Imaging Fiber Research Articles

Fiber finding algorithm using stepwise tracing to identify biopolymer fibers in noisy 3D images

We present a novel fiber finding algorithm (FFA) that will permit researchers to detect and return traces of individual biopolymers. Determining the biophysical properties and structural cues of biopolymers can permit researchers to assess the progression and severity of disease. Confocal microscopy images are a useful method for observing biopolymer structures in three dimensions, but their utility for identifying individual biopolymers is impaired by noise inherent in the acquisition process, including convolution from the point spread function (PSF). The new, iterative FFA we present here 1) measures a microscope’s PSF and uses it as a metric for identifying fibers against the background; 2) traces each fiber within a cone angle; and 3) blots out the identified trace before identifying another fiber. Blotting out the identified traces in each iteration allows the FFA to detect and return traces of single fibers accurately and efficiently—even within fiber bundles. We used the FFA to trace unlabeled collagen type I fibers—a biopolymer used to mimic the extracellular matrix in in vitro cancer assays—imaged by confocal reflectance microscopy in three dimensions, enabling quantification of fiber contour length, persistence length, and three-dimensional (3D) mesh size. Based on 3D confocal reflectance microscopy images and the PSF, we traced and measured the fibers to confirm that colder gelation temperatures increased fiber contour length, persistence length, and 3D mesh size—thereby demonstrating the FFA’s use in quantifying biopolymers’ structural and physical cues from noisy microscope images.

The principle and characteristics of an image fibre Background Oriented Schlieren (Fibre BOS) technique for time-resolved three-dimensional unsteady density measurements

The principle and characteristics of an image fibre Background Oriented Schlieren (Fibre BOS) technique for time-resolved three-dimensional unsteady density measurements

Microscopic Imaging and Optical Pressure Measurements of Detonations

AbstractThe microstructure of solid high explosives can affect their safety and performance. However, the extreme conditions in the vicinity of detonating explosives make high‐resolution imaging and data acquisition challenges. A new diagnostic method is presented here that allows microscopic imaging of self‐supported detonations while optically measuring pressures in an arbitrary confiner material nearby using an imaging fiber and an image intensifier at a safe distance. Tests with pressed pellets of HMX and PBX 9501 revealed features during pore collapse in engineered holes and detonation reaction zone morphology and thickness. Interface experiments allowed the measurement of pressure at the boundary between the explosive and a silicone polymer and the determination of the specific heat ratio for the gaseous products. The same methodology can be used to fit any form of equation‐of‐state and Hugoniot curves for arbitrary materials using few simple experiments.

Simultaneous confidence bands for functional data using the Gaussian Kinematic formula

We propose a construction of simultaneous confidence bands (SCBs) for functional parameters over arbitrary dimensional compact domains using the Gaussian Kinematic formula of t-processes (tGKF). Although the tGKF relies on Gaussianity, we show that a central limit theorem (CLT) for the parameter of interest is enough to obtain asymptotically precise covering even if the observations are non-Gaussian processes. As a proof of concept we study the functional signal-plus-noise model and derive a CLT for an estimator of the Lipshitz–Killing curvatures, the only data-dependent quantities in the tGKF. We further discuss extensions to discrete sampling with additive observation noise using scale space ideas from regression analysis. Our theoretical work is accompanied by a simulation study comparing different methods to construct SCBs for the population mean. We show that the tGKF outperforms state-of-the-art methods with precise covering for small sample sizes, and only a Rademacher multiplier-t bootstrap performs similarly well. A further benefit is that our SCBs are computational fast even for domains of dimension greater than one. Applications of SCBs to diffusion tensor imaging (DTI) fibers (1D) and spatio-temporal temperature data (2D) are discussed.

Asymmetric susceptibility tensor imaging.

To investigate the symmetry constraint in susceptibility tensor imaging. The linear relationship between the MRI frequency shift and the magnetic susceptibility tensor is derived without constraining the tensor to be symmetric. In the asymmetric case, the system matrix is shown to be maximally rank 6. Nonetheless, relaxing the symmetry constraint may still improve tensor estimation because noise and image artifacts do not necessarily follow the constraint. Gradient echo phase data are obtained from postmortem mouse brain and kidney samples. Both symmetric and asymmetric tensor reconstructions are applied to the data. The reconstructions are then used for susceptibility tensor imaging fiber tracking. Simulations with ground truth and at various noise levels are also performed. The reconstruction methods are compared qualitatively and quantitatively. Compared to regularized and unregularized symmetric reconstructions, the asymmetric reconstruction shows reduced noise and streaking artifacts, better contrast, and more complete fiber tracking. In simulation, the asymmetric reconstruction achieves better mean squared error and better angular difference in the presence of noise. Decomposing the asymmetric tensor into its symmetric and antisymmetric components confirms that the underlying susceptibility tensor is symmetric and that the main sources of asymmetry are noise and streaking artifacts. Whereas the susceptibility tensor is symmetric, asymmetric reconstruction is more effective in suppressing noise and artifacts, resulting in more accurate estimation of the susceptibility tensor.

