Generation of extended light-sheets for single and multi-photon fluorescence microscopy

We theoretically propose and computationally demonstrate the generation of extended light-sheet for fluorescence microscopy. This is made possible by the introduction of a specially designed double-window spatial filter that allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3.38 times for single photon excitation and 3.68 times for multiphoton excitation as compared to state-of-art single plane illumination microscopy system. This technique may facilitate the study of large biological specimens (such as Zebrafish embryo and tissue) with high spatial resolution and reduced photobleaching. (C) 2013 AIP Publishing LLC.

A MatLAB Based Virtual Phantom for 2D Electrical Impedance Tomography (MatVP2DEIT): Studying the Medical Electrical Impedance Tomography Reconstruction in Computer

Electrical Impedance Tomography (EIT) is a computerized medical imaging technique which reconstructs the electrical impedance images of a domain under test from the boundary voltage-current data measured by an EIT electronic instrumentation using an image reconstruction algorithm. Being a computed tomography technique, EIT injects a constant current to the patient's body through the surface electrodes surrounding the domain to be imaged (Omega) and tries to calculate the spatial distribution of electrical conductivity or resistivity of the closed conducting domain using the potentials developed at the domain boundary (partial derivative Omega). Practical phantoms are essentially required to study, test and calibrate a medical EIT system for certifying the system before applying it on patients for diagnostic imaging. Therefore, the EIT phantoms are essentially required to generate boundary data for studying and assessing the instrumentation and inverse solvers a in EIT. For proper assessment of an inverse solver of a 2D EIT system, a perfect 2D practical phantom is required. As the practical phantoms are the assemblies of the objects with 3D geometries, the developing of a practical 2D-phantom is a great challenge and therefore, the boundary data generated from the practical phantoms with 3D geometry are found inappropriate for assessing a 2D inverse solver. Furthermore, the boundary data errors contributed by the instrumentation are also difficult to separate from the errors developed by the 3D phantoms. Hence, the errorless boundary data are found essential to assess the inverse solver in 2D EIT. In this direction, a MatLAB-based Virtual Phantom for 2D EIT (MatVP2DEIT) is developed to generate accurate boundary data for assessing the 2D-EIT inverse solvers and the image reconstruction accuracy. MatVP2DEIT is a MatLAB-based computer program which simulates a phantom in computer and generates the boundary potential data as the outputs by using the combinations of different phantom parameters as the inputs to the program. Phantom diameter, inhomogeneity geometry (shape, size and position), number of inhomogeneities, applied current magnitude, background resistivity, inhomogeneity resistivity all are set as the phantom variables which are provided as the input parameters to the MatVP2DEIT for simulating different phantom configurations. A constant current injection is simulated at the phantom boundary with different current injection protocols and boundary potential data are calculated. Boundary data sets are generated with different phantom configurations obtained with the different combinations of the phantom variables and the resistivity images are reconstructed using EIDORS. Boundary data of the virtual phantoms, containing inhomogeneities with complex geometries, are also generated for different current injection patterns using MatVP2DEIT and the resistivity imaging is studied. The effect of regularization method on the image reconstruction is also studied with the data generated by MatVP2DEIT. Resistivity images are evaluated by studying the resistivity parameters and contrast parameters estimated from the elemental resistivity profiles of the reconstructed phantom domain. Results show that the MatVP2DEIT generates accurate boundary data for different types of single or multiple objects which are efficient and accurate enough to reconstruct the resistivity images in EIDORS. The spatial resolution studies show that, the resistivity imaging conducted with the boundary data generated by MatVP2DEIT with 2048 elements, can reconstruct two circular inhomogeneities placed with a minimum distance (boundary to boundary) of 2 mm. It is also observed that, in MatVP2DEIT with 2048 elements, the boundary data generated for a phantom with a circular inhomogeneity of a diameter less than 7% of that of the phantom domain can produce resistivity images in EIDORS with a 1968 element mesh. Results also show that the MatVP2DEIT accurately generates the boundary data for neighbouring, opposite reference and trigonometric current patterns which are very suitable for resistivity reconstruction studies. MatVP2DEIT generated data are also found suitable for studying the effect of the different regularization methods on reconstruction process. Comparing the reconstructed image with an original geometry made in MatVP2DEIT, it would be easier to study the resistivity imaging procedures as well as the inverse solver performance. Using the proposed MatVP2DEIT software with modified domains, the cross sectional anatomy of a number of body parts can be simulated in PC and the impedance image reconstruction of human anatomy can be studied.

