Image Processing Challenges in the Creation of Spatiotemporal Gene Expression Atlases of Developing Embryos

To properly understand and model animal embryogenesis it is crucial to obtain detailed measurements, both in time and space, about their gene expression domains and cell dynamics. Such challenge has been confronted in recent years by a surge of atlases which integrate a statistically relevant number of different individuals to get robust, complete information about their spatiotemporal locations of gene patterns. This paper will discuss the fundamental image analysis strategies required to build such models and the most common problems found along the way. We also discuss the main challenges and future goals in the field.

Nonrigid Motion Compensation of Free Breathing Acquired Myocardial Perfusion Data

In this work, we present a novel method to compensate the movement in images acquired during free breathing using first-pass gadolinium enhanced, myocardial perfusion magnetic resonance imaging (MRI). First, we use independent component analysis (ICA) to identify the optimal number of independent components (ICs) that separate the breathing motion from the intensity change induced by the contrast agent. Then, synthetic images are created by recombining the ICs, but other then in previously published work (Milles et al. 2008), we omit the component related to motion, and therefore, the resulting reference image series is free of motion. Motion compensation is then achieved by using a multi-pass non-rigid image registration scheme. We tested our method on 15 distinct image series (5 patients) consisting of 58 images each and we validated our method by comparing manually tracked intensity profiles of the myocardial sections to automatically generated ones before and after registration. The average correlation to the manually obtained curves before registration 0:89 0:11 was increased to 0:98 0:02

Processing Pipeline for Digitalizing the Lineage Tree of Early Zebrafish Embryogenesis from Multiharmonic Imaging

The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and μm spatial resolution

Optimal Multiresolution 3D Level-Set Method for Liver Segmentation incorporating Local Curvature Constraints

Advanced liver surgery requires a precise pre-operative planning, where liver segmentation and remnant liver volume are key elements to avoid post-operative liver failure. In that context, level-set algorithms have achieved better results than others, especially with altered liver parenchyma or in cases with previous surgery. In order to improve functional liver parenchyma volume measurements, in this work we propose two strategies to enhance previous level-set algorithms: an optimal multi-resolution strategy with fine details correction and adaptive curvature, as well as an additional semiautomatic step imposing local curvature constraints. Results show more accurate segmentations, especially in elongated structures, detecting internal lesions and avoiding leakages to close structures

Image Processing Challenges in the Creation of Spatiotemporal Gene Expression Atlases of Developing Embryos

To properly understand and model animal embryogenesis it is crucial to obtain detailed measurements, both in time and space, about their gene expression domains and cell dynamics. Such challenge has been confronted in recent years by a surge of atlases which integrate a statistically relevant number of different individuals to get robust, complete information about their spatiotemporal locations of gene patterns. This paper will discuss the fundamental image analysis strategies required to build such models and the most common problems found along the way. We also discuss the main challenges and future goals in the field.

Characterization and Test of a Data Acquisition System for PET

A small Positron Emission Tomography demonstrator based on LYSO slabs and Silicon Photomultiplier matrices is under construction at the University and INFN of Pisa. In this paper we present the characterization results of the read-out electronics and of the detection system. Two SiPM matrices, composed by 8 × 8 SiPM pixels, 1.5 mm pitch, have been coupled one to one to a LYSO crystals array. Custom Front-End ASICs were used to read the 64 channels of each matrix. Data from each Front-End were multiplexed and sent to a DAQ board for the digital conversion; a motherboard collects the data and communicates with a host computer through a USB port. Specific tests were carried out on the system in order to assess its performance. Futhermore we have measured some of the most important parameters of the system for PET application.

