Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Plantar flexion force induced by amplitude-modulated tendon vibration and associated soleus V/F-waves as an evidence of a centrally-mediated mechanism contributing to extra torque generation in humans

Background: High-frequency trains of electrical stimulation applied over the human muscles can generate forces higher than would be expected by direct activation of motor axons, as evidenced by an unexpected relation between the stimuli and the evoked contractions, originating what has been called “extra forces”. This phenomenon has been thought to reflect nonlinear input/output neural properties such as plateau potential activation in motoneurons. However, more recent evidence has indicated that extra forces generated during electrical stimulation are mediated primarily, if not exclusively, by an intrinsic muscle property, and not from a central mechanism as previously thought. Given the inherent differences between electrical and vibratory stimuli, this study aimed to investigate: (a) whether the generation of vibration-induced muscle forces results in an unexpected relation between the stimuli and the evoked contractions (i.e. extra forces generation) and (b) whether these extra forces are accompanied by signs of a centrally-mediated mechanism or whether intrinsic muscle properties are the redominant mechanisms. Methods: Six subjects had their Achilles tendon stimulated by 100 Hz vibratory stimuli that linearly increased in amplitude (with a peak-to-peak displacement varying from 0 to 5 mm) for 10 seconds and then linearly decreased to zero for the next 10 seconds. As a measure of motoneuron excitability taken at different times during the vibratory stimulation, short-latency compound muscle action potentials (V/F-waves) were recorded in the soleus muscle in response to supramaximal nerve stimulation. Results: Plantar flexion torque and soleus V/F-wave amplitudes were increased in the second half of the stimulation in comparison with the first half. Conclusion: The present findings provide evidence that vibratory stimuli may trigger a centrally-mediated mechanism that contributes to the generation of extra torques. The vibration-induced increased motoneuron excitability (leading to increased torque generation) presumably activates spinal motoneurons following the size principle, which is a desirable feature for stimulation paradigms involved in rehabilitation programs and exercise training.

Femtosecond laser processing of glassy and polymeric matrices containing metals and semiconductor nanostructures

Tailoring properties of materials by femtosecond laser processing has been proposed in the last decade as a powerful approach for technological applications, ranging from optics to biology. Although most of the research output in this field is related to femtosecond laser processing of single either organic or inorganic materials, more recently a similar approach has been proposed to develop advanced hybrid nanomaterials. Here, we report results on the use of femtosecond lasers to process hybrid nanomaterials, composed of polymeric and glassy matrices containing metal or semiconductor nanostructures. We present results on the use of femtosecond pulses to induce Cu and Ag nanoparticles in the bulk of borate and borosilicate glasses, which can be applied for a new generation of waveguides. We also report on 3D polymeric structures, fabricated by two-photon polymerization, containing Au and ZnO nanostructures, with intense two-photon fluorescent properties. The approach based on femtosecond laser processing to fabricate hybrid materials containing metal or semiconductor nanostructures is promising to be exploited for optical sensors and photonics devices.

Hypoxia and the cardiovascular response to dynamic knee-extensor exercise

[EN] Hypoxia affects O2 transport and aerobic exercise capacity. In two previous studies, conflicting results have been reported regarding whether O2 delivery to the muscle is increased with hypoxia or whether there is a more efficient O2 extraction to allow for compensation of the decreased O2 availability at submaximal and maximal exercise. To reconcile this discrepancy, we measured limb blood flow (LBF), cardiac output, and O2 uptake during two-legged knee-extensor exercise in eight healthy young men. They completed studies at rest, at two submaximal workloads, and at peak effort under normoxia (inspired O2 fraction 0.21) and two levels of hypoxia (inspired O2 fractions 0.16 and 0.11). During submaximal exercise, LBF increased in hypoxia and compensated for the decrement in arterial O2 content. At peak effort, however, our subjects did not achieve a higher cardiac output or LBF. Thus O2 delivery was not maintained and peak power output and leg O2 uptake were reduced proportionately. These data are consistent then with the findings of an increased LBF to compensate for hypoxemia at submaximal exercise, but no such increase occurs at peak effort despite substantial cardiac capacity for an elevation in LBF.