The geometry and the number of contacts of monodisperse sphere packs using X-ray tomography

The three-dimensional structure of very large samples of monodisperse bead packs is studied by means of X-Ray Computed Tomography. We retrieve the coordinatesofeach bead inthe pack and wecalculate the average coordination number by using the tomographic images to single out the neighbors in contact. The results are compared with the average coordination number obtained in Aste et al. (2005) by using a deconvolution technique. We show that the coordination number increases with the packing fraction, varying between 6.9 and 8.2 for packing fractions between 0.59 and 0.64. © 2005 Taylor & Francis Group.

Antibunching and blinking from a single colloidal CdSe quantum dot

We have investigated the optical properties of single CdSe/ZnS nanocrystals by conducting combinations of experiments on antibunching and photoluminescence intermittence under different experimental conditions. Based on photoluminescence in an antibunching experiment, we analyzed the emission lifetime of QDs by using stretched exponentials. The difference between the parameters obtained from average lifetimes and stretched exponents were analyzed by considering the effect of nonradiative emission. An Auger-assisted tunneling model was used to explain the power law exponents of off time distribution. The power law exponent under high excitation power was correlated with a higher Auger ionization rate. Using the parameters obtained from stretched exponential function and power law, the antibunching phenomena at different time and under different excitation intensity were analyzed.

Experimental study on K alpha X-ray emission from intense femtosecond laser-solid interactions

The characteristics of K alpha X-ray sources generated by p-polarized femtosecond laser-solid interactions are experimentally studied in the relativistic regime. By use of knife-edge image technique and a single-photon-counting X-ray CCD camera, we obtaine the source size, the spectrum and the conversion efficiency of the Ka X-ray sources. The experimental results show that the conversion efficiency of Ka photons reaches an optimum value of 7.08 x 10(-6)/sr at the laser intensity of 1.6 x 10(18) W/cm(2), which is different from the Reich's simulation results (Reich et al., 2000 Phys. Rev. Lett. 84 4846). We find that about 10% of laser energy is converted into the forward hot electrons at the laser intensity of 1.6 x 10(18) W/cm(2).

Impact of geometric variations on delivered dose in highly focused single vocal cord IMRT

Purpose. To investigate the robustness of single vocal cord intensity modulated radiation therapy (IMRT) treatment plans for set-up errors, respiration, and deformation. Material and methods. Four-dimensional computed tomography (4D-CT) scans of 10 early glottic carcinoma patients, previously treated with conventional techniques, were used in this simulation study. For each patient a pre-treatment 4D-CT was used for IMRT planning, generating a reference dose distribution. Prescribed PTV dose was 66 Gy. The impact of systematic set-up errors was simulated by applying shifts of ± 2 mm to the planning CT scans, followed by dose re-calculation with original beam segments, MUs, etc. Effects of respiration and deformation were determined utilizing extreme inhale and exhale CT scans, and repeat scans acquired after 22 Gy, 44 Gy, and 66 Gy, respectively. All doses were calculated using Monte Carlo dose simulations. Results. Considering all investigated geometrical perturbations, reductions in the clinical target volume (CTV) V95%, D98%, D2%, and generalized equivalent uniform dose (gEUD) were limited to 1.2 ± 2.2%, 2.4 ± 2.9%, 0.2 ± 1.8%, and 0.6 ± 1.1 Gy, respectively. The near minimum dose, D98%, was always higher than 89%, and gEUD always remained higher than 66 Gy. Planned contra-lateral (CL) vocal cord DMean, gEUD, and V40 Gy were 38.2 ± 6.0 Gy, 43.4 ± 5.6 Gy, and 42.7 ± 14.9%. With perturbations these values changed by -0.1 ± 4.3 Gy, 0.1 ± 4.0 Gy, and -1.0 ± 9.6%, respectively. Conclusions. On average, CTV dose reductions due to geometrical perturbations were very low, and sparing of the CL vocal cord was maintained. In a few observations (6 of 103 simulated situations), the near-minimum CTV-dose was around 90%, requiring attention in deciding on a future clinical protocol. 