Simulation Model for Sea Clutter in Airborne Radars

This paper presents the architecture and the methods used to dynamically simulate the sea backscatter of an airborne radar operating in a medium repetition frequency mode (MPRF). It offers a method of generating a sea backscatter signal which fulfills the intensity statistics of real clutter in time domain, spatial correlation and local Doppler spectrum of real data. Three antenna channels (sum, guard and difference) and their cross-correlation properties are simulated. The objective of this clutter generator is to serve as the signal source for the simulation of complex airborne pulsed radar signal processors

Ku band transmitarray lens for microwave applications

In this document a microstrip constrained lens device for Ku band, for microwave purpose, is presented. This paper offers an overview of artificial lens-type devices and the proposed transmitarray lens is thoroughly studied in terms of design and manufacturing, with architecture discussion and selection, along with the design, manufacturing and validation of all the forming components of the transmitarray (transmission circuits, radiating elements, etc.). Each element is properly characterized and assembled properly in the complete transmitarray prototype. Eventually, radiation pattern measurements as well as gain and directivity values, are provided to show the proper behaviour of the proposed transmitarray lens.

One dimensional exciton luminescence induced by extended defects in nonpolar (Al,Ga)N/GaN quantum wells

In this study, we present the optical properties of nonpolar GaN/(Al,Ga)N single quantum wells (QWs) grown on either a- or m-plane GaN templates for Al contents set below 15%. In order to reduce the density of extended defects, the templates have been processed using the epitaxial lateral overgrowth technique. As expected for polarization-free heterostructures, the larger the QW width for a given Al content, the narrower the QW emission line. In structures with an Al content set to 5 or 10%, we also observe emission from excitons bound to the intersection of I1-type basal plane stacking faults (BSFs) with the QW. Similarly to what is seen in bulk material, the temperature dependence of BSF-bound QW exciton luminescence reveals intra-BSF localization. A qualitative model evidences the large spatial extension of the wavefunction of these BSF-bound QW excitons, making them extremely sensitive to potential fluctuations located in and away from BSF. Finally, polarization-dependent measurements show a strong emission anisotropy for BSF-bound QW excitons, which is related to their one-dimensional character and that confirms that the intersection between a BSF and a GaN/(Al,Ga)N QW can be described as a quantum wire.

Room temperature absorption in laterally biased Quantum Infrared Detectors fabricated by MBE regrowth

In this paper, we show room temperature operation of a quantum well infrared photodetector (QWIP) using lateral conduction through ohmic contacts deposited at both sides of two n-doped quantum wells. To reduce the dark current due to direct conduction in the wells, we apply an electric field between the quantum wells and two pinch-off Schottky gates, in a fashion similar to a field effect device. Since the normal incidence absorption is strongly reduced in intersubband transitions in quantum wells, we first analyze the response of a detector based on quantum dots (QD). This QD device shows photocurrent signal up to 150 K when it is processed in conventional vertical detector. However, it is possible to observe room temperature signal when it is processed in a lateral structure. Finally, the room temperature photoresponse of the QWIP is demonstrated, and compared with theory. An excellent agreement between the estimated and measured characteristics of the device is found

PubDNA Finder in a Nutshell. Searching the Life Sciences Literature with Sequences of Nucleic Acids

Biomedical researchers and clinicians working with molecular technologies in routine clinical practice often need to review the available literature to gather information regarding specific sequences of nucleic acids. This includes, for instance, finding articles related to a concrete DNA sequence, or identifying empirically-validated primer/probe sequences to evaluate the presence of different micro-organisms. Unfortunately, these hard and time-consuming tasks often need to be manually performed by researchers themselves since no publicly available biomedical literature search engine, e.g. PubMed, PubMed Central (PMC), etc., provides the required search functionalities. In this article, we describe PubDNA Finder, a web service that enables users to perform advanced searches on PubMed Central-indexed full text articles with sequences of nucleic acids

Methods and Tools for Objective Assessment of Psychomotor Skills in Laparoscopic Surgery

