Automatic Generation of Analog Hardware Description Language (AHDL) Code from Cell Culture Images

This paper presents a computer tool for automatic analysis of cell culture images. The program allows the extraction of relevant information from biological images for pre and post system analysis. In particular, this tool is being used for electrical characterization of electrode-solution-cell systems in which bio-impedance is the main parameter to be known. The correct modeling of this kind of systems enables both electronic system characterization for circuit design specifications and data decoding from measurements. The developed program can be used in cell culture image processing for geographic information extraction and sensor sizing, generating cell count and Analog Hardware Description Language (AHDL) equivalent circuits useful for whole system electrical simulations.Ministerio de Ciencia e Innovación TEC2007-6807

ELECTRICAL IMPEDANCE SPECTROSCOPY AND TOMOGRAPHY: APPLICATIONS ON PLANT CHARACTERIZATION

World population will grow to 9.6 billion by 2050 and global food production needs to be increased by 70% to feed the increased population. Hence, better insight into plant physiology can impart better quality in fruits, vegetables, and crops, and eventually contribute to food security and sustainability. In this direction, this thesis utilizes electrical sensing technology, electrical impedance spectroscopy (EIS) and tomography (EIT), for better understanding and characterization of a number of physiological and structural aspects of the plant. It investigates the dehydration process in onion and ripening process in avocado by EIS, and perform 3D structural imaging of root by EIT. The thesis tracks and analyzes the dynamics of natural dehydration in onion and also assesses its moisture content using EIS. The work develops an equivalent electrical circuit that simulates the response of the onion undergoing natural drying for a duration of three weeks. The developed electrical model shows better congruence with the experimental data when compared to other conventional models for plant tissue with a mean absolute error of 0.42% and root mean squared error of 0.55%. Moreover, the study attempts to find a correlation between the measured impedance data and the actual moisture content of the onions under test (measured by weighing) and develops a simple mathematical model. This model provides an alternative tool for assessing the moisture content of onion nondestructively. The model shows excellent correlation with the ground truth data with a deterministic coefficient of 0.977, root mean square error of 0.030 and sum of squared error of 0.013. Next, the thesis presents an approach that will integrate EIS and machine learning technique that allows us to monitor ripening degree of avocado. It is evident from this study that the impedance absolute magnitude of avocado gradually decreases as the ripening stages (firm, breaking, ripe and overripe) proceed at a particular frequency. In addition, Principal component analysis shows that impedance magnitude (two principal components combined explain 99.95% variation) has better discrimination capabilities for ripening degrees compared to impedance phase angle, impedance real part, and impedance imaginary part. The developed classifier utilizes two principal component features over 100 EIS responses and demonstrate classification over firm, breaking, ripe and overripe stages with an accuracy of 90%, precision of 93%, recall of 90%, f1-score of 90% and an area under ROC curve (AUC) of 88%. Later on, this thesis presents the design, development, and implementation of a low-cost EIT system and analyzes root imaging as well. The designed prototype consists of an electrode array system, an Impedance analyzer board, 2 multiplexer units, and an Arduino. The Eval-Ad5933-EBZ is used for measuring the bio-impedance of the root, and two CD74HC4067 Multiplexers are used as electrode switching unit. Measuring and data collecting are controlled by the Arduino, and data storage is performed in a PC. By performing Finite Element Analysis and solving forward and inverse problem, the tomographic image of the root is reconstructed. The system is able to localize and build 2D and 3D tomographic image of root in a liquid medium. This proposed low-cost and easy-to-access system enables the users to capture the repetitive, noninvasive and non-destructive image of a plant root. Furthermore, the study proposes a simple mathematical model, based on ridge regression, which can predict root biomass from EIT data nondestructively with an accuracy of more than 93%. Thus, this study offers plant scientists and crop consultants the ability to better understand plant physiology nondestructively and noninvasively

Towards Bio-impedance Based Labs: A Review

In this article, some of the main contributions to BI (Bio-Impedance) parameter-based systems for medical, biological and industrial fields, oriented to develop micro laboratory systems are summarized. These small systems are enabled by the development of new measurement techniques and systems (labs), based on the impedance as biomarker. The electrical properties of the life mater allow the straightforward, low cost and usually non-invasive measurement methods to define its status or value, with the possibility to know its time evolution. This work proposes a review of bio-impedance based methods being employed to develop new LoC (Lab-on-a-Chips) systems, and some open problems identified as main research challenges, such as, the accuracy limits of measurements techniques, the role of the microelectrode-biological impedance modeling in measurements and system portability specifications demanded for many applications.Spanish founded Project: TEC 2013-46242-C3-1-P: Integrated Microsystem for Cell Culture AssaysFEDE