Single vocal cord irradiation:a competitive treatment strategy in early glottic cancer

INTRODUCTION: The treatment of choice for early glottic cancer is still being debated; ultimately it relies on the functional outcome. This paper reports on a novel sparing 4D conformal technique for single vocal cord irradiation (SVCI).

MATERIAL AND METHODS: The records of 164 T1a patients with SCC of the vocal cord, irradiated in the Erasmus MC between 2000 and 2008, were analyzed for local control and overall survival. The quality of life was determined by EORTC H&N35 questionnaires. Also the VHI (voice handicap index), and the TSH (thyroid stimulating hormone) blood levels, were established. On-line image guided SVCI, using cone beam CT or stereotactic radiation therapy (SRT) techniques, were developed.

RESULTS: A LC rate at five-years of 93% and a VHI of 12.7 (0-63) was determined. It appeared feasible to irradiate one vocal cord within 1-2mm accuracy. This way sparing of the contralateral (CL) vocal cord and CL normal tissues, could be achieved.

CONCLUSIONS: Given the accuracy (1-2mm) and small volume disease (CTV limited to one vocal cord), for the use of stereotactic RT techniques SVCI with large fraction sizes is currently being investigated in clinic. It is argued that hypofractionated SVCI can be a competitive alternative to laser surgery.

Inter- and Intrafraction Target Motion in Highly Focused Single Vocal Cord Irradiation of T1a Larynx Cancer Patients

PURPOSE: The purpose of this study was to verify clinical target volume-planning target volume (CTV-PTV) margins in single vocal cord irradiation (SVCI) of T1a larynx tumors and characterize inter- and intrafraction target motion.

METHODS AND MATERIALS: For 42 patients, a single vocal cord was irradiated using intensity modulated radiation therapy at a total dose of 58.1 Gy (16 fractions × 3.63 Gy). A daily cone beam computed tomography (CBCT) scan was performed to online correct the setup of the thyroid cartilage after patient positioning with in-room lasers (interfraction motion correction). To monitor intrafraction motion, CBCT scans were also acquired just after patient repositioning and after dose delivery. A mixed online-offline setup correction protocol ("O2 protocol") was designed to compensate for both inter- and intrafraction motion.

RESULTS: Observed interfraction, systematic (Σ), and random (σ) setup errors in left-right (LR), craniocaudal (CC), and anteroposterior (AP) directions were 0.9, 2.0, and 1.1 mm and 1.0, 1.6, and 1.0 mm, respectively. After correction of these errors, the following intrafraction movements derived from the CBCT acquired after dose delivery were: Σ = 0.4, 1.3, and 0.7 mm, and σ = 0.8, 1.4, and 0.8 mm. More than half of the patients showed a systematic non-zero intrafraction shift in target position, (ie, the mean intrafraction displacement over the treatment fractions was statistically significantly different from zero; P<.05). With the applied CTV-PTV margins (for most patients 3, 5, and 3 mm in LR, CC, and AP directions, respectively), the minimum CTV dose, estimated from the target displacements observed in the last CBCT, was at least 94% of the prescribed dose for all patients and more than 98% for most patients (37 of 42). The proposed O2 protocol could effectively reduce the systematic intrafraction errors observed after dose delivery to almost zero (Σ = 0.1, 0.2, 0.2 mm).

CONCLUSIONS: With adequate image guidance and CTV-PTV margins in LR, CC, and AP directions of 3, 5, and 3 mm, respectively, excellent target coverage in SVCI could be ensured.

Improved fluorescent proteins for single-molecule research in molecular tracking and co-localization

Three promising variants of autofluorescent proteins have been analyzed photophysically for their proposed use in single-molecule microscopy studies in living cells to compare their superiority to other fluorescent proteins previously reported regarding the number of photons emitted. The first variant under investigation the F46L mutant of eYFP has a 10% greater photon emission rate and > 50% slower photobleaching rate on average than the standard eYFP fluorophore. The monomeric red fluorescent protein (mRFP) has a fivefold lower photon emission rate, likely due to the monomeric content, and also a tenfold faster photobleaching rate than the DsRed fluorescent protein. In contrast, the previously reported eqfp611 has a 50% lower emission rate yet photobleaches more than a factor 2 slowly. We conclude that the F46L YFP and the eqfp611 are superior new options for single molecule imaging and tracking studies in living cells. Studies were also performed on the effects of forced quenching of multiple fluorescent proteins in sub-micrometer regions that would show the effects of dimerization at low concentration levels of fluorescent proteins and also indicate corrections to stoichiometry patterns with fluorescent proteins previously in print. We also introduce properties at the single molecule level of new FRET pairs with combinations of fluorescent proteins and artificial fluorophores.

