Large Biological Samples Research Articles

Planar Airy beam light-sheet for two-photon microscopy.

We demonstrate the first planar Airy light-sheet microscope. Fluorescence light-sheet microscopy has become the method of choice to study large biological samples with cellular or sub-cellular resolution. The propagation-invariant Airy beam enables a ten-fold increase in field-of-view with single-photon excitation; however, the characteristic asymmetry of the light-sheet limits its potential for multi-photon excitation. Here we show how a planar light-sheet can be formed from the curved propagation-invariant Airy beam. The resulting symmetric light sheet excites two-photon fluorescence uniformly across an extended field-of-view without the need for deconvolution. We demonstrate the method for rapid two-photon imaging of large volumes of neuronal tissue.

Remote scanning for ultra-large field of view in wide-field microscopy and full-field OCT.

Imaging specimens over large scales and with a sub-micron resolution is instrumental to biomedical research. Yet, the number of pixels to form such an image usually exceeds the number of pixels provided by conventional cameras. Although most microscopes are equipped with a motorized stage to displace the specimen and acquire the image tile-by-tile, we propose an alternative strategy that does not require to move any part in the sample plane. We propose to add a scanning mechanism in the detection unit of the microscope to collect sequentially different sub-areas of the field of view. Our approach, called remote scanning, is compatible with all camera-based microscopes. We evaluate the performances in both wide-field microscopy and full-field optical coherence tomography and we show that a field of view of 2.2 × 2.2 mm2 with a 1.1 μm resolution can be acquired. We finally demonstrate that the method is especially suited to image motion-sensitive samples and large biological samples such as millimetric engineered tissues.

Micrometer-resolution X-ray tomographic full-volume reconstruction of an intact post-mortem juvenile rat lung

In this article, we present an X-ray tomographic imaging method that is well suited for pulmonary disease studies in animal models to resolve the full pathway from gas intake to gas exchange. Current state-of-the-art synchrotron-based tomographic phase-contrast imaging methods allow for three-dimensional microscopic imaging data to be acquired non-destructively in scan times of the order of seconds with good soft tissue contrast. However, when studying multi-scale hierarchically structured objects, such as the mammalian lung, the overall sample size typically exceeds the field of view illuminated by the X-rays in a single scan and the necessity for achieving a high spatial resolution conflicts with the need to image the whole sample. Several image stitching and calibration techniques to achieve extended high-resolution fields of view have been reported, but those approaches tend to fail when imaging non-stable samples, thus precluding tomographic measurements of large biological samples, which are prone to degradation and motion during extended scan times. In this work, we demonstrate a full-volume three-dimensional reconstruction of an intact rat lung under immediate post-mortem conditions and at an isotropic voxel size of (2.75 µm)3. We present the methodology for collecting multiple local tomographies with 360° extended field of view scans followed by locally non-rigid volumetric stitching. Applied to the lung, it allows to resolve the entire pulmonary structure from the trachea down to the parenchyma in a single dataset. The complete dataset is available online (https://doi.org/10.16907/7eb141d3-11f1-47a6-9d0e-76f8832ed1b2).

Gold Nanoparticles for X-ray Microtomography of Neurons.

Commonly used methods to visualize the biological structure of brain tissues at subcellular resolution are confocal microscopy and two-photon microscopy. Both require slicing the sample into sections of a few tens of micrometers. The recent developments in X-ray microtomography enable three-dimensional imaging at sub-micrometer and isotropic resolution with larger biological samples. In this work, we developed and compared original microtomography methods and staining protocols to improve the contrast for in vitro mouse neuron imaging. Using Golgi's method to stain neurons randomly, we imaged the whole set of mouse brain structures. For specific and nonrandom neuron labeling, we conjugated 20 nm gold nanoparticles to antibodies used in the immunohistochemistry (IHC) method, using anti-NeuN to label specifically neuronal nuclei. We applied an original subtraction dual-energy method for microtomography in the vicinity of the Au L-III absorption edge and compared image reconstructions to confocal microscopy images acquired on the same samples. The results show the possibility to characterize the 3D entire brain structure of mice. They demonstrated a high contrast and neuron detection improvement by applying the dual-energy method coupled to IHC staining.

Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution.

The speed of high-resolution optical imaging has been a rate-limiting factor for meso-scale mapping of brain structures and functional circuits, which is of fundamental importance for neuroscience research. Here, we describe a new microscopy method of Volumetric Imaging with Synchronized on-the-fly-scan and Readout (VISoR) for high-throughput, high-quality brain mapping. Combining synchronized scanning beam illumination and oblique imaging over cleared tissue sections in smooth motion, the VISoR system effectively eliminates motion blur to obtain undistorted images. By continuously imaging moving samples without stopping, the system achieves high-speed 3D image acquisition of an entire mouse brain within 1.5 hours, at a resolution capable of visualizing synaptic spines. A pipeline is developed for sample preparation, imaging, 3D image reconstruction and quantification. Our approach is compatible with immunofluorescence methods, enabling flexible cell-type specific brain mapping and is readily scalable for large biological samples such as primate brains. Using this system, we examined behaviorally relevant whole-brain neuronal activation in 16 c-Fos-shEGFP mice under resting or forced swimming conditions. Our results indicate the involvement of multiple subcortical areas in stress response. Intriguingly, neuronal activation in these areas exhibits striking individual variability among different animals, suggesting the necessity of sufficient cohort size for such studies.

Multicolor fluorescence microscopy using static light sheets and a single-channel detection.

.We present a multicolor fluorescence microscope system, under a selective plane illumination microscopy (SPIM) configuration, using three continuous wave-lasers and a single-channel-detection camera. The laser intensities are modulated with three time-delayed pulse trains that operate synchronously at one third of the camera frame rate, allowing a sequential excitation and an image acquisition of up to three different biomarkers. The feasibility of this imaging acquisition mode is demonstrated by acquiring single-plane multicolor images of living hyphae of Neurospora crassa. This allows visualizing simultaneously the localization and dynamics of different cellular components involved in apical growth in living hyphae. The configuration presented represents a noncommercial, cost-effective alternative microscopy system for the rapid and simultaneous acquisition of multifluorescent images and can be potentially useful for three-dimensional imaging of large biological samples.

Fluorescence time-resolved macroimaging.

While laser scanning fluorescence lifetime imaging (FLIM) is a powerful approach for cell biology, its small field of view (typically less than 1mm) makes it impractical for the imaging of large biological samples that is often required for biomedical applications. Here we present a system that allows performing FLIM on macroscopic samples as large as 18mm with a lateral resolution of 15μm. The performance of the system is verified with FLIM of endogenous metabolic cofactor reduced nicotinamide adenine dinucleotide (phosphate), NAD(P)H, and genetically encoded fluorescent protein mKate2 in a mouse tumor in vivo.

Sensitivity of Transmission Raman Spectroscopy Signals to Temperature of Biological Tissues

Optical properties of biological tissues can be influenced by their temperature, thus affecting light transport inside the sample. This could potentially be exploited to deliver more photons inside large biological samples, when compared with experiments at room temperature, overcoming some of difficulties due to highly scattering nature of the tissue. Here we report a change in light transmitted inside biological tissue with temperature elevation from 20 to 40 °C, indicating a considerable enhancement of photons collected by the detector in transmission geometry. The measurement of Raman signals in porcine tissue samples, as large as 40 mm in thickness, indicates a considerable increase in signal ranging from 1.3 to 2 fold, subject to biological variability. The enhancements observed are ascribed to phase transitions of lipids in biological samples. This indicates that: 1) experiments performed on tissue at room temperature can lead to an underestimation of signals that would be obtained at depth in the body in vivo and 2) that experiments at room temperature could be modified to increase detection limits by elevating the temperature of the material of interest.

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples

BackgroundAdvances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination.ResultsTo address this fundamental limitation, we have developed light sheet theta microscopy (LSTM), which uniformly illuminates samples from the same side as the detection objective, thereby eliminating limits on lateral dimensions without sacrificing the imaging resolution, depth, and speed. We present a detailed characterization of LSTM, and demonstrate its complementary advantages over LSM for rapid high-resolution quantitative imaging of large intact samples with high uniform quality.ConclusionsThe reported LSTM approach is a significant step for the rapid high-resolution quantitative mapping of the structure and function of very large biological systems, such as a clarified thick coronal slab of human brain and uniformly expanded tissues, and also for rapid volumetric calcium imaging of highly motile animals, such as Hydra, undergoing non-isomorphic body shape changes.