3D Anatomy of the Jaw Muscles of the Spiny‐Tailed Dogfish ( Squalus acanthius )

New technologies are enabling anatomists to see inside animals to better understand the organization and function of the musculoskeletal system. Among the great transformations in vertebrate evolution is the acquisition and diversification of jaws and jaw musculature. Sharks are key species used in anatomy courses as well as research in organismal evolutionary biology where there is considerable diversity in cranial function and feeding behavior in the clade. Here, we use contrast imaging and 3D muscle fiber architecture visualization approaches to model and demonstrate the jaws and jaw muscles of the spinytailed dogfish (Sqaulus acanthius). A specimen was microCTed following immersion in an iodine-ethanol solution. Muscles and cartilages were segmented using Avizo. Muscle fascicles were then modeled using automated methods followed by manual noise reduction approaches. Colors of modeled fascicles were modeled to reflect orientations of muscles to reveal qualitative patterns in fiber organization. These segmented models of fascicles were then projected in quantitative space to show the orientations of muscle fascicles and moments of the quadratomandibularis, preorbitalis and levator hyomandibulae muscles among others. This 3D model will be shared with educators to include in comparative vertebrate anatomy courses. The results from the muscle architecture and mechanics data will be used to compare with other fishes and tetrapods as part of a growing study on the evolution of jaw muscles in vertebrates.

Phonon imaging in 3D with a fibre probe

We show for the first time that a single ultrasonic imaging fibre is capable of simultaneously accessing 3D spatial information and mechanical properties from microscopic objects. The novel measurement system consists of two ultrafast lasers that excite and detect high-frequency ultrasound from a nano-transducer that was fabricated onto the tip of a single-mode optical fibre. A signal processing technique was also developed to extract nanometric in-depth spatial measurements from GHz frequency acoustic waves, while still allowing Brillouin spectroscopy in the frequency domain. Label-free and non-contact imaging performance was demonstrated on various polymer microstructures. This singular device is equipped with optical lateral resolution, 2.5 μm, and a depth-profiling precision of 45 nm provided by acoustics. The endoscopic potential for this device is exhibited by extrapolating the single fibre to tens of thousands of fibres in an imaging bundle. Such a device catalyses future phonon endomicroscopy technology that brings the prospect of label-free in vivo histology within reach.

Visible wide-angle view imaging system for the first plasma on the HL-2M tokamak.

The wide-angle view imaging system, in terms of a tangential view diagnostic with field of view (FOV) of 56.8° and a downward-looking diagnostic from the top of the machine with FOV of 94.7°, has been newly constructed for the first plasma of the HL-2M tokamak achieved in December 2020. Its mission in this stage is to monitor the plasma evolution during its startup, sustainment, and disruption in the visible spectral range as well as the plasma-wall interaction. For the latter ultrawide view diagnostic, nearly three-quarters of the divertor region and half the area of the inner wall are in the view range. Both the diagnostics are characterized by a similar optical structure, i.e., the light emission from the plasma is collected by a front-end lens and transferred through an imaging fiber bundle to the camera. This optical structure is suitable for application in the complex tokamak environment mainly because the fiber bundle is flexible. Photos of glow discharges are acquired prior to the first plasma for testing the FOVs in the vacuum vessel. The spatial resolution is ∼4mm for the tangential view diagnostic and ∼10mm for the downward-looking diagnostic. The temporal resolutions, ranging from 90 to 360 Hz by changing the region of interest or binning acquisition mode of the color camera, are applied to record the plasma evolutions and/or dust creation events during the first plasma campaign.