Focal cystic high-attenuation lesions: characterization in renal phantom by using photon-counting spectral CT--improved differentiation of lesion composition

To evaluate the capability of spectral computed tomography (CT) to improve the characterization of cystic high-attenuation lesions in a renal phantom and to test the hypothesis that spectral CT will improve the differentiation of cystic renal lesions with high protein content and those that have undergone hemorrhage or malignant contrast-enhancing transformation.

Importance of 3D-CT imaging in single-bullet cranioencephalic gunshot wounds

PURPOSE: The aim of this paper is to demonstrate that computed tomography (CT) and three-dimensional (3D) CT imaging techniques can be useful tools for evaluating gunshot wounds of the skull in forensic medicine. Three purposes can be achieved: (1) identifying and recognising the bullet entrance wound - and exit wound, if present; (2) recognising the bullet's intracranial course by studying damage to bone and brain tissue; (3) suggesting hypotheses as to the dynamics of the event. MATERIALS AND METHODS: Ten cadavers of people who died of a fatal head injury caused by a single gunshot were imaged with total-body CT prior to conventional autoptic examination. Three-dimensional-CT reconstructions were obtained with the volume-rendering technique, and data were analysed by two independent observers and compared with autopsy results. RESULTS: In our experience, CT analysis and volumetric reconstruction techniques allowed the identification of the bullet entrance and exit wounds and intracranial trajectory, as well as helping to formulate a hypothesis on the extracranial trajectory to corroborate circumstantial evidence. CONCLUSIONS: CT imaging techniques are excellent tools for addressing the most important questions of forensic medicine in the case of gunshot wounds of the skull, with results as good as (or sometimes better than) traditional autoptic methods.

PET-CT-guided interventions in the management of FDG-positive lesions in patients suffering from solid malignancies: initial experiences

Positron emission tomography-computed tomography (PET-CT) has gained widespread acceptance as a staging investigation in the diagnostic workup of malignant tumours and may be used to visualize metabolic changes before the evolution of morphological changes. To make histology of PET findings without distinctive structural changes available for treatment decisions, we developed a protocol for multimodal image-guided interventions using an integrated PET-CT machine. We report our first experience in 12 patients admitted for staging and restaging of breast cancer, non-small cell lung cancer, cervical cancer, soft tissue sarcoma, and osteosarcoma. Patients were repositioned according to the findings in PET-CT and intervention was planned based on a subsequent single-bed PET-CT acquisition of the region concerned. The needle was introduced under CT guidance in a step-by-step technique and correct needle position in the centre of the FDG avid lesion was assured by repetition of a single-bed PET-CT acquisition before sampling. The metabolically active part of lesions was accurately targeted in all patients and representative samples were obtained in 92%. No major adverse effects occurred. We conclude that PET-CT guidance for interventions is feasible and may be promising to optimize the diagnostic yield of CT-guided interventions and to make metabolically active lesions without morphological correlate accessible to percutaneous interventions.

Transconvolution and the virtual positron emission tomograph--a new method for cross calibration in quantitative PET∕CT imaging

