Assembling models of embryo development: Image analysis and the construction of digital atlases

Digital atlases of animal development provide a quantitative description of morphogenesis, opening the path toward processes modeling. Prototypic atlases offer a data integration framework where to gather information from cohorts of individuals with phenotypic variability. Relevant information for further theoretical reconstruction includes measurements in time and space for cell behaviors and gene expression. The latter as well as data integration in a prototypic model, rely on image processing strategies. Developing the tools to integrate and analyze biological multidimensional data are highly relevant for assessing chemical toxicity or performing drugs preclinical testing. This article surveys some of the most prominent efforts to assemble these prototypes, categorizes them according to salient criteria and discusses the key questions in the field and the future challenges toward the reconstruction of multiscale dynamics in model organisms.

A low cost and widely applicable methodology of digital imagen analysis of ores for mineral and envirommental engineering

Technological and environmental problems related to ore processing are a serious limitation for sustainable development of mineral resources, particularly for countries / companies rich in ores, but with little access to sophisticated technology, e.g. in Latin America. Digital image analysis (DIA) can provide a simple, unexpensive and broadly applicable methodology to assess these problems, but this methodology has to be carefully defined, to produce reproducible and relevant information.

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

Computational methods to create and analyze a digital gene expression atlas of embryo development from microscopy images

