting the blood absorption spectrum due to pigment packaging is discussed along with the potential applications of the proposed formulation.

Development and testing of a sedation protocol for Neocaridina davidi.

Neocaridina davidi, a small freshwater shrimp native to Asia, specifically China, Japan, Korea, and Vietnam, possesses remarkable resistance to poor water quality and offers various advantages over other invertebrate species to examine crucial issues in neuroscience and other related areas. These advantages include robustness, ease of maintenance, and transparency, making them useful for in vivo studies with optical imaging techniques. Despite its suitability for research purposes, particularly in the fields of imaging and fluorescent techniques, the lack of attention given to this species has resulted in the absence of a robust and replicable sedation protocol for immobilization and safe manipulation. Consequently, researchers face challenges in performing experimental procedures while minimizing harm to this specimen. In this study, we have developed and evaluated a simple sedation protocol specifically designed for Neocaridina davidi, assessing its effectiveness using light microscopy and image processing.

Multispectral imaging for characterizing autofluorescent tissues.

Selective Plane Illumination Microscopy (SPIM) has become an emerging technology since its first application for 3D in-vivo imaging of the development of a living organism. An extensive number of works have been published, improving both the speed of acquisition and the resolution of the systems. Furthermore, multispectral imaging allows the effective separation of overlapping signals associated with different fluorophores from the spectrum over the whole field-of-view of the analyzed sample. To eliminate the need of using fluorescent dyes, this technique can also be applied to autofluorescence imaging. However, the effective separation of the overlapped spectra in autofluorescence imaging necessitates the use of mathematical tools. In this work, we explore the application of a method based on Principal Component Analysis (PCA) that enables tissue characterization upon spectral autofluorescence data without the use of fluorophores. Thus, enabling the separation of different tissue types in fixed and living samples with no need of staining techniques. Two procedures are described for acquiring spectral data, including a single excitation based method and a multi-excitation scanning approach. In both cases, we demonstrate the effective separation of various tissue types based on their unique autofluorescence spectra.

Diffuse optical tomography of the brain: effects of inaccurate baseline optical parameters and refinements using learned post-processing.

Diffuse optical tomography (DOT) uses near-infrared light to image spatially varying optical parameters in biological tissues. In functional brain imaging, DOT uses a perturbation model to estimate the changes in optical parameters, corresponding to changes in measured data due to brain activity. The perturbation model typically uses approximate baseline optical parameters of the different brain compartments, since the actual baseline optical parameters are unknown. We simulated the effects of these approximate baseline optical parameters using parameter variations earlier reported in literature, and brain atlases from four adult subjects. We report the errors in estimated activation contrast, localization, and area when incorrect baseline values were used. Further, we developed a post-processing technique based on deep learning methods that can reduce the effects due to inaccurate baseline optical parameters. The method improved imaging of brain activation changes in the presence of such errors.

Helical optical projection tomography.

A new technique termed Helical Optical Projection Tomography (hOPT) has been developed with the aim to overcome some of the limitations of current 3D optical imaging techniques. hOPT is based on Optical Projection Tomography (OPT) with the major difference that there is a translation of the sample in the vertical direction during the image acquisition process, requiring a new approach to image reconstruction. Contrary to OPT, hOPT makes possible to obtain 3D-optical images of intact long samples without imposing limits on the sample length. This has been tested using hOPT to image long murine tissue samples such as spinal cords and large intestines. Moreover, 3D-reconstructed images of the colon of DSS-treated mice, a model for Inflammatory Bowel Disease, allowed the identification of the structural alterations. Finally, the geometry of the hOPT device facilitates the addition of a Selective Plane Illumination Microscopy (SPIM) arm, providing the possibility of delivering high resolution images of selected areas together with complete volumetric information.

A new in vivo model to test anti-tuberculosis drugs using fluorescence imaging.