Producción e impacto de las instituciones españolas de investigación en Arts and Humanities Citation Index (2003-2012)

[EN]This essay reviews both the scholarly output and impact factor of Spanish research institutions in the Arts & Humanities Citation Index (A&HCI) database, managed by the Thomson-Reuters Web of Science. Based on a bibliometric analysis of a range of variables it has been possible to identify those institutions with the best performance indicators, the journals publishing the most articles, the most productive areas of research, and other relevant data on publishing patterns in the Humanities. The study reveals that the most productive Spanish institutions in the Humanities are the same as those that lead the performance figures in other areas; it also highlights the outstanding production of the Spanish National Research Council (CSIC).

Management and routing algorithms for ad-hoc and sensor networks

Large scale wireless adhoc networks of computers, sensors, PDAs etc. (i.e. nodes) are revolutionizing connectivity and leading to a paradigm shift from centralized systems to highly distributed and dynamic environments. An example of adhoc networks are sensor networks, which are usually composed by small units able to sense and transmit to a sink elementary data which are successively processed by an external machine. Recent improvements in the memory and computational power of sensors, together with the reduction of energy consumptions, are rapidly changing the potential of such systems, moving the attention towards datacentric sensor networks. A plethora of routing and data management algorithms have been proposed for the network path discovery ranging from broadcasting/floodingbased approaches to those using global positioning systems (GPS). We studied WGrid, a novel decentralized infrastructure that organizes wireless devices in an adhoc manner, where each node has one or more virtual coordinates through which both message routing and data management occur without reliance on either flooding/broadcasting operations or GPS. The resulting adhoc network does not suffer from the deadend problem, which happens in geographicbased routing when a node is unable to locate a neighbor closer to the destination than itself. WGrid allow multidimensional data management capability since nodes' virtual coordinates can act as a distributed database without needing neither special implementation or reorganization. Any kind of data (both single and multidimensional) can be distributed, stored and managed. We will show how a location service can be easily implemented so that any search is reduced to a simple query, like for any other data type. WGrid has then been extended by adopting a replication methodology. We called the resulting algorithm WRGrid. Just like WGrid, WRGrid acts as a distributed database without needing neither special implementation nor reorganization and any kind of data can be distributed, stored and managed. We have evaluated the benefits of replication on data management, finding out, from experimental results, that it can halve the average number of hops in the network. The direct consequence of this fact are a significant improvement on energy consumption and a workload balancing among sensors (number of messages routed by each node). Finally, thanks to the replications, whose number can be arbitrarily chosen, the resulting sensor network can face sensors disconnections/connections, due to failures of sensors, without data loss. Another extension to {WGrid} is {W*Grid} which extends it by strongly improving network recovery performance from link and/or device failures that may happen due to crashes or battery exhaustion of devices or to temporary obstacles. W*Grid guarantees, by construction, at least two disjoint paths between each couple of nodes. This implies that the recovery in W*Grid occurs without broadcasting transmissions and guaranteeing robustness while drastically reducing the energy consumption. An extensive number of simulations shows the efficiency, robustness and traffic road of resulting networks under several scenarios of device density and of number of coordinates. Performance analysis have been compared to existent algorithms in order to validate the results.

Sicurezza di rete, analisi del traffico e monitoraggio.

