scholarly journals A Sparsity-Constrained Preconditioned Kaczmarz Reconstruction Method for Fluorescence Molecular Tomography

2016 ◽  
Vol 2016 ◽  
pp. 1-15
Author(s):  
Duofan Chen ◽  
Jimin Liang ◽  
Yao Li ◽  
Guanghui Qiu
Keyword(s):  
Low Cost ◽  
Biological Tissues ◽  
Reconstruction Method ◽  
Fluorescence Molecular Tomography ◽  
In Vivo Experiments ◽  
Fluorescent Markers ◽  
Ill Posed ◽  
Kaczmarz Method ◽  
Memory Efficient

Fluorescence molecular tomography (FMT) is an imaging technique that can localize and quantify fluorescent markers to resolve biological processes at molecular and cellular levels. Owing to a limited number of measurements and a large number of unknowns as well as the diffusive transport of photons in biological tissues, the inverse problem in FMT is usually highly ill-posed. In this work, a sparsity-constrained preconditioned Kaczmarz (SCP-Kaczmarz) method is proposed to reconstruct the fluorescent target for FMT. The SCP-Kaczmarz method uses the preconditioning strategy to minimize the correlation between the rows of the forward matrix and constrains the Kaczmarz iteration results to be sparse. Numerical simulation and phantom and in vivo experiments were performed to test the efficiency of the proposed method. The results demonstrate that both the convergence and accuracy of the proposed method are improved compared with the classical memory-efficient low-cost Kaczmarz method.

scholarly journals Effective and robust approach for fluorescence molecular tomography based on CoSaMP and SP3 model

2016 ◽  
Vol 09 (06) ◽  
pp. 1650024 ◽  
Author(s):  
Xiaowei He ◽  
Hongbo Guo ◽  
Jingjing Yu ◽  
Xu Zhang ◽  
Yuqing Hou
Keyword(s):  
3D Reconstruction ◽  
Light Propagation ◽  
Matching Pursuit ◽  
Reconstruction Algorithm ◽  
Biological Tissues ◽  
Signal Recovery ◽  
Reconstruction Method ◽  
Fluorescence Molecular Tomography ◽  
Reconstruction Accuracy

Fluorescence molecular tomography (FMT) allows the detection and quantification of various biological processes in small animals in vivo, which expands the horizons of pre-clinical research and drug development. Efficient three-dimensional (3D) reconstruction algorithm is the key to accurate localization and quantification of fluorescent target in FMT. In this paper, 3D reconstruction of FMT is regarded as a sparse signal recovery problem and the compressive sampling matching pursuit (CoSaMP) algorithm is adopted to obtain greedy recovery of fluorescent signals. Moreover, to reduce the modeling error, the simplified spherical harmonics approximation to the radiative transfer equation (RTE), more specifically [Formula: see text], is utilized to describe light propagation in biological tissues. The performance of the proposed reconstruction method is thoroughly evaluated by simulations on a 3D digital mouse model by comparing it with three representative greedy methods including orthogonal matching pursuit (OMP), stagewise OMP(StOMP), and regularized OMP (ROMP). The CoSaMP combined with [Formula: see text] shows an improvement in reconstruction accuracy and exhibits distinct advantages over the comparative algorithms in multiple targets resolving. Stability analysis suggests that CoSaMP is robust to noise and performs stably with reduction of measurements. The feasibility and reconstruction accuracy of the proposed method are further validated by phantom experimental data.

scholarly journals Fast and Robust Reconstruction for Fluorescence Molecular Tomography viaL1-2Regularization

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Haibo Zhang ◽  
Guohua Geng ◽  
Xiaodong Wang ◽  
Xuan Qu ◽  
Yuqing Hou ◽  
...  
Keyword(s):  
Simulated Data ◽  
Alternating Direction Method ◽  
Reconstruction Method ◽  
System Matrix ◽  
Fluorescence Molecular Tomography ◽  
Alternating Direction ◽  
Adaptive Penalty ◽  
Difference Of Convex ◽  
The Difference