Ultrastretchable Kirigami Bioprobes.

An ultrastretchable film device is developed that can follow the shape of spherical and large deformable biological samples such as heart and brain tissues. Although the film is composed of biocompatible parylene for the device substrate and metal layers of platinum (Pt)/titanium (Ti), which are unstretchable materials, the film shows a high stretchability by patterning slits as a "Kirigami" design. A Pt/Ti-microelectrode array embedded in 11 µm thick parylene film with 5 × 91 slits exhibits a film strain of ≈250% at 9 mN strain-force (0.08 MPa in stress) with a Young's modulus of 23 kPa, while the 3 × 91-slit film shows a Young's modulus of 3.6 kPa. The maximum strains of these devices are ≈470% and ≈840%, respectively. It is demonstrated that the Kirigami-based microelectrode device can simultaneously record in vivo electrocorticogram signals from the visual and barrel cortices of a mouse by stretching the film and tuning the electrode gap. Moreover, wrapping the Kirigami device around a beating mouse's heart, which shows large and rapid changes in the volume and the surface area, can record the in vivo epicardial electrocardiogram signals. Such a small Young's modulus for a stretchable device reduces the device's strain-force, minimizing the device-induced stress to soft biological tissues.

High sensitivity non-invasive detection of calcifications deep inside biological tissue using Transmission Raman Spectroscopy.

The aim of this research was to develop a novel approach to probe non-invasively the composition of inorganic chemicals buried deep in large volume biological samples. The method is based on advanced Transmission Raman Spectroscopy (TRS) permitting chemical specific detection within a large sampling volume. The approach could be beneficial to chemical identification of the breast calcifications detected during mammographic X-ray procedures. The chemical composition of a breast calcification reflects the pathology of the surrounding tissue, malignant or benign and potentially the grade of malignancy. However, this information is not available from mammography, leading to excisional biopsy and histopathological assessment for a definitive diagnosis. Here we present, for the first time, a design of a new high performance deep Raman instrument and demonstrate its capability to detect type II calcifications (calcium hydroxyapatite) at clinically relevant concentrations and depths of around 40 mm in phantom tissue. This is around double the penetration depth achieved with our previous instrument design and around two orders of magnitude higher than that possible when using conventional Raman spectroscopy.

High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis

Zebrafish testis has become a powerful model for reproductive biology of teleostean fishes and other vertebrates and encompasses multiple applications in applied and basic research. Many studies have focused on 2D images, which is time consuming and implies extrapolation of results. Three-dimensional imaging of whole organs recently became an important challenge to better understand their architecture and allow cell enumeration. Several protocols have thus been developed to enhance sample transparency, a limiting step for imaging large biological samples. However, none of these methods has been applied to the zebrafish testis. We tested five clearing protocols to determine if some of them could be applied with only small modifications to the testis. We compared clearing efficiency at both macroscopic and microscopic levels. CUBIC and PACT were suitable for an efficient transparency, an optimal optical penetration, the GFP fluorescence preservation and avoiding meaningful tissue deformation. Finally, we succeeded in whole testis 3D capture at a cellular resolution with both CUBIC and PACT, which will be valuable in a standard workflow to investigate the 3D architecture of the testis and its cellular content. This paves the way for further development of high content phenotyping studies in several fields including development, genetic or toxicology.

A beginner’s guide to tissue clearing

The last decade has seen a proliferation of tissue clearing methods that render large biological samples transparent and allow unprecedented three-dimensional views of enormous volumes of tissue. For a scientist wondering whether these methods will be useful to address their research problems, it can be bewildering to sort through the ever-increasing number of papers introducing new clearing methods. Here, I provide a concise summary for the novice describing what tissue clearing is, which research problems it can be applied to, how to decide on a clearing method, and where the field is headed in the future.

Fluorescence polarization-based method with bisulfite conversion-specific one-label extension for quantification of single CpG dinucleotide methylation.