Il lavoro è stato suddiviso in tre macro-aree. Una prima riguardante un'analisi teorica di come funzionano le intrusioni, di quali software vengono utilizzati per compierle, e di come proteggersi (usando i dispositivi che in termine generico si possono riconoscere come i firewall). Una seconda macro-area che analizza un'intrusione avvenuta dall'esterno verso dei server sensibili di una rete LAN. Questa analisi viene condotta sui file catturati dalle due interfacce di rete configurate in modalità promiscua su una sonda presente nella LAN. Le interfacce sono due per potersi interfacciare a due segmenti di LAN aventi due maschere di sotto-rete differenti. L'attacco viene analizzato mediante vari software. Si può infatti definire una terza parte del lavoro, la parte dove vengono analizzati i file catturati dalle due interfacce con i software che prima si occupano di analizzare i dati di contenuto completo, come Wireshark, poi dei software che si occupano di analizzare i dati di sessione che sono stati trattati con Argus, e infine i dati di tipo statistico che sono stati trattati con Ntop. Il penultimo capitolo, quello prima delle conclusioni, invece tratta l'installazione di Nagios, e la sua configurazione per il monitoraggio attraverso plugin dello spazio di disco rimanente su una macchina agent remota, e sui servizi MySql e DNS. Ovviamente Nagios può essere configurato per monitorare ogni tipo di servizio offerto sulla rete.

Development of muliplexed analytical methods based on bioluminescent whole-cell biosensors

The subject of this Ph.D. research thesis is the development and application of multiplexed analytical methods based on bioluminescent whole-cell biosensors. One of the main goals of analytical chemistry is multianalyte testing in which two or more analytes are measured simultaneously in a single assay. The advantages of multianalyte testing are work simplification, high throughput, and reduction in the overall cost per test. The availability of multiplexed portable analytical systems is of particular interest for on-field analysis of clinical, environmental or food samples as well as for the drug discovery process. To allow highly sensitive and selective analysis, these devices should combine biospecific molecular recognition with ultrasensitive detection systems. To address the current need for rapid, highly sensitive and inexpensive devices for obtaining more data from each sample,genetically engineered whole-cell biosensors as biospecific recognition element were combined with ultrasensitive bioluminescence detection techniques. Genetically engineered cell-based sensing systems were obtained by introducing into bacterial, yeast or mammalian cells a vector expressing a reporter protein whose expression is controlled by regulatory proteins and promoter sequences. The regulatory protein is able to recognize the presence of the analyte (e.g., compounds with hormone-like activity, heavy metals…) and to consequently activate the expression of the reporter protein that can be readily measured and directly related to the analyte bioavailable concentration in the sample. Bioluminescence represents the ideal detection principle for miniaturized analytical devices and multiplexed assays thanks to high detectability in small sample volumes allowing an accurate signal localization and quantification. In the first chapter of this dissertation is discussed the obtainment of improved bioluminescent proteins emitting at different wavelenghts, in term of increased thermostability, enhanced emission decay kinetic and spectral resolution. The second chapter is mainly focused on the use of these proteins in the development of whole-cell based assay with improved analytical performance. In particular since the main drawback of whole-cell biosensors is the high variability of their analyte specific response mainly caused by variations in cell viability due to aspecific effects of the sample’s matrix, an additional bioluminescent reporter has been introduced to correct the analytical response thus increasing the robustness of the bioassays. The feasibility of using a combination of two or more bioluminescent proteins for obtaining biosensors with internal signal correction or for the simultaneous detection of multiple analytes has been demonstrated by developing a dual reporter yeast based biosensor for androgenic activity measurement and a triple reporter mammalian cell-based biosensor for the simultaneous monitoring of two CYP450 enzymes activation, involved in cholesterol degradation, with the use of two spectrally resolved intracellular luciferases and a secreted luciferase as a control for cells viability. In the third chapter is presented the development of a portable multianalyte detection system. In order to develop a portable system that can be used also outside the laboratory environment even by non skilled personnel, cells have been immobilized into a new biocompatible and transparent polymeric matrix within a modified clear bottom black 384 -well microtiter plate to obtain a bioluminescent cell array. The cell array was placed in contact with a portable charge-coupled device (CCD) light sensor able to localize and quantify the luminescent signal produced by different bioluminescent whole-cell biosensors. This multiplexed biosensing platform containing whole-cell biosensors was successfully used to measure the overall toxicity of a given sample as well as to obtain dose response curves for heavy metals and to detect hormonal activity in clinical samples (PCT/IB2010/050625: “Portable device based on immobilized cells for the detection of analytes.” Michelini E, Roda A, Dolci LS, Mezzanotte L, Cevenini L , 2010). At the end of the dissertation some future development steps are also discussed in order to develop a point of care (POCT) device that combine portability, minimum sample pre-treatment and highly sensitive multiplexed assays in a short assay time. In this POCT perspective, field-flow fractionation (FFF) techniques, in particular gravitational variant (GrFFF) that exploit the earth gravitational field to structure the separation, have been investigated for cells fractionation, characterization and isolation. Thanks to the simplicity of its equipment, amenable to miniaturization, the GrFFF techniques appears to be particularly suited for its implementation in POCT devices and may be used as pre-analytical integrated module to be applied directly to drive target analytes of raw samples to the modules where biospecifc recognition reactions based on ultrasensitive bioluminescence detection occurs, providing an increase in overall analytical output.