Training and assessment paradigms for laparoscopic surgical skills are evolving from traditional mentor–trainee tutorship towards structured, more objective and safer programs. Accreditation of surgeons requires reaching a consensus on metrics and tasks used to assess surgeons’ psychomotor skills. Ongoing development of tracking systems and software solutions has allowed for the expansion of novel training and assessment means in laparoscopy. The current challenge is to adapt and include these systems within training programs, and to exploit their possibilities for evaluation purposes. This paper describes the state of the art in research on measuring and assessing psychomotor laparoscopic skills. It gives an overview on tracking systems as well as on metrics and advanced statistical and machine learning techniques employed for evaluation purposes. The later ones have a potential to be used as an aid in deciding on the surgical competence level, which is an important aspect when accreditation of the surgeons in particular, and patient safety in general, are considered. The prospective of these methods and tools make them complementary means for surgical assessment of motor skills, especially in the early stages of training. Successful examples such as the Fundamentals of Laparoscopic Surgery should help drive a paradigm change to structured curricula based on objective parameters. These may improve the accreditation of new surgeons, as well as optimize their already overloaded training schedules.

A New Multidisciplinary Home Care Telemedicine System to Monitor Stable Chronic Human Immunodeficiency Virus-Infected Patients: A Randomized Study

BACKGROUND: Antiretroviral therapy has changed the natural history of human immunodeficiency virus (HIV) infection in developed countries, where it has become a chronic disease. This clinical scenario requires a new approach to simplify follow-up appointments and facilitate access to healthcare professionals. METHODOLOGY: We developed a new internet-based home care model covering the entire management of chronic HIV-infected patients. This was called Virtual Hospital. We report the results of a prospective randomised study performed over two years, comparing standard care received by HIV-infected patients with Virtual Hospital care. HIV-infected patients with access to a computer and broadband were randomised to be monitored either through Virtual Hospital (Arm I) or through standard care at the day hospital (Arm II). After one year of follow up, patients switched their care to the other arm. Virtual Hospital offered four main services: Virtual Consultations, Telepharmacy, Virtual Library and Virtual Community. A technical and clinical evaluation of Virtual Hospital was carried out. FINDINGS: Of the 83 randomised patients, 42 were monitored during the first year through Virtual Hospital (Arm I) and 41 through standard care (Arm II). Baseline characteristics of patients were similar in the two arms. The level of technical satisfaction with the virtual system was high: 85% of patients considered that Virtual Hospital improved their access to clinical data and they felt comfortable with the videoconference system. Neither clinical parameters [level of CD4+ T lymphocytes, proportion of patients with an undetectable level of viral load (p = 0.21) and compliance levels >90% (p = 0.58)] nor the evaluation of quality of life or psychological questionnaires changed significantly between the two types of care. CONCLUSIONS: Virtual Hospital is a feasible and safe tool for the multidisciplinary home care of chronic HIV patients. Telemedicine should be considered as an appropriate support service for the management of chronic HIV infection. TRIAL REGISTRATION: Clinical-Trials.gov: NCT01117675.

Planar compact array with parasitic elements for MIMO systems

A compact planar array with parasitic elements is studied to be used in MIMO systems. Classical compact arrays suffer from high coupling which makes correlation and matching efficiency to be worse. A proper matching network improves these lacks although its bandwidth is low and may increase the antenna size. The proposed antenna makes use of parasitic elements to improve both correlation and efficiency. A specific software based on MoM has been developed to analyze radiating structures with several feed points. The array is optimized through a Genetic Algorithm to determine parasitic elements position in order to fulfill different figures of merit. The proposed design provides the required correlation and matching efficiency to have a good performance over a significant bandwidth.

A New Method to Reduce Truncation Errors in Partial Spherical Near-Field Measurements

A new and effective method for reduction of truncation errors in partial spherical near-field (SNF) measurements is proposed. The method is useful when measuring electrically large antennas, where the measurement time with the classical SNF technique is prohibitively long and an acquisition over the whole spherical surface is not practical. Therefore, to reduce the data acquisition time, partial sphere measurement is usually made, taking samples over a portion of the spherical surface in the direction of the main beam. But in this case, the radiation pattern is not known outside the measured angular sector as well as a truncation error is present in the calculated far-field pattern within this sector. The method is based on the Gerchberg-Papoulis algorithm used to extrapolate functions and it is able to extend the valid region of the calculated far-field pattern up to the whole forward hemisphere. To verify the effectiveness of the method, several examples are presented using both simulated and measured truncated near-field data.