A hybrid clustering algorithm for multiple‐source resolving in bioluminescence tomography

Bioluminescence tomography is a preclinical imaging modality to locate and quantify internal bioluminescent sources from surface measurements, which experienced rapid growth in the last 10 years. However, multiple‐source resolving remains a challenging issue in BLT. In this study, it is treated as an unsupervised pattern recognition problem based on the reconstruction result, and a novel hybrid clustering algorithm combining the advantages of affinity propagation (AP) and K‐means is developed to identify multiple sources automatically. Moreover, we incorporate the clustering analysis into a general multiple‐source reconstruction framework, which can provide stable reconstruction and accurate resolving result without providing the number of targets. Numerical simulations and in vivo experiments on 4T1‐luc2 mouse model were conducted to assess the performance of the proposed method in multiple‐source resolving. The encouraging results demonstrate significant effectiveness and potential of our method in preclinical BLT applications.      

Integrated photoacoustic and diffuse optical tomography system for imaging of human finger joints in vivo

In this study, we developed a dual‐modality tomographic system that integrated photoacoustic imaging (PAI) and diffuse optical tomography (DOT) into a single platform for imaging human finger joints with fine structures and associated optical properties. In PAI, spherical focused transducers were utilized to collect acoustic signals, and the concept of virtual detector was applied in a conventional back‐projection algorithm to improve the image quality. A finite‐element based reconstruction algorithm was employed to quantitatively recover optical property distribution in the objects for DOT. The phantom results indicate that PAI has a maximum lateral resolution of 70 µm in resolving structures of targets. DOT was able to recover both optical absorption and reduced scattering coefficients of targets accurately. To validate the potential of this system in clinical diagnosis of joint diseases, the distal interphalangeal (DIP) joints of 4 healthy female volunteers were imaged. We successfully obtained high‐resolution images of the phalanx and the surrounding soft tissue via PAI, and recovered both optical absorption and reduced scattering coefficients of phalanx using DOT. The in vivo results suggest that this dual‐modality system has the potential for the early diagnosis of joint diseases such as osteoarthritis (OA) and rheumatoid arthritis (RA).

Integrated PAI/DOT imaging interface (top) and typical reconstruction of structures and associated optical properties of a female finger joint via PAI and DOT (bottom).     

Evaluation of a commercial Model Based Iterative reconstruction algorithm in computed tomography

IntroductionIterative reconstruction algorithms have been introduced in clinical practice to obtain dose reduction without compromising the diagnostic performance.PurposeTo investigate the commercial Model Based IMR algorithm by means of patient dose and image quality, with standard Fourier and alternative metrics.Materials and methodsA Catphan phantom, a commercial density phantom and a cylindrical water filled phantom were scanned both varying CTDI_vol and reconstruction thickness. Images were then reconstructed with Filtered Back Projection and both statistical (iDose) and Model Based (IMR) Iterative reconstruction algorithms.Spatial resolution was evaluated with Modulation Transfer Function and Target Transfer Function. Noise reduction was investigated with Standard Deviation. Furthermore, its behaviour was analysed with 3D and 2D Noise Power Spectrum. Blur and Low Contrast Detectability were investigated.Patient dose indexes were collected and analysed.ResultsAll results, related to image quality, have been compared to FBP standard reconstructions.Model Based IMR significantly improves Modulation Transfer Function with an increase between 12% and 64%. Target Transfer Function curves confirm this trend for high density objects, while Blur presents a sharpness reduction for low density details.Model Based IMR underlines a noise reduction between 44% and 66% and a variation in noise power spectrum behaviour. Low Contrast Detectability curves underline an averaged improvement of 35–45%; these results are compatible with an achievable reduction of 50% of CTDI_vol.A dose reduction between 25% and 35% is confirmed by median values of CTDI_vol.ConclusionIMR produces an improvement in image quality and dose reduction.     

Isotropic high resolution optoacoustic imaging with linear detector arrays in bi‐directional scanning

Optoacoustic (photoacoustic) imaging is often performed with one‐dimensional transducer arrays, in analogy to ultrasound imaging. Optoacoustic imaging using linear arrays offers ease of implementation but comes with several performance drawbacks, in particular poor elevation resolution, i.e. the resolution along the axis perpendicular to the focal plane. Herein, we introduce and investigate a bi‐directional scanning approach using linear arrays that can improve the imaging performance to quasi‐isotropic transverse resolution. We study the approach theoretically and perform numerical simulations and phantom measurements to evaluate its performance under defined conditions. Finally, we discuss the features and the limitations of the proposed method.