Abstract The creation of atlases, or digital models where information from different subjects can be combined, is a field of increasing interest in biomedical imaging. When a single image does not contain enough information to appropriately describe the organism under study, it is then necessary to acquire images of several individuals, each of them containing complementary data with respect to the rest of the components in the cohort. This approach allows creating digital prototypes, ranging from anatomical atlases of human patients and organs, obtained for instance from Magnetic Resonance Imaging, to gene expression cartographies of embryo development, typically achieved from Light Microscopy. Within such context, in this PhD Thesis we propose, develop and validate new dedicated image processing methodologies that, based on image registration techniques, bring information from multiple individuals into alignment within a single digital atlas model. We also elaborate a dedicated software visualization platform to explore the resulting wealth of multi-dimensional data and novel analysis algo-rithms to automatically mine the generated resource in search of bio¬logical insights. In particular, this work focuses on gene expression data from developing zebrafish embryos imaged at the cellular resolution level with Two-Photon Laser Scanning Microscopy. Disposing of quantitative measurements relating multiple gene expressions to cell position and their evolution in time is a fundamental prerequisite to understand embryogenesis multi-scale processes. However, the number of gene expressions that can be simultaneously stained in one acquisition is limited due to optical and labeling constraints. These limitations motivate the implementation of atlasing strategies that can recreate a virtual gene expression multiplex. The developed computational tools have been tested in two different scenarios. The first one is the early zebrafish embryogenesis where the resulting atlas constitutes a link between the phenotype and the genotype at the cellular level. The second one is the late zebrafish brain where the resulting atlas allows studies relating gene expression to brain regionalization and neurogenesis. The proposed computational frameworks have been adapted to the requirements of both scenarios, such as the integration of partial views of the embryo into a whole embryo model with cellular resolution or the registration of anatom¬ical traits with deformable transformation models non-dependent on any specific labeling. The software implementation of the atlas generation tool (Match-IT) and the visualization platform (Atlas-IT) together with the gene expression atlas resources developed in this Thesis are to be made freely available to the scientific community. Lastly, a novel proof-of-concept experiment integrates for the first time 3D gene expression atlas resources with cell lineages extracted from live embryos, opening up the door to correlate genetic and cellular spatio-temporal dynamics. La creación de atlas, o modelos digitales, donde la información de distintos sujetos puede ser combinada, es un campo de creciente interés en imagen biomédica. Cuando una sola imagen no contiene suficientes datos como para describir apropiadamente el organismo objeto de estudio, se hace necesario adquirir imágenes de varios individuos, cada una de las cuales contiene información complementaria respecto al resto de componentes del grupo. De este modo, es posible crear prototipos digitales, que pueden ir desde atlas anatómicos de órganos y pacientes humanos, adquiridos por ejemplo mediante Resonancia Magnética, hasta cartografías de la expresión genética del desarrollo de embrionario, típicamente adquiridas mediante Microscopía Optica. Dentro de este contexto, en esta Tesis Doctoral se introducen, desarrollan y validan nuevos métodos de procesado de imagen que, basándose en técnicas de registro de imagen, son capaces de alinear imágenes y datos provenientes de múltiples individuos en un solo atlas digital. Además, se ha elaborado una plataforma de visualization específicamente diseñada para explorar la gran cantidad de datos, caracterizados por su multi-dimensionalidad, que resulta de estos métodos. Asimismo, se han propuesto novedosos algoritmos de análisis y minería de datos que permiten inspeccionar automáticamente los atlas generados en busca de conclusiones biológicas significativas. En particular, este trabajo se centra en datos de expresión genética del desarrollo embrionario del pez cebra, adquiridos mediante Microscopía dos fotones con resolución celular. Disponer de medidas cuantitativas que relacionen estas expresiones genéticas con las posiciones celulares y su evolución en el tiempo es un prerrequisito fundamental para comprender los procesos multi-escala característicos de la morfogénesis. Sin embargo, el número de expresiones genéticos que pueden ser simultáneamente etiquetados en una sola adquisición es reducido debido a limitaciones tanto ópticas como del etiquetado. Estas limitaciones requieren la implementación de estrategias de creación de atlas que puedan recrear un multiplexado virtual de expresiones genéticas. Las herramientas computacionales desarrolladas han sido validadas en dos escenarios distintos. El primer escenario es el desarrollo embrionario temprano del pez cebra, donde el atlas resultante permite constituir un vínculo, a nivel celular, entre el fenotipo y el genotipo de este organismo modelo. El segundo escenario corresponde a estadios tardíos del desarrollo del cerebro del pez cebra, donde el atlas resultante permite relacionar expresiones genéticas con la regionalización del cerebro y la formación de neuronas. La plataforma computacional desarrollada ha sido adaptada a los requisitos y retos planteados en ambos escenarios, como la integración, a resolución celular, de vistas parciales dentro de un modelo consistente en un embrión completo, o el alineamiento entre estructuras de referencia anatómica equivalentes, logrado mediante el uso de modelos de transformación deformables que no requieren ningún marcador específico. Está previsto poner a disposición de la comunidad científica tanto la herramienta de generación de atlas (Match-IT), como su plataforma de visualización (Atlas-IT), así como las bases de datos de expresión genética creadas a partir de estas herramientas. Por último, dentro de la presente Tesis Doctoral, se ha incluido una prueba conceptual innovadora que permite integrar los mencionados atlas de expresión genética tridimensionales dentro del linaje celular extraído de una adquisición in vivo de un embrión. Esta prueba conceptual abre la puerta a la posibilidad de correlar, por primera vez, las dinámicas espacio-temporales de genes y células.

3D + t Morphological Processing: Applications to Embryogenesis Image Analysis

We propose to directly process 3D + t image sequences with mathematical morphology operators, using a new classi?cation of the 3D+t structuring elements. Several methods (?ltering, tracking, segmentation) dedicated to the analysis of 3D + t datasets of zebra?sh embryogenesis are introduced and validated through a synthetic dataset. Then, we illustrate the application of these methods to the analysis of datasets of zebra?sh early development acquired with various microscopy techniques. This processing paradigm produces spatio-temporal coherent results as it bene?ts from the intrinsic redundancy of the temporal dimension, and minimizes the needs for human intervention in semi-automatic algorithms.

