Image processing on reconfigurable hardware for continuous monitoring of fluorescent biomarkers in cell cultures

Fluorescence microscopy is a widespread tool in biological research. It is the primary modality for bioimaging and empowers the study and analysis of multitudes of biological processes. It can be applied to fixed biosamples, that is samples with frozen biological features by mean of chemical linkers, or live biosamples providing useful insights on the spatio-temporal behavior of fluorescently stained biomarkers. Current fluorescent microscopy techniques use digital image sensors which are used to leverage quantitative studies instead qualitative outcomes. However, state-of-the-art techniques are not suitable for integration in small, contained and (semi-)autonomous systems. They remain costly, bulky and rather quantitatively inefficient methods for monitoring fluorescent biomarkers, which is not on par with the design constraints found in modern Lab-on-a-Chip or Point-of-Use systems requiring the use of miniaturized and integrated fluroscence microscopy. In this thesis, I summarize my research and engineering efforts in bringing an embedded image processing system capable of monitoring fluorescent biomarkers in cell cultures in a continuous and real-time manner. Three main areas related to the problem at hand were explored in the course of this work: simulation, segmentation algorithms and embedded image processing. n the area of simulation, a novel approach for generating synthetic fluorescent 2D images of cell cultures is presented. This approach is dichotomized in a first part focusing on the modeling and generation of synthetic populations of cells (i.e. cell cultures) at the level of single fluorescent biomarkers and in a second part simulating the imaging process occurring in a traditional digital fluorescent microscope to produce realistic images of the synthetic cell cultures. The objective of the proposed approach aims at providing synthetic data at will in order to test and validate image processing systems and algorithms. Various image segmentation algorithms are considered and compared for the purpose of segmenting fluorescent spots in microscopic images. The study presented in this thesis includes a novel image thresholding technique for spot extraction along with three well-known spot segmentation techniques. The comparison is undertaken on two aspects. The segmentation masks provided by the methods are used to extract further metrics related to the fluorescent signals in order to (i) evaluate how well the segmentation masks can provide data for classifying real fluorescent biological samples from negative control samples and (ii) quantitatively compare the segmentations masks based on simulated data from the previously stated simulation tool. Finally, the design of an embedded image processing system based on FPGA technologies is showcased. A semi-autonomous smart camera is conceived for the continuous monitoring of fluorescent biomarkers based on one of the segmentation methods incorporated in the previously stated comparison. Keeping the focus on the need for integration in fluorescence microscopy, the image processing core at the heart of the smart camera results from the use of a novel image processing suite; a suite of IP cores developed under the constraints dictated by the bioimaging needs of fluorescence microscopy for use in FPGA and SoC technologies. As a proof of concept, the smart camera is applied to the monitoring of the kinetics of the uptake of fluorescent silica nano-particles in cell cultures.

Rate allocation and optimized decoding in inter-session network coding

Eirina Bourtsoulatze

Recent advances in data processing and communication systems have led to a continuous increase in the amount of data communicated over today’s networks. These large volumes of data pose new challenges on the current networking infrastructure that only offers a best effort mechanism for data delivery. The emergence of new distributed network architectures, such as peer-to-peer networks and wireless mesh networks, and the need for efficient data delivery mechanisms have motivated researchers to reconsider the way that information is communicated and processed in the networks. This has given rise to a new research field called network coding. The network coding paradigm departs from the traditional routing principle where information is simply relayed by the network nodes towards the destination, and introduces some intelligence in the network through coding at the intermediate nodes. This in-network data processing has been proved to substantially improve the performance of data delivery systems in terms of throughput and error resilience in networks with high path diversity. Motivated by the promising results in the network coding research, we focus in this thesis on the design of network coding algorithms for simultaneous transmission of multiple data sources in overlay networks. We investigate several problems that arise in the context of inter-session network coding, namely (i) decoding delay minimization in inter-session network coding, (ii) distributed rate allocation for inter-session network coding and (iii) correlation-aware decoding of incomplete network coded data. We start by proposing a novel framework for data delivery from multiple sources to multiple clients in an overlay wireline network, where intermediate nodes employ randomized inter-session network coding. We consider networks with high resource diversity, which creates network coding opportunities with possibly large gains in terms of throughput, delay and error robustness. However, the coding operations in the intermediate nodes must be carefully designed in order to enable efficient data delivery. We look at the problem from the decoding delay perspective and design solutions that lead to a small decoding delay at clients through proper coding and rate allocation. We cast the optimization problem as a rate allocation problem, which seeks for the coding operations that minimize the average decoding delay in the client population. We demonstrate the validity of our algorithm through simulations in representative network topologies. The results show that an effective combination of intra- and inter-session network coding based on randomized linear coding permits to reach small decoding delays and to better exploit the available network resources even in challenging network settings. Next, we design a distributed rate allocation algorithm where the users decide locally how many intra- and inter-session network coded packets should be requested from the parent nodes in order to get minimal decoding delay. The capability to take coding decisions locally with only a partial knowledge of the network statistics is of crucial importance for applications where users are organized in dynamic overlay networks. We propose a receiver-driven communication protocol that operates in two rounds. First, the users request and obtain information regarding the network conditions and packet availability in their local neighborhood. Then, every user independently optimizes the rate allocation among different possible intra- and inter-session packet combinations to be requested from its parents. We also introduce the novel concept of equivalent flows, which permits to efficiently estimate the expected number of packets that are necessary for decoding and hence to simplify the rate allocation process. Experimental results indicate that our algorithm is capable of eliminating the bottlenecks and reducing the decoding delay of users with limited resources. We further investigate the application of the proposed distributed rate allocation algorithm to the transmission of video sequences and validate the performance of our system using the NS-3 simulator. The simulation results show that the proposed rate allocation algorithm is successful in improving the quality of the delivered video compared to intra-session network coding based solutions. Finally, we investigate the problem of decoding the source information from an incomplete set of network coded data with the help of source priors in a finite algebraic field. The inability to form a complete decoding system can be often caused by transmission losses or timing constraints imposed by the application. In this case, exact reconstruction of the source data by conventional algorithms such as Gaussian elimination is not feasible; however, partial recovery of the source data may still be possible, which can be useful in applications where approximate reconstruction is informative. We use the statistical characteristics of the source data in order to perform approximate decoding. We first analyze the performance of a hypothetical maximum a posteriori decoder, which recovers the source data from an incomplete set of network coded data given the joint statistics of the sources. We derive an upper bound on the probability of erroneous source sequence decoding as a function of the system parameters. We then propose a constructive solution to the approximate decoding problem and design an iterative decoding algorithm based on message passing, which jointly considers the network coding and the correlation constraints. We illustrate the performance of our decoding algorithm through extensive simulations on synthetic and real data sets. The results demonstrate that, even by using a simple correlation model expressed as a correlation noise between pairs of sources, the original source data can be partially decoded in practice from an incomplete set of network coded symbols. Overall, this thesis addresses several important issues related to the design of efficient data delivery methods with inter-session network coding. Our novel framework for decoding delay minimization can impact the development of practical inter-session network coding algorithms that are appropriate for applications with low delay requirements. Our rate allocation algorithms are able to exploit the high resource diversity of modern networking systems and represent an effective alternative in the development of distributed communication systems. Finally, our algorithm for data recovery from incomplete network coded data using correlation priors can contribute significantly to the improvement of the delivered data quality and provide new insights towards the design of joint source and network coding algorithms.