A longitudinal comparison in cynomolgus macaques of the effect of brimonidine on optic nerve neuropathy using diffusion tensor imaging magnetic resonance imaging and spectral domain optical coherence tomography

Early detection of optic neuropathy is crucial for initiating treatment that could delay or prevent visual field loss. Preclinical studies have advanced a number of potential neuroprotective strategies to prevent retinal ganglion cell (RGC) degeneration, but none have successfully completed clinical trials. One issue related to the lack of preclinical to clinical translation is the lack of preclinical morphometric assessments that could be used to track neuroprotection, as well as neurodegeneration, over time within the same animal. Thus, to assess whether clinically used morphometric assessments can identify neuroprotection of RGC, the current study compared optic nerve fractional anisotropy (FA) obtained with diffusion tensor imaging (DTI) and retinal nerve fiber layer (RNFL) thickness measured with spectral domain optical coherence tomography (SD-OCT) to observe not only the early progression of RGC axonal degeneration but to also discern which imaging modality identifies signs of neuroprotection during treatment with the alpha-adrenoceptor agonist brimonidine. Elevated and sustained intraocular pressure (IOP) was observed following laser photocoagulation of the trabecular meshwork in one eye of nonhuman primates (NHP). Either brimonidine (0.1%) or control treatment was instilled twice daily for two months. In control-treated eyes, increased IOP, increased vertical cup-to-disc (C/D), reduced rim-to-disc (R/D) ratio, decreased RNFL thickness and decreased FA were observed. While IOP remained elevated during the course of the study, brimonidine tended to delay the progression of RNFL thinning. However, in the same animal, optic nerve FA did not appear to decline. Brimonidine treatment did not affect other measures of RGC axonal degeneration. The current findings demonstrate that early progression of optic neuropathy can be tracked over time in a nonhuman primate model of ocular hypertension using either DTI or SD-OCT. Furthermore, the delayed changes to RNFL thickness and FA appear to be a neuroprotective effect of brimonidine independent of its effect on IOP.

A Signaled Locomotor Avoidance Action Is Fully Represented in the Neural Activity of the Midbrain Tegmentum

Animals, including humans, readily learn to avoid harmful and threatening situations by moving in response to cues that predict the threat (e.g., fire alarm, traffic light). During a negatively reinforced sensory-guided locomotor action, known as signaled active avoidance, animals learn to avoid a harmful unconditioned stimulus (US) by moving away when signaled by a harmless conditioned stimulus (CS) that predicts the threat. CaMKII-expressing neurons in the pedunculopontine tegmentum area (PPT) of the midbrain locomotor region have been shown to play a critical role in the expression of this learned behavior, but the activity of these neurons during learned behavior is unknown. Using calcium imaging fiber photometry in freely behaving mice, we show that PPT neurons sharply activate during presentation of the auditory CS that predicts the threat before onset of avoidance movement. PPT neurons activate further during the succeeding CS-driven avoidance movement, or during the faster US-driven escape movement. PPT neuron activation was weak during slow spontaneous movements but correlated sharply with movement speed and, therefore, with the urgency of the behavior. Moreover, using optogenetics, we found that these neurons must discharge during the signaled avoidance interval for naive mice to effectively learn the active avoidance behavior. As an essential hub for signaled active avoidance, neurons in the midbrain tegmentum process the conditioned cue that predicts the threat and discharge sharply relative to the speed or apparent urgency of the avoidance (learned) and escape (innate) responses.SIGNIFICANCE STATEMENTDuring signaled active avoidance behavior, subjects move away to avoid a threat when directed by an innocuous sensory stimulus. Using imaging methods in freely behaving mice, we found that the activity of neurons in a part of the midbrain, known as the pedunculopontime tegmentum, increases during the presentation of the innocuous sensory stimulus that predicts the threat and also during the expression of the learned behavior as mice move away to avoid the threat. In addition, inhibiting these neurons abolishes the ability of mice to learn the behavior. Thus, neurons in this part of the midbrain code and are essential for signaled active avoidance behavior.

Diffusion Kurtosis Imaging Fiber Tractography of Major White Matter Tracts in Neurosurgery.

Diffusion tensor imaging (DTI)-based fiber tractography is routinely used in clinical applications to visualize major white matter tracts, such as the corticospinal tract (CST), optic radiation (OR), and arcuate fascicle (AF). Nevertheless, DTI is limited due to its capability of resolving intra-voxel multi-fiber populations. Sophisticated models often require long acquisition times not applicable in clinical practice. Diffusion kurtosis imaging (DKI), as an extension of DTI, combines sophisticated modeling of the diffusion process with short acquisition times but has rarely been investigated in fiber tractography. In this study, DTI- and DKI-based fiber tractography of the CST, OR, and AF was investigated in healthy volunteers and glioma patients. For the CST, significantly larger tract volumes were seen in DKI-based fiber tractography. Similar results were obtained for the OR, except for the right OR in patients. In the case of the AF, results of both models were comparable with DTI-based fiber tractography showing even significantly larger tract volumes in patients. In the case of the CST and OR, DKI-based fiber tractography contributes to advanced visualization under clinical time constraints, whereas for the AF, other models should be considered.