A scalable evolvable hardware processing array

Evolvable hardware (EH) is an interesting alternative to conventional digital circuit design, since autonomous generation of solutions for a given task permits self-adaptivity of the system to changing environments, and they present inherent fault tolerance when evolution is intrinsically performed. Systems based on FPGAs that use Dynamic and Partial Reconfiguration (DPR) for evolving the circuit are an example. Also, thanks to DPR, these systems can be provided with scalability, a feature that allows a system to change the number of allocated resources at run-time in order to vary some feature, such as performance. The combination of both aspects leads to scalable evolvable hardware (SEH), which changes in size as an extra degree of freedom when trying to achieve the optimal solution by means of evolution. The main contributions of this paper are an architecture of a scalable and evolvable hardware processing array system, some preliminary evolution strategies which take scalability into consideration, and to show in the experimental results the benefits of combined evolution and scalability. A digital image filtering application is used as use case.

Logarithmical hopping encoding: a low computational complexity algorithm for image compression

LHE (logarithmical hopping encoding) is a computationally efficient image compression algorithm that exploits the Weber–Fechner law to encode the error between colour component predictions and the actual value of such components. More concretely, for each pixel, luminance and chrominance predictions are calculated as a function of the surrounding pixels and then the error between the predictions and the actual values are logarithmically quantised. The main advantage of LHE is that although it is capable of achieving a low-bit rate encoding with high quality results in terms of peak signal-to-noise ratio (PSNR) and image quality metrics with full-reference (FSIM) and non-reference (blind/referenceless image spatial quality evaluator), its time complexity is O( n) and its memory complexity is O(1). Furthermore, an enhanced version of the algorithm is proposed, where the output codes provided by the logarithmical quantiser are used in a pre-processing stage to estimate the perceptual relevance of the image blocks. This allows the algorithm to downsample the blocks with low perceptual relevance, thus improving the compression rate. The performance of LHE is especially remarkable when the bit per pixel rate is low, showing much better quality, in terms of PSNR and FSIM, than JPEG and slightly lower quality than JPEG-2000 but being more computationally efficient.

Area-Efficient Linear Regression Architecture for Real-Time Signal Processing on FPGAs

Linear regression is a technique widely used in digital signal processing. It consists on finding the linear function that better fits a given set of samples. This paper proposes different hardware architectures for the implementation of the linear regression method on FPGAs, specially targeting area restrictive systems. It saves area at the cost of constraining the lengths of the input signal to some fixed values. We have implemented the proposed scheme in an Automatic Modulation Classifier, meeting the hard real-time constraints this kind of systems have.

Bio-inspired FPGA Architecture for Self-Calibration of an Image Compression Core based on Wavelet Transforms in Embedded Systems

A generic bio-inspired adaptive architecture for image compression suitable to be implemented in embedded systems is presented. The architecture allows the system to be tuned during its calibration phase. An evolutionary algorithm is responsible of making the system evolve towards the required performance. A prototype has been implemented in a Xilinx Virtex-5 FPGA featuring an adaptive wavelet transform core directed at improving image compression for specific types of images. An Evolution Strategy has been chosen as the search algorithm and its typical genetic operators adapted to allow for a hardware friendly implementation. HW/SW partitioning issues are also considered after a high level description of the algorithm is profiled which validates the proposed resource allocation in the device fabric. To check the robustness of the system and its adaptation capabilities, different types of images have been selected as validation patterns. A direct application of such a system is its deployment in an unknown environment during design time, letting the calibration phase adjust the system parameters so that it performs efcient image compression. Also, this prototype implementation may serve as an accelerator for the automatic design of evolved transform coefficients which are later on synthesized and implemented in a non-adaptive system in the final implementation device, whether it is a HW or SW based computing device. The architecture has been built in a modular way so that it can be easily extended to adapt other types of image processing cores. Details on this pluggable component point of view are also given in the paper.