Dynamic power management: from portable devices to high performance computing

Electronic applications are nowadays converging under the umbrella of the cloud computing vision. The future ecosystem of information and communication technology is going to integrate clouds of portable clients and embedded devices exchanging information, through the internet layer, with processing clusters of servers, data-centers and high performance computing systems. Even thus the whole society is waiting to embrace this revolution, there is a backside of the story. Portable devices require battery to work far from the power plugs and their storage capacity does not scale as the increasing power requirement does. At the other end processing clusters, such as data-centers and server farms, are build upon the integration of thousands multiprocessors. For each of them during the last decade the technology scaling has produced a dramatic increase in power density with significant spatial and temporal variability. This leads to power and temperature hot-spots, which may cause non-uniform ageing and accelerated chip failure. Nonetheless all the heat removed from the silicon translates in high cooling costs. Moreover trend in ICT carbon footprint shows that run-time power consumption of the all spectrum of devices accounts for a significant slice of entire world carbon emissions. This thesis work embrace the full ICT ecosystem and dynamic power consumption concerns by describing a set of new and promising system levels resource management techniques to reduce the power consumption and related issues for two corner cases: Mobile Devices and High Performance Computing.

Role of nitric oxide and endocannabinoids in synaptic plasticity in the perirhinal cortex and in visual recognition memory

Introduction and aims of the research Nitric oxide (NO) and endocannabinoids (eCBs) are major retrograde messengers, involved in synaptic plasticity (long-term potentiation, LTP, and long-term depression, LTD) in many brain areas (including hippocampus and neocortex), as well as in learning and memory processes. NO is synthesized by NO synthase (NOS) in response to increased cytosolic Ca2+ and mainly exerts its functions through soluble guanylate cyclase (sGC) and cGMP production. The main target of cGMP is the cGMP-dependent protein kinase (PKG). Activity-dependent release of eCBs in the CNS leads to the activation of the Gαi/o-coupled cannabinoid receptor 1 (CB1) at both glutamatergic and inhibitory synapses. The perirhinal cortex (Prh) is a multimodal associative cortex of the temporal lobe, critically involved in visual recognition memory. LTD is proposed to be the cellular correlate underlying this form of memory. Cholinergic neurotransmission has been shown to play a critical role in both visual recognition memory and LTD in Prh. Moreover, visual recognition memory is one of the main cognitive functions impaired in the early stages of Alzheimer’s disease. The main aim of my research was to investigate the role of NO and ECBs in synaptic plasticity in rat Prh and in visual recognition memory. Part of this research was dedicated to the study of synaptic transmission and plasticity in a murine model (Tg2576) of Alzheimer’s disease. Methods Field potential recordings. Extracellular field potential recordings were carried out in horizontal Prh slices from Sprague-Dawley or Dark Agouti juvenile (p21-35) rats. LTD was induced with a single train of 3000 pulses delivered at 5 Hz (10 min), or via bath application of carbachol (Cch; 50 μM) for 10 min. LTP was induced by theta-burst stimulation (TBS). In addition, input/output curves and 5Hz-LTD were carried out in Prh slices from 3 month-old Tg2576 mice and littermate controls. Behavioural experiments. The spontaneous novel object exploration task was performed in intra-Prh bilaterally cannulated adult Dark Agouti rats. Drugs or vehicle (saline) were directly infused into the Prh 15 min before training to verify the role of nNOS and CB1 in visual recognition memory acquisition. Object recognition memory was tested at 20 min and 24h after the end of the training phase. Results Electrophysiological experiments in Prh slices from juvenile rats showed that 5Hz-LTD is due to the activation of the NOS/sGC/PKG pathway, whereas Cch-LTD relies on NOS/sGC but not PKG activation. By contrast, NO does not appear to be involved in LTP in this preparation. Furthermore, I found that eCBs are involved in LTP induction, but not in basal synaptic transmission, 5Hz-LTD and Cch-LTD. Behavioural experiments demonstrated that the blockade of nNOS impairs rat visual recognition memory tested at 24 hours, but not at 20 min; however, the blockade of CB1 did not affect visual recognition memory acquisition tested at both time points specified. In three month-old Tg2576 mice, deficits in basal synaptic transmission and 5Hz-LTD were observed compared to littermate controls. Conclusions The results obtained in Prh slices from juvenile rats indicate that NO and CB1 play a role in the induction of LTD and LTP, respectively. These results are confirmed by the observation that nNOS, but not CB1, is involved in visual recognition memory acquisition. The preliminary results obtained in the murine model of Alzheimer’s disease indicate that deficits in synaptic transmission and plasticity occur very early in Prh; further investigations are required to characterize the molecular mechanisms underlying these deficits.