General image fiber tool: A concept for automated evaluation of fiber diameters in SEM images

Fiber imaging is becoming increasingly important in various fields. The current standard method of quality assurance is the manual quantification of fiber diameters in Scanning Electron Microscope (SEM) images, which is time consuming and introduces bias. However, due to partly insufficient reliability of automated software, improved concepts are required. We introduce an innovative routine for computerized evaluation of fiber diameters in SEM images with improved accuracy. This General Image Fiber Tool (GIFT) automatically calculates the average fiber diameter and standard deviation by statistical analysis. In a comparative study, GIFT was benchmarked to an existing popular fiber analysis tool, DiameterJ, and manual quantification. GIFT has detected fiber diameters with improved accuracy in numerous SEM images, and has been shown to be a remarkably sound method when challenged with difficult image types. The work presented here validates the GIFT concept and demonstrates its potential for applications in biomedicine and various other fields.

Multimodal Functional Analysis Platform: 1. Ultrathin Fluorescence Endoscope Imaging System Enables Flexible Functional Brain Imaging.

To elucidate the expression mechanisms of brain functions, we have developed an ultrathin fluorescence endoscope imaging system (U-FEIS) that can image cells in the brain at any depth while minimizing the invasion. The endoscope part of U-FEIS consists of a GRIN lens and a 10,000-pixel image fiber with a diameter of 450μm. The specialized microscope of U-FEIS is within 30cm square and includes lenses and optical filters optimized for the endoscope. Using U-FEIS, we successfully visualized neurons expressing GFP with single-cell resolution and recorded the multineuronal activities in vitro and in vivo. U-FEIS can also perform imaging and optical stimulation simultaneously. Therefore, U-FEIS should be a powerful optical tool in neuroscience research.

Fatigue of buried dented pipeline specimens

This paper reports the results of fatigue tests performed on dented steel pipeline specimens that were buried and subjected to cyclic internal pressure. Hot-spot cyclic strain amplitudes were measured using two experimental techniques: Digital Image Correlation (DIC) and Fiber Optic Bragg Strain Gages (FBSG). First, full-field measurements were taken using DIC identified strain concentration sites that were potential locations or hot-spots for fatigue cracks to initiate. Close to these point-locations, measurements of strains using FBSG were also taken, and the results were then compared with the DIC results. These fiber gages were also used during the cyclic pressure loading process while the specimens were buried, in such a way as to monitor any possible influence that might be caused by soil coverture restricting the free deformation occurring in the dented areas. These cyclic strain values were used to demonstrate that a simple uniaxial Coffin-Manson fatigue equation that uses the universal exponents proposed by Manson and the circumferential strain amplitude can be used to predict the life of the dented specimens. Moreover, it was determined that the measured strains at the hot-spot locations were not influenced by the soil coverture.

High Contrast Imaging through Infrared Chalcogenide Imaging Fiber Bundle Illuminated by Quantum Cascade Laser

High Contrast Imaging through Infrared Chalcogenide Imaging Fiber Bundle Illuminated by Quantum Cascade Laser

DTI for brain targeting: Diffusion weighted imaging fiber tractography-Assisted deep brain stimulation.

Fiber tractography assisted Deep Brain Stimulation (DBS) has been performed by different groups for more than 10 years to now. Groups around the world have adapted initial approaches to currently embrace the fiber tractography technology mainly for treating tremor (DBS and lesions), psychiatric indications (OCD and major depression) and pain (DBS). Despite the advantages of directly visualizing the target structure, the technology is demanding and is vulnerable to inaccuracies especially since it is performed on individual level. In this contribution, we will focus on tremor and psychiatric indications, and will show future applications of sophisticated tractography applications for subthalamic nucleus (STN) DBS surgery and stimulation steering as an example.

A miniaturized pre-calibration based Lissajous scanning fiber probe for endoscopic optical coherence tomography