A Multiresolution Image Alignment Technique Based on Direct Methods for Pose Estimation of Aerial Vehicles

In this paper, we seek to expand the use of direct methods in real-time applications by proposing a vision-based strategy for pose estimation of aerial vehicles. The vast majority of approaches make use of features to estimate motion. Conversely, the strategy we propose is based on a MR (Multi-Resolution) implementation of an image registration technique (Inverse Compositional Image Alignment ICIA) using direct methods. An on-board camera in a downwards-looking configuration, and the assumption of planar scenes, are the bases of the algorithm. The motion between frames (rotation and translation) is recovered by decomposing the frame-to-frame homography obtained by the ICIA algorithm applied to a patch that covers around the 80% of the image. When the visual estimation is required (e.g. GPS drop-out), this motion is integrated with the previous known estimation of the vehicles' state, obtained from the on-board sensors (GPS/IMU), and the subsequent estimations are based only on the vision-based motion estimations. The proposed strategy is tested with real flight data in representative stages of a flight: cruise, landing, and take-off, being two of those stages considered critical: take-off and landing. The performance of the pose estimation strategy is analyzed by comparing it with the GPS/IMU estimations. Results show correlation between the visual estimation obtained with the MR-ICIA and the GPS/IMU data, that demonstrate that the visual estimation can be used to provide a good approximation of the vehicle's state when it is required (e.g. GPS drop-outs). In terms of performance, the proposed strategy is able to maintain an estimation of the vehicle's state for more than one minute, at real-time frame rates based, only on visual information.

Image sub-segmentation by PFCM and Artificial Neural Networks to detect pore space in 2D and 3D CT soil images

The image by Computed Tomography is a non-invasive alternative for observing soil structures, mainly pore space. The pore space correspond in soil data to empty or free space in the sense that no material is present there but only fluids, the fluid transport depend of pore spaces in soil, for this reason is important identify the regions that correspond to pore zones. In this paper we present a methodology in order to detect pore space and solid soil based on the synergy of the image processing, pattern recognition and artificial intelligence. The mathematical morphology is an image processing technique used for the purpose of image enhancement. In order to find pixels groups with a similar gray level intensity, or more or less homogeneous groups, a novel image sub-segmentation based on a Possibilistic Fuzzy c-Means (PFCM) clustering algorithm was used. The Artificial Neural Networks (ANNs) are very efficient for demanding large scale and generic pattern recognition applications for this reason finally a classifier based on artificial neural network is applied in order to classify soil images in two classes, pore space and solid soil respectively.

An image segmentation based on a genetic algorithm for determining soil coverage by crop residues

Determination of the soil coverage by crop residues after ploughing is a fundamental element of Conservation Agriculture. This paper presents the application of genetic algorithms employed during the fine tuning of the segmentation process of a digital image with the aim of automatically quantifying the residue coverage. In other words, the objective is to achieve a segmentation that would permit the discrimination of the texture of the residue so that the output of the segmentation process is a binary image in which residue zones are isolated from the rest. The RGB images used come from a sample of images in which sections of terrain were photographed with a conventional camera positioned in zenith orientation atop a tripod. The images were taken outdoors under uncontrolled lighting conditions. Up to 92% similarity was achieved between the images obtained by the segmentation process proposed in this paper and the templates made by an elaborate manual tracing process. In addition to the proposed segmentation procedure and the fine tuning procedure that was developed, a global quantification of the soil coverage by residues for the sampled area was achieved that differed by only 0.85% from the quantification obtained using template images. Moreover, the proposed method does not depend on the type of residue present in the image. The study was conducted at the experimental farm “El Encín” in Alcalá de Henares (Madrid, Spain).