The poor elevation resolution in a linear scan (left image) is overcome by the proposed bi‐directional scanning approach that yields isotropic transverse resolution (right).     

Sparse‐graph manifold learning method for bioluminescence tomography

In preclinical researches, bioluminescence tomography (BLT) has widely been used for tumor imaging and monitoring, imaged‐guided tumor therapy, and so forth. For these biological applications, both tumor spatial location and morphology analysis are the leading problems needed to be taken into account. However, most existing BLT reconstruction methods were proposed for some specific applications with a focus on sparse representation or morphology recovery, respectively. How to design a versatile algorithm that can simultaneously deal with both aspects remains an impending problem. In this study, a Sparse‐Graph Manifold Learning (SGML) method was proposed to balance the source sparseness and morphology, by integrating non‐convex sparsity constraint and dynamic Laplacian graph model. Furthermore, based on the nonconvex optimization theory and some iterative approximation, we proposed a novel iteratively reweighted soft thresholding algorithm (IRSTA) to solve the SGML model. Numerical simulations and in vivo experiments result demonstrated that the proposed SGML method performed much superior to the comparative methods in spatial localization and tumor morphology recovery for various source settings. It is believed that the SGML method can be applied to the related optical tomography and facilitate the development of optical molecular tomography.     

Quantitative and rapid estimations of human sub‐surface skin mass using ultra‐high‐resolution spectral domain optical coherence tomography

Non‐invasive and quantitative estimations for the delineation of sub‐surface tumor margins could greatly aid in the early detection and monitoring of the morphological appearances of tumor growth, ensure complete tumor excision without the unnecessary sacrifice of healthy tissue, and facilitate post‐operative follow‐up for recurrence. In this study, a high‐speed, non‐invasive, and ultra‐high‐resolution spectral domain optical coherence tomography (UHR‐SDOCT) imaging platform was developed for the quantitative measurement of human sub‐surface skin mass. With a proposed robust, semi‐automatic analysis, the system can rapidly quantify lesion area and shape regularity by an en‐face‐oriented algorithm. Various sizes of nylon sutures embedded in pork skin were used first as a phantom to verify the accuracy of our algorithm, and then in vivo, feasibility was proven using benign human angiomas and pigmented nevi. Clinically, this is the first step towards an automated skin lesion measurement system.

In vivo optical coherence tomography (OCT) image of angioma (A). Thin red arrows point to a blood vessel (BV).     

Dual‐wavelength‐assisted thermal hemostasis for treatment of benign prostate hyperplasia

Laser treatment on a large size of prostate gland often encounters significant bleeding that can prolong the entire procedure and cause urinary complications. The current study investigates the feasibility of dual‐wavelength (532 and 980 nm) application to achieve rapid hemostasis for 532‐nm laser prostatectomy. Porcine kidney and bleeding phantom models were tested to quantify the degree of the irreversible tissue coagulation and to estimate the time for the complete hemostasis, respectively. The ex vivo kidney testing verifies that the dual‐wavelength created up to 40% deeper and 25% wider coagulation regions than a single wavelength does. The bleeding phantom testing demonstrates that due to the enhanced thermal effects, the simultaneous irradiation yields the complete photocoagulation (~11 seconds) whereas 532 or 980 nm hardly stops bleeders. Numerical simulations validate that the combined optical‐thermal characteristics of both the wavelengths account for the augmented thermal coagulation. The dual‐wavelength‐assisted coagulation can be a feasible treatment to entail the rapid hemostasis and to facilitate the laser prostatectomy in an effective manner.      

Validation of delay‐multiply‐and‐standard‐deviation weighting factor for improved photoacoustic imaging of sentinel lymph node

Delay‐and‐sum (DAS) is one of the most common algorithms used to construct the photoacoustic images due to its low complexity. However, it results in images with high sidelobes and low resolution. Delay‐and‐standard‐deviation (DASD) weighting factor can improve the contrast of the images compared to DAS. However, it still suffers from high sidelobes. In this work, a new weighting factor, named delay‐multiply‐and‐standard‐deviation (DMASD) is introduced to enhance the contrast of the reconstructed images compared to other mentioned methods. In the proposed method, the SD of the mutual multiplied delayed signals are calculated, normalized and multiplied to DAS beamformed data. The results show that DMASD improves the signal‐to‐noise‐ratio about 19.29 and 7.3 dB compared to DAS and DASD, respectively, for in vivo imaging of the sentinel lymph node. Moreover, the contrast ratio is improved by the DMASD about 23.61 and 10.81 dB compared to DAS and DASD, respectively.      