OBJECTIVES: The current method for testing new drugs against tuberculosis in vivo is the enumeration of bacteria in organs by cfu assay. Owing to the slow growth rate of Mycobacterium tuberculosis (Mtb), these assays can take months to complete. Our aim was to develop a more efficient, fluorescence-based imaging assay to test new antibiotics in a mouse model using Mtb reporter strains. METHODS: A commercial IVIS Kinetic® system and a custom-built laser scanning system with fluorescence molecular tomography (FMT) capability were used to detect fluorescent Mtb in living mice and lungs ex vivo. The resulting images were analysed and the fluorescence was correlated with data from cfu assays. RESULTS: We have shown that fluorescent Mtb can be visualized in the lungs of living mice at a detection limit of ∼8 × 107 cfu/lung, whilst in lungs ex vivo a detection limit of ∼2 × 105 cfu/lung was found. These numbers were comparable between the two imaging systems. Ex vivo lung fluorescence correlated to numbers of bacteria in tissue, and the effect of treatment of mice with the antibiotic moxifloxacin could be visualized and quantified after only 9 days through fluorescence measurements, and was confirmed by cfu assays. CONCLUSIONS: We have developed a new and efficient method for anti-tuberculosis drug testing in vivo, based on fluorescent Mtb reporter strains. Using this method instead of, or together with, cfu assays will reduce the time required to assess the preclinical efficacy of new drugs in animal models and enhance the progress of these candidates into clinical trials against human tuberculosis.

Tomographic imaging with polarized light.

We report three-dimensional tomographic reconstruction of optical parameters for the mesoscopic light scattering regime from experimentally obtained datasets by using polarized light. We present a numerically inexpensive approximation to the radiative transfer equation governing the polarized light transport. This approximation is employed in the reconstruction algorithm, which computes two optical parameters by using parallel and perpendicular polarizations of transmitted light. Datasets were obtained by imaging a scattering phantom embedding highly absorbing inclusions. Reconstruction results are presented and discussed.

Non-invasive visualization of amyloid-beta deposits in Alzheimer amyloidosis mice using magnetic resonance imaging and fluorescence molecular tomography.

Abnormal cerebral accumulation of amyloid-beta peptide (Aß) is a major hallmark of Alzheimer's disease. Non-invasive monitoring of Aß deposits enables assessing the disease burden in patients and animal models mimicking aspects of the human disease as well as evaluating the efficacy of Aß-modulating therapies. Previous in vivo assessments of plaque load have been predominantly based on macroscopic fluorescence reflectance imaging (FRI) and confocal or two-photon microscopy using Aß-specific imaging agents. However, the former method lacks depth resolution, whereas the latter is restricted by the limited field of view preventing a full coverage of the large brain region. Here, we utilized a fluorescence molecular tomography (FMT)-magnetic resonance imaging (MRI) pipeline with the curcumin derivative fluorescent probe CRANAD-2 to achieve full 3D brain coverage for detecting Aß accumulation in the arcAß mouse model of cerebral amyloidosis. A homebuilt FMT system was used for data acquisition, whereas a customized software platform enabled the integration of MRI-derived anatomical information as prior information for FMT image reconstruction. The results obtained from the FMT-MRI study were compared to those from conventional planar FRI recorded under similar physiological conditions, yielding comparable time courses of the fluorescence intensity following intravenous injection of CRANAD-2 in a region-of-interest comprising the brain. In conclusion, we have demonstrated the feasibility of visualizing Aß deposition in 3D using a multimodal FMT-MRI strategy. This hybrid imaging method provides complementary anatomical, physiological and molecular information, thereby enabling the detailed characterization of the disease status in arcAß mouse models, which can also facilitate monitoring the efficacy of putative treatments targeting Aß.

Single Plane Illumination Microscopy for Microfluidic Device Imaging.