Sparse reconstruction inspired by compressed sensing has attracted considerable attention in fluorescence molecular tomography (FMT). However, the columns of system matrix used for FMT reconstruction tend to be highly coherent, which meansL1minimization may not produce the sparsest solution. In this paper, we propose a novel reconstruction method by minimization of the difference ofL1andL2norms. To solve the nonconvexL1-2minimization problem, an iterative method based on the difference of convex algorithm (DCA) is presented. In each DCA iteration, the update of solution involves anL1minimization subproblem, which is solved by the alternating direction method of multipliers with an adaptive penalty. We investigated the performance of the proposed method with both simulated data andin vivoexperimental data. The results demonstrate that the DCA forL1-2minimization outperforms the representative algorithms forL1,L2,L1/2, andL0when the system matrix is highly coherent.

scholarly journals Sutureless repair of corneal injuries using naturally derived bioadhesive hydrogels

2019 ◽  
Vol 5 (3) ◽  
pp. eaav1281 ◽  
Author(s):  
Ehsan Shirzaei Sani ◽  
Ahmad Kheirkhah ◽  
Devyesh Rana ◽  
Zhongmou Sun ◽  
William Foulsham ◽  
...  
Keyword(s):  
Low Cost ◽  
Unmet Need ◽  
Defect Model ◽  
Sutureless Repair ◽  
In Vivo Experiments ◽  
High Adhesion ◽  
Common Causes ◽  
Corneal Regeneration

Corneal injuries are common causes of visual impairment worldwide. Accordingly, there is an unmet need for transparent biomaterials that have high adhesion, cohesion, and regenerative properties. Herein, we engineer a highly biocompatible and transparent bioadhesive for corneal reconstruction using a visible light cross-linkable, naturally derived polymer, GelCORE (gel for corneal regeneration). The physical properties of GelCORE could be finely tuned by changing prepolymer concentration and photocrosslinking time. GelCORE revealed higher tissue adhesion compared to commercial adhesives. Furthermore, in situ photopolymerization of GelCORE facilitated easy delivery to the cornea, allowing for bioadhesive curing precisely according to the required geometry of the defect. In vivo experiments, using a rabbit stromal defect model, showed that bioadhesive could effectively seal corneal defects and induce stromal regeneration and re-epithelialization. Overall, GelCORE has many advantages including low cost and ease of production and use. This makes GelCORE a promising bioadhesive for corneal repair.

scholarly journals A High-Efficiency Super-Resolution Reconstruction Method for Ultrasound Microvascular Imaging

2018 ◽  
Vol 8 (7) ◽  
pp. 1143 ◽  
Author(s):  
Wei Guo ◽  
Yusheng Tong ◽  
Yurong Huang ◽  
Yuanyuan Wang ◽  
Jinhua Yu
Keyword(s):  
Time Resolution ◽  
High Efficiency ◽  
Gaussian Function ◽  
Super Resolution ◽  
Reconstruction Method ◽  
Image Deconvolution ◽  
Clinical Use ◽  
In Vivo Experiments ◽  
Resolution Imaging

The emergence of super-resolution imaging makes it possible to display the microvasculatures clearly using ultrasound imaging, which is of great importance in the early diagnosis of cancer. At present, the super-resolution performance can only be achieved when the sampling signal is long enough (usually more than 10,000 frames). Thus, the imaging time resolution is not suitable for clinical use. In this paper, we proposed a novel super-resolution reconstruction method, which is proved to have a satisfactory resolution using shorter sampling signal sequences. In the microbubble localization step, the integrated form of the 2D Gaussian function is innovatively adopted for image deconvolution in our method, which enhances the accuracy of microbubble positioning. In the trajectory tracking step, for the first time the averaged shifted histogram technique is presented for the visualization, which greatly improves the precision of reconstruction. In vivo experiments on rabbits were conducted to verify the effectiveness of the proposed method. Compared to the conventional reconstruction method, our method significantly reduces the Full-Width-at-Half-Maximum (FWHM) by 50% using only 400-frame signals. Besides, there is no significant increase in the running time using the proposed method. Considering its imaging performance and used frame number, the conclusion can be drawn that the proposed method advances the application of super-resolution imaging to the clinical use with a much higher time resolution.