Hyperspectral scanning laser optical tomography

In order to study physical relationships within tissue volumes or even organism‐level systems, the spatial distribution of multiple fluorescent markers needs to be resolved efficiently in three dimensions. Here, rather than acquiring discrete spectral images sequentially using multiple emission filters, a hyperspectral scanning laser optical tomography system is developed to obtain hyperspectral volumetric data sets with 2‐nm spectral resolution of optically transparent mesoscopic (millimeter‐centimeter) specimens. This is achieved by acquiring a series of point‐scanning hyperspectral extended depth of field images at different angles and subsequently tomographically reconstructing the 3D intensity distribution for each wavelength. This technique is demonstrated to provide robust measurements via the comparison of spectral and intensity profiles of fluorescent bead phantoms. Due to its enhanced spectral resolving ability, this technique is also demonstrated to resolve largely overlapping fluorophores, as demonstrated by the 3D fluorescence hyperspectral reconstruction of a dual‐labeled mouse thymus gland sample and the ability to distinguish tumorous and normal tissues of an unlabeled mouse intestine sample.      

Monte Carlo method for bioluminescence tomography

Bioluminescence imaging plays an important role in the areas of cancer biology, cell biology, gene therapy, and so on. The 2D planar bioluminescent imaging has been transformed into a 3D framework by bioluminescence tomography (BLT) that enables bioluminescent source reconstruction in a mouse using a modality fusion approach. To solve this BLT problem, a geometrical model of the mouse is usually built from a CT/micro-CT/micro-MRI scan, which facilitates the assignment of optical parameters to various anatomical regions in the model. This optical model is then used to facilitate BLT. The forward model is based on Monte Carlo simulation to calculate the diffuse light flux on the surface of the mouse. The forward model data are used to define the imaging system and perform the BLT reconstruction. In this paper, we report the reconstruction of sources inside a heterogeneous highly scattering physical phantom to demonstrate the feasibility of this Monte Carlo based BLT method.     

Depth‐resolved multimodal imaging: Wavelength modulated spatially offset Raman spectroscopy with optical coherence tomography

A major challenge in biophotonics is multimodal imaging to obtain both morphological and molecular information at depth. We demonstrate a hybrid approach integrating optical coherence tomography (OCT) with wavelength modulated spatially offset Raman spectroscopy (WM‐SORS). With depth colocalization obtained from the OCT, we can penetrate 1.2‐mm deep into strong scattering media (lard) to acquire up to a 14‐fold enhancement of a Raman signal from a hidden target (polystyrene) with a spatial offset. Our approach is capable of detecting both Raman and OCT signals for pharmaceutical particles embedded in turbid media and revealing the white matter at depth within a 0.6‐mm thick brain tissue layer. This depth resolved label‐free multimodal approach is a powerful route to analyze complex biomedical samples.      

Sensitivity and accuracy of hybrid fluorescence‐mediated tomography in deep tissue regions

Fluorescence‐mediated tomography (FMT) enables noninvasive assessment of the three‐dimensional distribution of near‐infrared fluorescence in mice. The combination with micro‐computed tomography (µCT) provides anatomical data, enabling improved fluorescence reconstruction and image analysis. The aim of our study was to assess sensitivity and accuracy of µCT‐FMT under realistic in vivo conditions in deeply‐seated regions. Accordingly, we acquired fluorescence reflectance images (FRI) and µCT‐FMT scans of mice which were prepared with rectal insertions with different amounts of fluorescent dye. Default and high‐sensitivity scans were acquired and background signal was analyzed for three FMT channels (670 nm, 745 nm, and 790 nm). Analysis was performed for the original and an improved FMT reconstruction using the µCT data. While FRI and the original FMT reconstruction could detect 100 pmol, the improved FMT reconstruction could detect 10 pmol and significantly improved signal localization. By using a finer sampling grid and increasing the exposure time, the sensitivity could be further improved to detect 0.5 pmol. Background signal was highest in the 670 nm channel and most prominent in the gastro‐intestinal tract and in organs with high relative amounts of blood. In conclusion, we show that µCT‐FMT allows sensitive and accurate assessment of fluorescence in deep tissue regions.