Three-dimensional imaging of live processes at a cellular level is a challenging task. It requires high-speed acquisition capabilities, low phototoxicity, and low mechanical disturbances. Three-dimensional imaging in microfluidic devices poses additional challenges as a deep penetration of the light source is required, along with a stationary setting, so the flows are not perturbed. Different types of fluorescence microscopy techniques have been used to address these limitations; particularly, confocal microscopy and light sheet fluorescence microscopy (LSFM). This manuscript proposes a novel architecture of a type of LSFM, single-plane illumination microscopy (SPIM). This custom-made microscope includes two mirror galvanometers to scan the sample vertically and reduce shadowing artifacts while avoiding unnecessary movement. In addition, two electro-tunable lenses fine-tune the focus position and reduce the scattering caused by the microfluidic devices. The microscope has been fully set up and characterized, achieving a resolution of 1.50 µm in the x-y plane and 7.93 µm in the z-direction. The proposed architecture has risen to the challenges posed when imaging microfluidic devices and live processes, as it can successfully acquire 3D volumetric images together with time-lapse recordings, and it is thus a suitable microscopic technique for live tracking miniaturized tissue and disease models.

Feasibility of U-curve method to select the regularization parameter for fluorescence diffuse optical tomography in phantom and small animal studies.

When dealing with ill-posed problems such as fluorescence diffuse optical tomography (fDOT) the choice of the regularization parameter is extremely important for computing a reliable reconstruction. Several automatic methods for the selection of the regularization parameter have been introduced over the years and their performance depends on the particular inverse problem. Herein a U-curve-based algorithm for the selection of regularization parameter has been applied for the first time to fDOT. To increase the computational efficiency for large systems an interval of the regularization parameter is desirable. The U-curve provided a suitable selection of the regularization parameter in terms of Picard's condition, image resolution and image noise. Results are shown both on phantom and mouse data.

Light, sound, chemistry action: state of the art optical methods for animal imaging.

During recent years, macroscopic optical methods have been promoted from backstage to main actors in biological imaging. Many possible forms of energy conservation have been explored that involve light, including fluorescence emission, sound generated through absorption and bioluminescence, that is light generated through a chemical reaction. These physicochemical approaches for contrast generation have resulted in optical imaging methods that come with potent performance characteristics over simple epi-illumination optical imaging approaches of the past, and can play a central role in imaging applications in vivo as it pertains to modern biological and drug discovery, pre-clinical imaging and clinical applications. This review focuses on state of the art optical and opto-acoustic (photo-acoustic) imaging methods and discusses key performance characteristics that convert optical imaging from a qualitative modality to a powerful high-resolution and quantitative volumetric interrogation tool for operation through several millimeters of tissue depth.:

Derivation of the scalar radiative transfer equation from energy conservation of Maxwell's equations in the far field.

In this paper the expression for the radiative transfer equation (RTE) commonly used when describing light propagation in biological tissues is derived directly from the equation of energy conservation of Maxwell's equations (Poynting's theorem) by making use of a volume-averaged expression for the time-averaged flow of energy. The derivation is presented step by step with Maxwell's equations as the starting point, analyzing all approximations taken in order to arrive at the expression of the scalar RTE employed in biomedical applications, which neglects particle nonsphericity and orientation, depolarization, and coherence effects.

Improved reconstructions and generalized filtered back projection for optical projection tomography.

Optical projection tomography (OPT) is a noninvasive imaging technique that enables imaging of small specimens (<1 cm), such as organs or animals in early developmental stages. In this paper, we present a set of computational methods that can be applied to the acquired data sets in order to correct for (a) unknown background or illumination intensity distributions over the field of view, (b) intensity spikes in single CCD pixels (so-called "hot pixels"), and (c) refractive index mismatch between the media in which the specimens are embedded and the environment. We have tested these correction methods using a variety of samples and present results obtained from Parhyale hawaiensis embedded in glycerol and in sea water. Successful reconstructions of fluorescence and absorption OPT images have been obtained for weakly scattering specimens embedded in media with nonmatched refractive index, thus advancing OPT toward routine in vivo imaging.