scholarly journals Normalized Born Approximation-Based Two-Stage Reconstruction Algorithm for Quantitative Fluorescence Molecular Tomography

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Huangjian Yi ◽  
Duofang Chen ◽  
Wei Li ◽  
Shuang Zhou ◽  
Miao Ning ◽  
...  
Keyword(s):  
Born Approximation ◽  
Small Animal Imaging ◽  
Small Animal ◽  
Reconstruction Algorithm ◽  
Reconstruction Technique ◽  
Reconstruction Method ◽  
Fluorescence Molecular Tomography ◽  
Two Stage ◽  
Quantitative Reconstruction

Fluorescence molecular tomography (FMT) is a promising technique forin vivosmall animal imaging. In this paper, a two-stage reconstruction method based on normalized Born approximation is developed for FMT, which includes two steps for quantitative reconstruction. First, the localization of fluorescent fluorophore is determined byl1-norm regularization method. Then, in the location region of fluorophore, which is provided by the first stage, algebraic reconstruction technique (ART) is utilized for the fluorophore concentration reconstruction. The validity of the two-stage quantitative reconstruction algorithm is testified by simulation experiments on a 3D digital mouse atlas and physical experiments on a phantom. The results suggest that we are able to recover the fluorophore location and concentration.

scholarly journals Controlled neighbor exchanges drive glassy behavior, intermittency and cell streaming in epithelial tissues

2020 ◽  
Author(s):  
Amit Das ◽  
Srikanth Sastry ◽  
Dapeng Bi
Keyword(s):  
Glass Transition ◽  
Biological Tissues ◽  
Cell Junctions ◽  
Pupal Development ◽  
In Vivo Experiments ◽  
Cell Property ◽  
Time Required ◽  
Rate Limiting ◽  
Cell Cell

Cell neighbor exchanges are integral to tissue rearrangements in biology, including development and repair. Often these processes occur via topological T1 transitions analogous to those observed in foams, grains and colloids. However, in contrast to in non-living materials the T1 transitions in biological tissues are rate-limited and cannot occur instantaneously due to the finite time required to remodel complex structures at cell-cell junctions. Here we study how this rate-limiting process affects the mechanics and collective behavior of cells in a tissue by introducing this important biological constraint in a theoretical vertex-based model as an intrinsic single-cell property. We report in the absence of this time constraint, the tissue undergoes a motility-driven glass transition characterized by a sharp increase in the intermittency of cell-cell rearrangements. Remarkably, this glass transition disappears as T1 transitions are temporally limited. As a unique consequence of limited rearrangements, we also find that the tissue develops spaitally correlated streams of fast and slow cells, in which the fast cells organize into stream-like patterns with leader-follower interactions, and maintain optimally stable cell-cell contacts. The predictions of this work is compared with existing in-vivo experiments in Drosophila pupal development.

scholarly journals Reconstruction Method for Optical Tomography Based on the Linearized Bregman Iteration with Sparse Regularization

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Chengcai Leng ◽  
Dongdong Yu ◽  
Shuang Zhang ◽  
Yu An ◽  
Yifang Hu
Keyword(s):  
A Priori ◽  
Optical Tomography ◽  
Reconstruction Method ◽  
Bregman Iteration ◽  
Sparse Regularization ◽  
Bioluminescence Tomography ◽  
Regularization Problem ◽  
Ill Posed ◽  
Linearized Bregman Iteration

Optical molecular imaging is a promising technique and has been widely used in physiology, and pathology at cellular and molecular levels, which includes different modalities such as bioluminescence tomography, fluorescence molecular tomography and Cerenkov luminescence tomography. The inverse problem is ill-posed for the above modalities, which cause a nonunique solution. In this paper, we propose an effective reconstruction method based on the linearized Bregman iterative algorithm with sparse regularization (LBSR) for reconstruction. Considering the sparsity characteristics of the reconstructed sources, the sparsity can be regarded as a kind ofa prioriinformation and sparse regularization is incorporated, which can accurately locate the position of the source. The linearized Bregman iteration method is exploited to minimize the sparse regularization problem so as to further achieve fast and accurate reconstruction results. Experimental results in a numerical simulation andin vivomouse demonstrate the effectiveness and potential of the proposed method.