     

Investigating the healing mechanisms of an angiogenesis‐promoting topical treatment for diabetic wounds using multimodal microscopy

Impaired skin wound healing is a significant comorbid condition of diabetes that is caused by poor microcirculation, among other factors. Studies have shown that angiogenesis, a critical step in the wound healing process in diabetic wounds, can be promoted under hypoxia. In this study, an angiogenesis‐promoting topical treatment for diabetic wounds, which promotes angiogenesis by mimicking a hypoxic environment via inhibition of prolyl hydroxylase resulting in elevation or maintenance of hypoxia‐inducible factor, was investigated utilizing a custom‐built multimodal microscopy system equipped with phase‐variance optical coherence tomography (PV‐OCT) and fluorescence lifetime imaging microscopy (FLIM). PV‐OCT was used to track the regeneration of the microvasculature network, and FLIM was used to assess the in vivo metabolic response of mouse epidermal keratinocytes to the treatment during healing. Results show a significant decrease in the fluorescence lifetime of intracellular reduced nicotinamide adenine dinucleotide, suggesting a hypoxic‐like environment in the wounded skin, followed by a quantitative increase in blood vessel density assessed by PV‐OCT. Insights gained in these studies could lead to new endpoints for evaluation of the efficacy and healing mechanisms of wound‐healing drugs in a setting where delayed healing does not permit available methods for evaluation to take place.      

Effects of various generations of iterative CT reconstruction algorithms on low-contrast detectability as a function of the effective abdominal diameter: A quantitative task-based phantom study

PurposeTo investigate how various generations of iterative reconstruction (IR) algorithms impact low-contrast detectability (LCD) in abdominal computed tomography (CT) for different patient effective diameters, using a quantitative task-based approach.MethodsInvestigations were performed using an anthropomorphic abdominal phantom with two optional additional rings to simulate varying patient effective diameters (25, 30, and 35 cm), and containing multiple spherical targets (5, 6, and 8 mm in diameter) with a 20-HU contrast difference. The phantom was scanned using routine abdominal protocols (CTDI_vol, 5.9–16 mGy) on four CT systems from two manufacturers. Images were reconstructed using both filtered back-projection (FBP) and various IR algorithms: ASiR 50%, SAFIRE 3 (both statistical IRs), ASiR-V 50%, ADMIRE 3 (both partial model-based IRs), or Veo (full model-based IR). Section thickness/interval was 2/1 mm or 2.5/1.25 mm, except 0.625/0.625 mm for Veo. We assessed LCD using a channelized Hotelling observer with 10 dense differences of Gaussian channels, with the area under the receiver operating characteristic curve (AUC) as a figure of merit.ResultsFor the smallest phantom (25-cm diameter) and smallest lesion size (5-mm diameter), AUC for FBP and the various IR algorithms did not significantly differ for any of the tested CT systems. For the largest phantom (35-cm diameter), Veo yielded the highest AUC improvement (8.5%). Statistical and partial model-based IR algorithms did not significantly improve LCD.ConclusionIn abdominal CT, switching from FBP to IR algorithms offers limited possibilities for achieving significant dose reductions while ensuring a constant objective LCD.     

Front Cover: Spectrally encoded coherence tomography and reflectometry: Simultaneous en face and cross‐sectional imaging at 2 gigapixels per second (J. Biophotonics 4/2018)

SECTR is a novel multimodal imaging platform for combined volumetric optical coherence tomography (OCT) and en face spectrally encoded reflectometry (SER). The authors demonstrate three‐dimensional motion‐tracking with millisecond temporal and micron spatial resolution using complementary data from OCT and SER, and preliminary algorithms and results showing real‐time image aiming and multi‐volumetric mosaicking for reconstruction of wide‐field composites. The image shows a noninvasively imaged nine‐field mosaic of in vivo human retina and depth‐resolved visualization of tissue microstructures. Further details can be found in the article by Mohamed T. El‐Haddad, Ivan Bozic, and Yuankai K. Tao ( e201700268 )

     

Development of a 3‐dimensional tissue lung phantom of a preterm infant for optical measurements of oxygen—Laser‐detector position considerations