Wheat and low-input agriculture: agronomic, nutritional and nutraceutical implications

Recently, the increasing interest in organic food products and environmental friendly practices has emphasized the importance of selecting crop varieties suitable for the low-input systems. Additionally, in recent years the relationship between diet and human health has gained much attention among consumers, favoring the investigations on food nutraceutical properties. Among cereals, wheat plays an important role in human nutrition around the world and contributes to the daily intake of essential nutrients such as starch and protein. Moreover, whole grain contains several bioactive compounds that confer to wheat-derived products unique nutraceutical properties (dietary fibre, antioxidants). The present research provided interesting insights for the selection of wheat genotypes suitable for low-input systems and the development of specific breeding programs dedicated to organic farming. The investigation involved 5 old not dwarf genotypes (Andriolo, Frassineto, Gentil rosso, Inallettabile, Verna) and 1 modern dwarf variety (Palesio), grown under biodynamic management, over two consecutive growing seasons (2009/2010, 2010/2011). Results evidenced that under low-input farming some investigated old wheat genotypes (Frassineto, Inallettabile) were comparable to the modern cultivar in terms of whole agronomic performance. As regards the nutritional and nutraceutical properties, some old genotypes (Andriolo, Gentil rosso, Verna) emerged for their relevant content of several investigated phytochemicals (such as insoluble dietary fibre, polyphenols, flavonoids, in vitro antioxidant activity) and nutrients (protein, lipid, minerals). Despite of the low technological features, the six wheat varieties grown under low-input management may efficiently provide raw material for the preparation of traditionally processed bread with valuable sensory and nutritional properties. Results highlighted that old wheat varieties have peculiar phytochemical composition and may be a valuable source of nutraceutical compounds. Some of the genetic material involved in the present study may be used in breeding programs aimed at selecting varieties suitable for low-input farming and rich in health-promoting compounds.