ELECTRICAL IMPEDANCE SPECTROSCOPY AND TOMOGRAPHY: APPLICATIONS ON PLANT CHARACTERIZATION

World population will grow to 9.6 billion by 2050 and global food production needs to be increased by 70% to feed the increased population. Hence, better insight into plant physiology can impart better quality in fruits, vegetables, and crops, and eventually contribute to food security and sustainability. In this direction, this thesis utilizes electrical sensing technology, electrical impedance spectroscopy (EIS) and tomography (EIT), for better understanding and characterization of a number of physiological and structural aspects of the plant. It investigates the dehydration process in onion and ripening process in avocado by EIS, and perform 3D structural imaging of root by EIT. The thesis tracks and analyzes the dynamics of natural dehydration in onion and also assesses its moisture content using EIS. The work develops an equivalent electrical circuit that simulates the response of the onion undergoing natural drying for a duration of three weeks. The developed electrical model shows better congruence with the experimental data when compared to other conventional models for plant tissue with a mean absolute error of 0.42% and root mean squared error of 0.55%. Moreover, the study attempts to find a correlation between the measured impedance data and the actual moisture content of the onions under test (measured by weighing) and develops a simple mathematical model. This model provides an alternative tool for assessing the moisture content of onion nondestructively. The model shows excellent correlation with the ground truth data with a deterministic coefficient of 0.977, root mean square error of 0.030 and sum of squared error of 0.013. Next, the thesis presents an approach that will integrate EIS and machine learning technique that allows us to monitor ripening degree of avocado. It is evident from this study that the impedance absolute magnitude of avocado gradually decreases as the ripening stages (firm, breaking, ripe and overripe) proceed at a particular frequency. In addition, Principal component analysis shows that impedance magnitude (two principal components combined explain 99.95% variation) has better discrimination capabilities for ripening degrees compared to impedance phase angle, impedance real part, and impedance imaginary part. The developed classifier utilizes two principal component features over 100 EIS responses and demonstrate classification over firm, breaking, ripe and overripe stages with an accuracy of 90%, precision of 93%, recall of 90%, f1-score of 90% and an area under ROC curve (AUC) of 88%. Later on, this thesis presents the design, development, and implementation of a low-cost EIT system and analyzes root imaging as well. The designed prototype consists of an electrode array system, an Impedance analyzer board, 2 multiplexer units, and an Arduino. The Eval-Ad5933-EBZ is used for measuring the bio-impedance of the root, and two CD74HC4067 Multiplexers are used as electrode switching unit. Measuring and data collecting are controlled by the Arduino, and data storage is performed in a PC. By performing Finite Element Analysis and solving forward and inverse problem, the tomographic image of the root is reconstructed. The system is able to localize and build 2D and 3D tomographic image of root in a liquid medium. This proposed low-cost and easy-to-access system enables the users to capture the repetitive, noninvasive and non-destructive image of a plant root. Furthermore, the study proposes a simple mathematical model, based on ridge regression, which can predict root biomass from EIT data nondestructively with an accuracy of more than 93%. Thus, this study offers plant scientists and crop consultants the ability to better understand plant physiology nondestructively and noninvasively

Generation of HDL models for bio-impedance sensor simulation based on microelectrodes

This paper presents a computer tool for automatic analysis of cell culture images. The program allows the extraction of relevant information from biological images for pre and post system analysis. In particular, this tool is being used for electrical characterization of electrode-solution-cell systems in which bio-impedance is the main parameter to be known. The correct modeling of this kind of systems enables both electronic system characterization for circuit design specifications and data decoding from measurements. The developed program allows cell culture image processing for geographic information extraction and sensor sizing, generating cell count and Analog Hardware Description Language (AHDL) equivalent circuits useful for whole system simulations

Remote Sensing of Cell-Culture Assays

This chapter describes a full system developed to perform the remote sensing of cell-culture experiments from any access point with internet connection. The proposed system allows the real-time monitoring of cell assays thanks to bioimpedance measurement circuits developed to count the number of cell present in a culture. Cell-culture characterization is performed through the measurement of the increasing bioimpedance parameter over time. The circuit implementation is based on the oscillation-based test (OBT) methodology. Bioimpedance of cell cultures is measured in terms of the oscillation parameters (frequency, amplitude, phase, etc.) and used as empirical markers to carry out an appropriate interpretation in terms of cell size identification, cell counting, cell growth, growth rhythm, etc. The device is capable of managing the whole sensing task and performs wireless communication through a Bluetooth module. Data are interpreted and displayed on a computer or a mobile phone through a web application. The system has its practical application in drug development processes, offering a label-free, high-throughput, and high-content screening method for cellular research, avoiding the classical end-point techniques and a significant workload and cost material reduction