scholarly journals In Vivo Recognition of Vascular Structures by Near-Infrared Transillumination

Proceedings ◽  
2019 ◽  
Vol 42 (1) ◽  
pp. 24
Author(s):  
Valentina Bello ◽  
Elisabetta Bodo ◽  
Sara Pizzurro ◽  
Sabina Merlo
Keyword(s):  
Semiconductor Lasers ◽  
Near Infrared ◽  
Low Cost ◽  
Full Range ◽  
Digital Camera ◽  
Biological Tissues ◽  
Dorsal Vein ◽  
Spatially Distributed ◽  
Vascular Structures

Transillumination is a very well-known non-invasive optical technique that relies on the use of non-ionizing radiation to obtain information about the internal morphology of biological tissues. In a previous work, we implemented a laser-based illuminator operating at a wavelength of 850 nm, combined with a CMOS digital camera and narrow-band optical detection that showed great potential for in vivo imaging. A great advantage is the use of low-cost semiconductor lasers, driven by a very low current (about 11 mA, spatially distributed as a 6-by-6 matrix covering a 25 cm2 area). Thanks to the strong absorption of hemoglobin at this wavelength, we have collected raw data of vascular structures that have been further processed to achieve images with much better quality. In particular, here we show that a higher contrast can be attained by the expansion of gray level histograms to exploit the full range, 0–255. This elaboration can be, for instance, exploited for the recognition of vascular structures with better resolution. Examples are reported relative to hand dorsal vein patterns and live chick embryos’ blood vessels. Analyses can be successfully performed without applying any thermal or mechanical stress to the human tissue under test and without damaging or puncturing any parts of the eggshell.

A technique for protecting delicate specimens during processing

1989 ◽  
Vol 47 ◽  
pp. 982-983
Author(s):  
R.J. Mount ◽  
R.V. Harrison
Keyword(s):  
Basilar Membrane ◽  
Low Cost ◽  
Organ Of Corti ◽  
Region Of Interest ◽  
Sensory Epithelium ◽  
Physical Damage ◽  
Air Drying ◽  
Specimen Handling ◽  
Two Component

The sensory end organ of the ear, the organ of Corti, rests on a thin basilar membrane which lies between the bone of the central modiolus and the bony wall of the cochlea. In vivo, the organ of Corti is protected by the bony wall which totally surrounds it. In order to examine the sensory epithelium by scanning electron microscopy it is necessary to dissect away the protective bone and expose the region of interest (Fig. 1). This leaves the fragile organ of Corti susceptible to physical damage during subsequent handling. In our laboratory cochlear specimens, after dissection, are routinely prepared by the O-T- O-T-O technique, critical point dried and then lightly sputter coated with gold. This processing involves considerable specimen handling including several hours on a rotator during which the organ of Corti is at risk of being physically damaged. The following procedure uses low cost, readily available materials to hold the specimen during processing ,preventing physical damage while allowing an unhindered exchange of fluids.Following fixation, the cochlea is dehydrated to 70% ethanol then dissected under ethanol to prevent air drying. The holder is prepared by punching a hole in the flexible snap cap of a Wheaton vial with a paper hole punch. A small amount of two component epoxy putty is well mixed then pushed through the hole in the cap. The putty on the inner cap is formed into a “cup” to hold the specimen (Fig. 2), the putty on the outside is smoothed into a “button” to give good attachment even when the cap is flexed during handling (Fig. 3). The cap is submerged in the 70% ethanol, the bone at the base of the cochlea is seated into the cup and the sides of the cup squeezed with forceps to grip it (Fig.4). Several types of epoxy putty have been tried, most are either soluble in ethanol to some degree or do not set in ethanol. The only putty we find successful is “DUROtm MASTERMENDtm Epoxy Extra Strength Ribbon” (Loctite Corp., Cleveland, Ohio), this is a blue and yellow ribbon which is kneaded to form a green putty, it is available at many hardware stores.

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