PURPOSE Positron emission tomography (PET)∕computed tomography (CT) measurements on small lesions are impaired by the partial volume effect, which is intrinsically tied to the point spread function of the actual imaging system, including the reconstruction algorithms. The variability resulting from different point spread functions hinders the assessment of quantitative measurements in clinical routine and especially degrades comparability within multicenter trials. To improve quantitative comparability there is a need for methods to match different PET∕CT systems through elimination of this systemic variability. Consequently, a new method was developed and tested that transforms the image of an object as produced by one tomograph to another image of the same object as it would have been seen by a different tomograph. The proposed new method, termed Transconvolution, compensates for differing imaging properties of different tomographs and particularly aims at quantitative comparability of PET∕CT in the context of multicenter trials. METHODS To solve the problem of image normalization, the theory of Transconvolution was mathematically established together with new methods to handle point spread functions of different PET∕CT systems. Knowing the point spread functions of two different imaging systems allows determining a Transconvolution function to convert one image into the other. This function is calculated by convolving one point spread function with the inverse of the other point spread function which, when adhering to certain boundary conditions such as the use of linear acquisition and image reconstruction methods, is a numerically accessible operation. For reliable measurement of such point spread functions characterizing different PET∕CT systems, a dedicated solid-state phantom incorporating (68)Ge∕(68)Ga filled spheres was developed. To iteratively determine and represent such point spread functions, exponential density functions in combination with a Gaussian distribution were introduced. Furthermore, simulation of a virtual PET system provided a standard imaging system with clearly defined properties to which the real PET systems were to be matched. A Hann window served as the modulation transfer function for the virtual PET. The Hann's apodization properties suppressed high spatial frequencies above a certain critical frequency, thereby fulfilling the above-mentioned boundary conditions. The determined point spread functions were subsequently used by the novel Transconvolution algorithm to match different PET∕CT systems onto the virtual PET system. Finally, the theoretically elaborated Transconvolution method was validated transforming phantom images acquired on two different PET systems to nearly identical data sets, as they would be imaged by the virtual PET system. RESULTS The proposed Transconvolution method matched different PET∕CT-systems for an improved and reproducible determination of a normalized activity concentration. The highest difference in measured activity concentration between the two different PET systems of 18.2% was found in spheres of 2 ml volume. Transconvolution reduced this difference down to 1.6%. In addition to reestablishing comparability the new method with its parameterization of point spread functions allowed a full characterization of imaging properties of the examined tomographs. CONCLUSIONS By matching different tomographs to a virtual standardized imaging system, Transconvolution opens a new comprehensive method for cross calibration in quantitative PET imaging. The use of a virtual PET system restores comparability between data sets from different PET systems by exerting a common, reproducible, and defined partial volume effect.

Quantification of pleural effusion from single area measurements on CT

The objective of this study was to determine if area measurements of pleural fluid on computed tomography (CT) reflect the actual pleural fluid volume (PEvol) as measured at autopsy, to establish a formula to estimate the volume of pleural effusion (PEest), and to test the accuracy and observer reliability of PEest.132 human cadavers, with pleural effusion were divided into phase 1 (n = 32) and phase 2 (n = 100). In phase 1, PEvol was compared to area measurements on axial (axA), sagittal (sagA), and coronal (corA) CT images. Linear regression analysis was used to create a formula to calculate PEest. In phase 2, intra-class correlation (ICC) was used to assess inter-reader reliability and determine the agreement between PEest and PEvol. PEvol correlated to a higher degree to axA (r s mean = 0.738; p < 0.001) than to sagA (r s mean = 0.679, p < 0.001) and corA (r s mean = 0.709; p < 0.001). PEest can be established with the following formula: axA × 0.1 = PEest. Mean difference between PEest and PEvol was less than 40 mL (ICC = 0.837-0.874; p < 0.001). Inter-reader reliability was higher between two experienced readers (ICC = 0.984-0.987; p < 0.001) than between an inexperienced reader and both experienced readers (ICC = 0.660-0.698; p < 0.001). Pleural effusions may be quantified in a rapid, reliable, and reasonably accurate fashion using single area measurements on CT.

Computed Ultrasound Tomography in Echo mode (CUTE) of speed of sound for diagnosis and for aberration correction in pulse-echo sonography

Sound speed as a diagnostic marker for various diseases of human tissue has been of interest for a while. Up to now, mostly transmission ultrasound computed tomography (UCT) was able to detect spatially resolved sound speed, and its promise as a diagnostic tool has been demonstrated. However, UCT is limited to acoustically transparent samples such as the breast. We present a novel technique where spatially resolved detection of sound speed can be achieved using conventional pulse-echo equipment in reflection mode. For this purpose, pulse-echo images are acquired under various transmit beam directions and a two-dimensional map of the sound speed is reconstructed from the changing phase of local echoes using a direct reconstruction method. Phantom results demonstrate that a high spatial resolution (1 mm) and contrast (0.5 % of average sound speed) can be achieved suitable for diagnostic purposes. In comparison to previous reflection-mode based methods, CUTE works also in a situation with only diffuse echoes, and its direct reconstruction algorithm enables real-time application. This makes it suitable as an addition to conventional clinical ultrasound where it has the potential to benefit diagnosis in a multimodal approach. In addition, knowledge of the spatial distribution of sound speed allows full aberration correction and thus improved spatial resolution and contrast of conventional B-mode ultrasound. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.