To quantify the methylation at individual CpG dinucleotide sites in large biological or clinical samples, we developed a bisulfite conversion-specific one-label extension (BS-OLE) method using visualization by fluorescence polarization (FP) measurement of methylation at single CpG sites in small amounts of genomic DNA. Genomic DNA was treated with sodium bisulfite to convert unmethylated cytosine to uracil leaving 5-methylcytosine unaltered, and BS-PCR was used to generate DNA template containing target CpG sites. BS-OLE uses a BS-primer hybridized immediately upstream of the target CpG site being examined and then fluorescent dCTP or dUTP is incorporated into the methylated (CpG) or unmethylated (TpG) form of the target site through single-nucleotide chain extension, yielding an FP ratio between the fluorescent dCTP- and dUTP-incorporated products as a measure of methylation. This provides stable estimates of the methylation level of human genomic DNA and of a 250-bp plasmid DNA segment containing a single TCGA TaqI cleavage site, in accordance with the results of a combined bisulfite restriction analysis method. We used BS-OLE to measure dose-dependent DNA hypomethylation in human embryonic kidney 293T cells treated with the DNA methyltransferase inhibitor 5-aza-dC. BS-OLE is well suited to high-throughput multi-sample applications in biological and medical studies.

Intense high repetition rate Mo Kα x-ray source generated from laser solid interaction for imaging application.

We report an efficient Mo Kα x-ray source produced by interaction of femtosecond Ti: sapphire laser pulses with a solid Molybdenum target working at 1 kHz repetition rate. The generated Mo Kα x-ray intensity reaches to 4.7 × 10(10) photons sr(-1) s(-1), corresponding to an average power of 0.8 mW into 2π solid angle. The spatial resolution of this x-ray source is measured to be 26 lp/mm. With the high flux and high spatial resolution characteristics, high resolving in-line x-ray radiography was realized on test objects and large size biological samples within merely half a minute. This experiment shows the possibility of laser plasma hard x-ray source as a new low cost and high resolution system for radiography and its ability of ultrafast x-ray pump-probe study of matter.

Optimized Routing and Pin-Constrained Design of Digital Micro-Fluidic Biochip

Digital micro-fluidic biochips have represented as a small integrated tool for large biological sample analysis. Only nanoliter volume of discrete fluid droplets (sample) is required to manipulate the integrated chips on an electrode array via electrical actuation. Each electrode activate with independent pin for direct addressing biochip. For low cost and disposal biochip, pin-constraint design is one of the main motivations of this paper. However the pin-count reductions are inescapably depend on the droplet routing stage. The emphasis here is on the concurrent routing with minimum number of cell used without any electrode interference. The paper presents a multi-objective optimization technique for concurrent routing on single source -single target net (2-pin net), two-source single target net (3-pin net) problem and integrates the routing result with masking based algorithm to select the compatible sequence without any electrode interference. The experimental result of benchmark Invitro, Protein show the significant reduction of control pins, number of used cells and routing time compare to crossreferencing and broadcast addressing, ant colony optimization and two-stage ILP method.

Gravity driven high throughput phase detecting cytometer based on quantitative interferometric microscopy

Phase distribution detection of cells and tissues is concerned since it is an important auxiliary method for observing biological samples. High speed and large amount cell detection is needed for its high detecting efficiency. In this paper, we have proposed a simple large scale biological sample phase detection device called gravity driven high throughput phase detecting cytometer based on quantitative interferometric microscopy to obtain flowing red blood cells phase. The system could realize high throughput phase detecting and statistical analysis with high detecting speed and in real time. The statistical characteristics of red blood cells could be obtained which might be helpful for biological analysis and disease detection. We believe this method is a powerful tool to quantitatively measure the phase distribution of biological samples.