PREGLED TEHNIKA SEIZMIČKE REFRAKCIJE I TOMOGRAFIJE ELEKTRIČNOM OTPORNOŠĆU U ISTRAŽIVANJU PODZEMLJA

Geophysical subsurface investigations use the principles of physics to unravel intrinsic Earth’s subsurface features and nature of the underlying geology. Over the past two decades, the use of Seismic Refraction Tomography (SRT) and Electrical Resistivity Tomography (ERT) for subsurface investigations has greatly improved the quality of acquired data for two- and three-dimensional (2D and 3D) surveys. SRT employs more shotpoints and receivers than the conventional seismic refraction for its imaging technique. ERT uses automated multi-electrode array systems to improve the confidence of large and dense data collection. SRT and ERT techniques use powerful inversion algorithms to achieve high resolution subsurface inversion models for resolving subsurface characteristics and geological conditions over a complex and larger area that may be difficult with the use of their conventional methods. The 2D and 3D inversion models (tomograms) generated from the field data sets of these techniques efficiently ameliorate inaccurate subsurface boundaries and structural delineation with higher depth resolution, especially the 3D inversion models for areas of complex geology. These state-of-the-art techniques have extensively been used for groundwater, environmental, engineering and mining investigations among others. This study provides insight from theories to data inversion techniques for the known tomography techniques (SRT and ERT) in use for subsurface investigations.Geofizičko istraživanje podzemlja temelji se na fizikalnim načelima kojima se objašnjava intrinistička priroda geoloških pojava. Tijekom zadnja dva desetljeća primjena seizmičke refrakcijske tomografije (skr. SRT) te one električne otpornosti (skr. ERT) značajno je povećala kvalitetu 2D i 3D interpretacije prikupljenih podataka. Tehnika SRT-a rabi veći broj točaka i prijamnika negoli konvencionalna seizmička refrakcija. Tehnika ERT-a koristi automatizirane višeelektrodne nizove s ciljem prikupljanja većega broja podataka na manjoj površini. Obje se temelje na naprednim algoritmima inverzije kako bi omogućile stvaranje visokorazlučivih modela podzemlja na kojima je moguće interpretirati složene geološke odnose. Stoga je primjena takvih 2D i 3D modela višestruka; za određivanje granica podzemnih tijela ili promjena u njima, opažanja podzemnih voda, rješavanje inženjersko-geoloških problema, u rudarskim istraživanjima itsl. Ova studija je obuhvatila teorijske osnove tih tehnika te nekoliko primjera njihove uporabe

Continuous Nondestructive Monitoring Method Using the Reconstructed Three-Dimensional Conductivity Images via GREIT for Tissue Engineering

A continuous Nondestructive monitoring method is required to apply proper feedback controls during tissue regeneration. Conductivity is one of valuable information to assess the physiological function and structural formation of regenerated tissues or cultured cells. However, conductivity imaging methods suffered from inherited ill-posed characteristics in image reconstruction, unknown boundary geometry, uncertainty in electrode position, and systematic artifacts. In order to overcome the limitation of microscopic electrical impedance tomography (micro-EIT), we applied a 3D-specific container with a fixed boundary geometry and electrode configuration to maximize the performance of Graz consensus reconstruction algorithm for EIT (GREIT). The separation of driving and sensing electrodes allows us to simplify the hardware complexity and obtain higher measurement accuracy from a large number of small sensing electrodes. We investigated the applicability of the GREIT to 3D micro-EIT images via numerical simulations and large-scale phantom experiments. We could reconstruct multiple objects regardless of the location. The resolution was 5 mm3 with 30 dB SNR and the position error was less than 2.54 mm. This shows that the new micro-EIT system integrated with GREIT is robust with the intended resolution. With further refinement and scaling down to a microscale container, it may be a continuous nondestructive monitoring tool for tissue engineering applications

Cell Biometrics Based on Bio-Impedance Measurements

Open Access.This work is in part supported by the funded Project: Auto-calibración y auto-test en circuitos analógicos, mixtos y de radio frecuencia: Andalusian Government project P0-TIC- 5386, co-financed with the FEDER program.Peer Reviewe

Geophysical assessment of soil and rock in the New Madrid seismic zone

The research presented here consists of two case studies: the first from a study site in Illinois and the second from a site in Arkansas. In both instances, geophysical investigations were conducted to characterize the subsurface. At the Illinois site, borehole control, downhole seismic (DHS), seismic refraction tomography (SRT) and multichannel analysis of surface waves (MASW) data were acquired for the purpose of seismic site characterization. Shear wave and compressional wave velocities were used to estimate depth to bedrock and to generate 1-D plots depicting variations in Poisson\u27s Ratio, elastic moduli and density. The average shear wave velocity in the upper 100 ft was calculated and the national earthquake hazards reduction program (NEHRP) class D was assigned to the site based on MASW and DHS data results. At the Arkansas site, borehole control, electrical resistivity tomography (ERT), seismic refraction tomography (SRT), and multichannel analysis of surface waves (MASW) data were acquired with the objective of verifying and mapping a postulated fault. A comparative evaluation of the overall usefulness of the ERT, SRT and MASW techniques was also performed. The comparison showed that ERT and SRT tools generated remarkably similar images of the fault. The MASW tool generated a slightly different image of the fault. The research demonstrates that integrated use of seismic (seismic refraction tomography, multichannel analysis of surface waves and downhole seismic) and electrical (electrical resistivity tomography) methods is an effective approach in terms of assessing soil and rock in the New Madrid Seismic Zone --Abstract, page iii