There is a need to further improve the clinical care of our most vulnerable patients—preterm infants. Novel diagnostic and treatment tools facilitate such advances. Here, we evaluate a potential percutaneous optical monitoring tool to assess the oxygen and water vapor content in the lungs of preterm babies. The aim is to prepare for further clinical studies by gaining a detailed understanding of how the measured light intensity and gas absorption signal behave for different possible geometries of light delivery and receiver. Such an experimental evaluation is conducted for the first time utilizing a specially developed 3‐dimensional‐printed optical phantom based on a geometry model obtained from computer tomography images of the thorax (chest) of a 1700‐g premature infant. The measurements yield reliable signals for source–detector distances up to about 50 mm, with stronger gas absorption signals at long separations and positions related to the lower part of the lung, consistent with a larger relative volume of this. The limitations of this study include the omission of scattering tissue within the lungs and that similar optical properties are used for the wavelengths employed for the 2 gases, yielding no indication on the optimal wavelength pair to use.      

Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms

Algorithms for three-dimensional (3D) reconstruction of objects based on their projections are essential in various biological and medical imaging modalities. In cryo-electron tomography (CET) a major challenge for reconstruction is the limited range of projection angles, which manifests itself as a “missing wedge” of data in Fourier space making the reconstruction problem ill-posed. Here, we apply an iterative reconstruction method that makes use of nonuniform fast Fourier transform (NUFFT) to the reconstruction of cryo-electron tomograms. According to several measures the reconstructions are superior to those obtained using conventional methods, most notably weighted backprojection. Most importantly, we show that it is possible to fill in partially the unsampled region in Fourier space with meaningful information without making assumptions about the data or applying prior knowledge. As a consequence, particles of known structure can be localized with higher confidence in cryotomograms and subtomogram averaging yields higher resolution densities.     

Automated three‐dimensional cell counting method for grading uveitis of rodent eye in vivo with optical coherence tomography

In preclinical vision research, cell grading in small animal models is essential for the quantitative evaluation of intraocular inflammation. Here, we present a new and practical optical coherence tomography (OCT) image analysis method for the automated detection and counting of aqueous cells in the anterior chamber (AC) of a rodent model of uveitis. Anterior segment OCT images are acquired with a 100 kHz swept‐source OCT system. The proposed method consists of 2 steps. In the first step, we first despeckle and binarize each OCT image. After removing AS structures in the binary image, we then apply area thresholding to isolate cell‐like objects. Potential cell candidates are selected based on their best fit to roundness. The second step performs the cell counting within the whole AC, in which additional cell tracking analysis is conducted on the successive OCT images to eliminate redundancy in cell counting. Finally, 3D cell grading using the proposed method is demonstrated in longitudinal OCT imaging of a mouse model of anterior uveitis in vivo. Rendering of anterior segment (orange) of mouse eye and automatically counted anterior chamber cells (green). Inset is a top view of the rendering, showing the cell distribution across the anterior chamber.      

Measuring polarization changes in the human outer retina with polarization‐sensitive optical coherence tomography

Morphological changes in the outer retina such as drusen are established biomarkers to diagnose age‐related macular degeneration. However, earlier diagnosis might be possible by taking advantage of more subtle changes that accompany tissues that bear polarization‐altering properties. To test this hypothesis, we developed a method based on polarization‐sensitive optical coherence tomography with which volumetric data sets of the macula were obtained from 10 young (<25 years) and 10 older (>54 years) subjects. All young subjects and 5 of the older subjects had retardance values induced by the retinal pigment epithelium and Bruch's membrane (RPE‐BM) complex that were just above the noise floor measurement (5°‐13° at 840 nm). In contrast, elevated retardance, up to 180°, was observed in the other 5 older subjects. Analysis of the degree of polarization uniformity (DOPU) demonstrates that reduced DOPU (<0.4) in the RPE is associated with elevated double pass phase retardation (DPPR) below the RPE‐BM complex, suggesting that the observed elevated DPPR in older subjects is the result of increased scattering or polarization scrambling. Collectively, our measurements show that the outer retina can undergo dramatic change in its polarization properties with age, and in some cases still retain its clinically normal appearance.      

A method to study the hemodynamics of chicken embryo's aortic arches using optical coherence tomography

Congenital cardiovascular defects are the leading cause of birth defect related death. It has been hypothesized that fluid mechanical forces of embryonic blood flow affect cardiovascular development and play a role in congenital malformations. Studies in small animal embryos can improve our understanding of congenital malformations and can lead to better treatment. We present a feasibility study in which high‐resolution optical coherence tomography (OCT) and computational fluid dynamics (CFD) are combined to provide quantitative analysis of the embryonic flow mechanics and the associated anatomy in a small animal model.