In this paper we present a miniaturized pre-calibration based forward-viewing Lissajous scanning fiber probe for endoscopic optical coherence tomography (OCT). The probe is based on an asymmetric fiber cantilever driven by the piezoelectric bender to realize the two-dimensional (2D) Lissajous scanning, which can realize a relatively large scanning range under a low driving voltage. A capillary metal tube is mounted at the end of the main fiber to reduce the resonant frequency of the fiber cantilever. The relationship between the filling rate and the side-lobe number of the Lissajous scanning pattern is studied, and a method of selecting the orthogonal resonant frequency of the Lissajous scanning is proposed. Through the numerical simulation by COMSOL software, the structural parameters of the asymmetric fiber cantilever are determined. The orthogonal resonant frequencies of the asymmetric fiber cantilever are 169 Hz and 122 Hz. The lengths of the main imaging fiber, the auxiliary fiber and the metal capillary tube are 15.94 mm, 4.49 mm and 2 mm, respectively. The probe is fully packaged in a metal tube for endoscopic imaging. The focal spot and the working distance are 25 µm and 5 mm, respectively. The field of view is larger than 1.5 mm × 1.5 mm. The total rigid length and the outer diameter of the probe are 35 mm and 3.5 mm, respectively. The stability and repeatability of the Lissajous scanning trajectory, and the imaging stability with the rotation of the probe are investigated and verified. The probe is incorporated into a 50 kHz swept source OCT system. The axial resolution of the endoscopic OCT is 10.3 μm, and the imaging frame rate is 1 FPS (frames per second). The maximum signal-to-noise ratio of the imaging system is 110 dB. The imaging performance of the probe is validated by the 2D <i>en-face</i> and three-dimensional volumetric OCT imaging of the high scattering sample and the biological tissue. The probe can be used for the endoscopic imaging of the human tooth. From the result we can distinguish the dental enamel, dental essence and the dental calculus. The developed forward-viewing Lissajous scanning fiber probe is expected to be used in dental applications such as early calculus detection.

Microsurgical and Tractographic Anatomical Study of Transtemporal-Transchoroidal Fissure Approaches to the Ambient Cistern.

Approaching ambient cistern lesions is still a challenge because of deep location and related white matter tracts (WMTs) and neural structures. To investigate the white matter anatomy in the course of 3 types of transtemporal-transchoroidal fissure approaches (TTcFA) to ambient cistern by using fiber dissection technique with translumination and magnetic resonance imaging fiber tractography. Eight formalin-fixed cerebral hemispheres were dissected on surgical corridor from the temporal cortex to the ambient cistern by using Klingler's method. The trans-middle temporal gyrus, trans-inferior temporal sulcus (TITS), and trans-inferior temporal gyrus (TITG) approaches were evaluated. WMTs that were identified during dissection were then reconstructed on the Human Connectome Project 1021 individual template for validation. The trans-middle gyrus approach interrupted the U fibers, arcuate fasciculus (AF), the ventral segment of inferior frontoocipital fasciculus (IFOF), the temporal extensions of the anterior commissure (AC) posterior crura, the tapetum (Tp) fibers, and the anterior loop of the optic radiation (OR). The TITS approach interrupted U fibers, inferior longitudinal fasciculus (ILF), IFOF, and OR. The TITG approach interrupted the U fibers, ILF, and OR. The middle longitudinal fasciculus, ILF, and uncinate fasciculus (UF) were not interrupted in the trans-middle gyrus approach and the AF, UF, AC, and Tp fibers were not interrupted in the TITS/gyrus approaches. Surgical planning of the ambient cistern lesions requires detailed knowledge about WMTs. Fiber dissection and tractography techniques improve the orientation during surgery and may help decrease surgical complications.

Mode decomposition of multimode optical fiber beams by phase-only spatial light modulator

Multimode optical fibers (MMF) recently attracted a renewed attention, because of their potential for spatial division multiplexing, medical imaging and high-power fiber lasers, thanks to the discovery of new nonlinear optical effects, such as Kerr beam self-cleaning, spatiotemporal mode-locking, and geometric parametric instability, to name a few. The main feature of these effects is that many transverse modes are involved in nonlinear interactions. To advance our understanding, it is necessary to analyse the modal content of beams at the output of MMFs. In this work, based on a computer digital holography method using a phase-only spatial light modulator (SLM) as a correlation filter, we experimentally demonstrate a method of mode decomposition involving a large (≃80) number of fiber modes. To obtain this, we carried out a SLM calibration, and numerically investigated the most critical parameters which affect the fidelity of the decomposition, by comparing experimental and reconstructed beam patterns in both the linear (speckled structures) and in the nonlinear (self-cleaned beams) propagation regime.

Core crosstalk in ordered imaging fiber bundles.

Coherent fiber bundles are used widely for imaging. Commonly, disordered arrays of randomly sized fiber cores avoid proximity between like-cores, which would otherwise result in increased core crosstalk and a negative impact on imaging. Recently, stack-and-draw fiber manufacture techniques have been used to produce fibers with a controlled core layout to minimize core crosstalk. However, one must take manufacturing considerations into account during stack-and-draw fiber design in order to avoid impractical or unachievable fabrication. This comes with a set of practical compromises, such as using only a small number of different core sizes. Through characterization of core crosstalk patterns, this Letter aims to aid the understanding of crosstalk limitations imposed by such compromises in the core layout made for ease of fabrication.