Beneficial effect of directional freezing on in vitro viability of cryopreserved sheep whole ovaries and ovarian cortical slices

Does directional freezing improve the structural and functional integrity of ovarian fragments compared with conventional slow freezing and to whole ovary cryopreservation? Compared with slow freezing, the use of directional freezing significantly improves all structural and functional parameters of ovarian fragments assessed in vitro and, overall, whole ovaries were better preserved than ovarian fragments. Directional freezing has been developed to provide an alternative way to cryopreserve large biological samples and it is known to improve the structural and functional integrity of whole ovaries. Conventional slow freezing of ovarian fragments is the procedure more widely used in clinical settings but it causes substantial structural damage that limits the functional period after transfer back into the patient. We performed a 2 × 2 factorial design experiment on a total of 40 sheep ovaries, divided into four groups (n = 10 ovaries per group): (i) directional freezing of whole ovary (DFwo); (ii) directional freezing of ovarian fragments (DFof); (iii) conventional freezing of whole ovary (CFwo); (iv) conventional freezing of ovarian fragments (CFof). An additional eight ovaries were used as fresh controls. Ewe ovaries were randomly assigned to one of the experimental groups and frozen accordingly. Upon thawing, ovarian tissue was examined morphologically and cultured in vitro for 7 days. Samples were analyzed for cell proliferation and apoptosis, for DNA damage and repair activity, and for the presence of a panel of heat shock proteins (HSPs) by immunohistochemistry. Most studied parameters were significantly improved (P < 0.05) in all samples cryopreserved with directional compared with slow freezing. The proportion of primordial follicles, which developed to the primary stage in whole ovaries (53 ± 1.7%) and in ovarian fragments (44 ± 1.8%) cryopreserved with directional freezing, was greater than with slow frozen whole ovaries (6 ± 0.5%, P = 0.001) or fragments (32 ± 1.5%, P = 0.004). After 7 days of culture, cell proliferation in DFwo (28 ± 0.73%) was the highest of all groups (P < 0.05) followed by DFof (23 ± 0.81%), CFof (20 ± 0.79%) and CFwo (9 ± 0.85%). Directional freezing also resulted in a better preservation of the cell capacity to repair DNA damage compared with slow freezing both in whole ovaries and ovarian fragments. Apoptosis and HSP protein levels were significantly increased only in the CFwo group. Direct comparison demonstrated that, overall, DFwo had better parameters than DFof and was no different from the fresh controls. The study is limited to an in vitro evaluation and uses sheep ovaries, which are smaller than human ovaries and therefore may withstand the procedures better. Improved integrity of ovarian morphology may translate to improved outcomes after transplantation. Alternatively, the particularly good preservation of whole ovaries suggests they could provide a source of ovarian follicles for in vitro culture in those cases when the presence of malignant cells poses a substantial risk for the patient. Supported by: Associazione Italiana per la Ricerca sul Cancro (AIRC) IG 10376, Carraresi Foundation and by Legge 7 Regione Autonoma Sardegna (R.A.S). There are no conflicts of interest.

Force-feedback high-speed atomic force microscope for studying large biological systems

We designed and developed a high-speed atomic force microscope (HSAFM) utilizing a force-feedback scheme for imaging large biological samples. The system collects three simultaneous images: a deflection image, a topographic image, and a force image. We demonstrated that this force-feedback HSAFM is capable of acquiring large topographic images of Escherichia coli biofilms at approximately one frame per second in air. We discuss how the self-actuating cantilever and the piezo tube follow those larger biological topographic features during the HSAFM imaging process.

Emerging technologies in mass spectrometry imaging

Mass spectrometry imaging (MSI) as an analytical tool for bio-molecular and bio-medical research targets accurate compound localization and identification. In terms of dedicated instrumentation, this translates into the demand for more detail in the image dimension (spatial resolution) and in the spectral dimension (mass resolution and accuracy), preferably combined in one instrument. At the same time, large area biological tissue samples require fast acquisition schemes, instrument automation and a robust data infrastructure. This review discusses the analytical capabilities of an "ideal" MSI instrument for bio-molecular and bio-medical molecular imaging. The analytical attributes of such an ideal system are contrasted with technological and methodological challenges in MSI. In particular, innovative instrumentation for high spatial resolution imaging in combination with high sample throughput is discussed. Detector technology that targets various shortcomings of conventional imaging detector systems is highlighted. The benefits of accurate mass analysis, high mass resolving power, additional separation strategies and multimodal three-dimensional data reconstruction algorithms are discussed to provide the reader with an insight in the current technological advances and the potential of MSI for bio-medical research.