EPFL2013

Adding limited reconfigurability to superscalar processors

Marc Epalza

For the last thirty years, electronics, at first built with discrete components, and then as Integrated Circuits (IC), have brought diverse and lasting improvements to our quality of life. Examples might include digital calculators, automotive and airplane control assistance, almost all electrical household appliances, and the almost ubiquitous Personal Computer. Application-Specific Integrated Circuits (ASICs) were traditionally used for their high performance and low manufacturing cost, and were designed specifically for a single application with large volumes. But as lower product lifetimes and the pressures of fast marketing increased, ASICs' high design cost pushed for their replacement by Microprocessors. These processors, capable of implementing any functionality through a change in software, are thus often called General Purpose Processors. General purpose processors are used for everyday computing tasks, and found in all personal computers. They are also often used as building blocks for scientific supercomputers. Superscalar processors such as these require ever more processing power to run complex simulations, video games or versatile telecoms services. In the case of embedded applications, e.g. for portable devices, both performance and power consumption must be taken into account. In a bid to adapt a processor to some extent to select applications, fully reconfigurable logic can greatly improve the performance of a processor, since it is shaped for the best possible execution with the available resources. However, as reconfigurable logic is far slower than custom logic, this gain is possible only for some specific applications with large parallelism, after a detailed study of the algorithm. Even though this process can be automated, it still requires large computing resources, and cannot be performed at run time. To reduce the loss in speed compared to custom logic, it is possible to limit the reconfigurability to increase the breadth of applications where performance can be improved. However, as the application space increases, a careful analysis and design of the reconfigurability is required to minimize the speed loss, notably when dynamic reconfiguration is considered. As a case study, we analyze the feasibility of adding limited reconfigurability to the Floating Point Units (FPUs) of a general purpose processor. These rather large units execute all floating point operations, and may also be used for integer multiplication. If an application contains few or infrequent instructions that must be executed by the FPU, this idle hardware only increases power consumption without enhancing performance. This is often the case in non-scientific applications and even many recent and detailed video games which make heavy use of hardware display accelerators for 3D graphics. In a fast multiplier such as can be found in the FPU of a high performance processor, the logic to perform multiplication is a large tree of compressors to add all the partial products together. It is possible to add logic to allow the reconfiguration of part of this tree as several extra Arithmetic and Logic Units (ALU). This requires a detailed timing analysis for both the reconfigurable FPU and the extra ALUs, taking into account effects such as added wires and longer critical paths. Finally, the algorithm to decide when and how to reconfigure must be studied, in terms of eciency and complexity. The results of adding this limited reconfigurability to a mainstream superscalar processor over a large set of compute intensive benchmarks show gains of up to 56% in the best case, with an average gain of 11%. The application to an idealized huge top processor still shows slightly positive average gains, as the limits of available parallelism are reached, bounded by both the application and many of the characteristics of the processor. In all cases, binary compatibility is maintained, allowing the re-use of all existing software. We show that adding limited reconfigurability to a general purpose superscalar processor can produce interesting gains over a wide range of applications while maintaining binary compatibility, and without large modifications to the original design. Limited reconfigurability is worthwhile as it increases the design space, allowing gains to apply to a larger set of applications. These gains are achieved through careful study and optimization of the reconfigurable logic and the decision algorithm.

EPFL2004

Rapid Scalable Distributed Power Flow with Open-Source Implementation

Yuning Jiang

This paper introduces a new method for solving the distributed AC power flow (PF) problem by further exploiting the problem formulation. We propose a new variant of the ALADIN algorithm devised specifically for this type of problem. This new variant is characterized by using a reduced modelling method of the distributed AC PF problem, which is reformulated as a zero-residual least-squares problem with consensus constraints. This PF is then solved by a Gauss-Newton based inexact ALADIN algorithm presented in the paper. An open-source implementation of this algorithm, called rapidPF, is provided. Simulation results, for which the power system's dimension varies from 53 to 10224 buses, show great potential of this combination in the aspects of both the computing time and scalability. Copyright (C) 2022 The Authors.