CT perfusion image processing: analysis of liver tumors

Perfusion CT imaging of the liver has potential to improve evaluation of tumour angiogenesis. Quantitative parameters can be obtained applying mathematical models to Time Attenuation Curve (TAC). However, there are still some difficulties for an accurate quantification of perfusion parameters due, for example, to algorithms employed, to mathematical model, to patient’s weight and cardiac output and to the acquisition system. In this thesis, new parameters and alternative methodologies about liver perfusion CT are presented in order to investigate the cause of variability of this technique. Firstly analysis were made to assess the variability related to the mathematical model used to compute arterial Blood Flow (BFa) values. Results were obtained implementing algorithms based on “ maximum slope method” and “Dual input one compartment model” . Statistical analysis on simulated data demonstrated that the two methods are not interchangeable. Anyway slope method is always applicable in clinical context. Then variability related to TAC processing in the application of slope method is analyzed. Results compared with manual selection allow to identify the best automatic algorithm to compute BFa. The consistency of a Standardized Perfusion Index (SPV) was evaluated and a simplified calibration procedure was proposed. At the end the quantitative value of perfusion map was analyzed. ROI approach and map approach provide related values of BFa and this means that pixel by pixel algorithm give reliable quantitative results. Also in pixel by pixel approach slope method give better results. In conclusion the development of new automatic algorithms for a consistent computation of BFa and the analysis and definition of simplified technique to compute SPV parameter, represent an improvement in the field of liver perfusion CT analysis.

Pervasive Sensing in Future Networks

Pervasive Sensing is a recent research trend that aims at providing widespread computing and sensing capabilities to enable the creation of smart environments that can sense, process, and act by considering input coming from both people and devices. The capabilities necessary for Pervasive Sensing are nowadays available on a plethora of devices, from embedded devices to PCs and smartphones. The wide availability of new devices and the large amount of data they can access enable a wide range of novel services in different areas, spanning from simple data collection systems to socially-aware collaborative filtering. However, the strong heterogeneity and unreliability of devices and sensors poses significant challenges. So far, existing works on Pervasive Sensing have focused only on limited portions of the whole stack of available devices and data that they can use, to propose and develop mainly vertical solutions. The push from academia and industry for this kind of services shows that time is mature for a more general support framework for Pervasive Sensing solutions able to enhance frail architectures, promote a well balanced usage of resources on different devices, and enable the widest possible access to sensed data, while ensuring a minimal energy consumption on battery-operated devices. This thesis focuses on pervasive sensing systems to extract design guidelines as foundation of a comprehensive reference model for multi-tier Pervasive Sensing applications. The validity of the proposed model is tested in five different scenarios that present peculiar and different requirements, and different hardware and sensors. The ease of mapping from the proposed logical model to the real implementations and the positive performance result campaigns prove the quality of the proposed approach and offer a reliable reference model, together with a direction for the design and deployment of future Pervasive Sensing applications.

Reverse Engineering tools: development and experimentation of innovative methods for physical and geometrical data integration and post-processing

In recent years, the use of Reverse Engineering systems has got a considerable interest for a wide number of applications. Therefore, many research activities are focused on accuracy and precision of the acquired data and post processing phase improvements. In this context, this PhD Thesis deals with the definition of two novel methods for data post processing and data fusion between physical and geometrical information. In particular a technique has been defined for error definition in 3D points’ coordinates acquired by an optical triangulation laser scanner, with the aim to identify adequate correction arrays to apply under different acquisition parameters and operative conditions. Systematic error in data acquired is thus compensated, in order to increase accuracy value. Moreover, the definition of a 3D thermogram is examined. Object geometrical information and its thermal properties, coming from a thermographic inspection, are combined in order to have a temperature value for each recognizable point. Data acquired by an optical triangulation laser scanner are also used to normalize temperature values and make thermal data independent from thermal-camera point of view.

Controllo ottico automatizzato di circuiti fotonici integrati: Progettazione, realizzazione e valutazione

In this report a new automated optical test for next generation of photonic integrated circuits (PICs) is provided by the test-bed design and assessment. After a briefly analysis of critical problems of actual optical tests, the main test features are defined: automation and flexibility, relaxed alignment procedure, speed up of entire test and data reliability. After studying varied solutions, the test-bed components are defined to be lens array, photo-detector array, and software controller. Each device is studied and calibrated, the spatial resolution, and reliability against interference at the photo-detector array are studied. The software is programmed in order to manage both PIC input, and photo-detector array output as well as data analysis. The test is validated by analysing state-of-art 16 ports PIC: the waveguide location, current versus power, and time-spatial power distribution are measured as well as the optical continuity of an entire path of PIC. Complexity, alignment tolerance, time of measurement are also discussed.