Técnicas de procesado digital de señal aplicadas a acelerómetros

En este proyecto se estudian y analizan las diferentes técnicas de procesado digital de señal aplicadas a acelerómetros. Se hace uso de una tarjeta de prototipado, basada en DSP, para realizar las diferentes pruebas. El proyecto se basa, principalmente, en realizar filtrado digital en señales provenientes de un acelerómetro en concreto, el 1201F, cuyo campo de aplicación es básicamente la automoción. Una vez estudiadas la teoría de procesado y las características de los filtros, diseñamos una aplicación basándonos sobre todo en el entorno en el que se desarrollaría una aplicación de este tipo. A lo largo del diseño, se explican las diferentes fases: diseño por ordenador (Matlab), diseño de los filtros en el DSP (C), pruebas sobre el DSP sin el acelerómetro, calibración del acelerómetro, pruebas finales sobre el acelerómetro... Las herramientas utilizadas son: la plataforma Kit de evaluación 21-161N de Analog Devices (equipado con el entorno de desarrollo Visual DSP 4.5++), el acelerómetro 1201F, el sistema de calibración de acelerómetros CS-18-LF de Spektra y los programas software MATLAB 7.5 y CoolEditPRO 2.0. Se realizan únicamente filtros IIR de 2º orden, de todos los tipos (Butterworth, Chebyshev I y II y Elípticos). Realizamos filtros de banda estrecha, paso-banda y banda eliminada, de varios tipos, dentro del fondo de escala que permite el acelerómetro. Una vez realizadas todas las pruebas, tanto simulaciones como físicas, se seleccionan los filtros que presentan un mejor funcionamiento y se analizan para obtener conclusiones. Como se dispone de un entorno adecuado para ello, se combinan los filtros entre sí de varias maneras, para obtener filtros de mayor orden (estructura paralelo). De esta forma, a partir de filtros paso-banda, podemos obtener otras configuraciones que nos darán mayor flexibilidad. El objetivo de este proyecto no se basa sólo en obtener buenos resultados en el filtrado, sino también de aprovechar las facilidades del entorno y las herramientas de las que disponemos para realizar el diseño más eficiente posible. In this project, we study and analize digital signal processing in order to design an accelerometer-based application. We use a hardware card of evaluation, based on DSP, to make different tests. This project is based in design digital filters for an automotion application. The accelerometer type is 1201F. First, we study digital processing theory and main parameters of real filters, to make a design based on the application environment. Along the application, we comment all the different steps: computer design (Matlab), filter design on the DSP (C language), simulation test on the DSP without the accelerometer, accelerometer calibration, final tests on the accelerometer... Hardware and software tools used are: Kit of Evaluation 21-161-N, based on DSP, of Analog Devices (equiped with software development tool Visual DSP 4.5++), 1201-F accelerometer, CS-18-LF calibration system of SPEKTRA and software tools MATLAB 7.5 and CoolEditPRO 2.0. We only perform 2nd orden IIR filters, all-type : Butterworth, Chebyshev I and II and Ellyptics. We perform bandpass and stopband filters, with very narrow band, taking advantage of the accelerometer's full scale. Once all the evidence, both simulations and physical, are finished, filters having better performance and analyzed and selected to draw conclusions. As there is a suitable environment for it, the filters are combined together in different ways to obtain higher order filters (parallel structure). Thus, from band-pass filters, we can obtain many configurations that will give us greater flexibility. The purpose of this project is not only based on good results in filtering, but also to exploit the facilities of the environment and the available tools to make the most efficient design possible.

Desarrollos para la explotación de datos integrados mediante fotogrametría y láser escáner en proyectos de patrimonio arquitectónico

La presente tesis doctoral describe los desarrollos realizados, y finalmente materializados en patentes con registro de la propiedad intelectual, para la integración de las nuevas tecnologías de documentación fotogramétrica y las bases de datos de los barredores láser terrestres, en los procesos de elaboración, redacción y ejecución de proyectos de restauración y rehabilitación arquitectónicos. Los avances tecnológicos aparecidos en control métrico, junto con las técnicas de imagen digital y los desarrollos fotogramétricos, pueden aportar mejoras significativas en el proceso proyectual y permiten aplicar nuevos procedimientos de extracción de datos para generar de forma sencilla, bajo el control directo y supervisión de los responsables del proyecto, la información métrica y documental más adecuada. Se establecen como principios, y por tanto como base para el diseño de dicha herramienta, que los desarrollos aparecidos sí han producido el uso extendido del sistema CAD (como instrumento de dibujo) así como el uso de la imagen digital como herramienta de documentación. La herramienta a diseñar se fundamenta por tanto en la imagen digital (imágenes digitales, imágenes rectificadas, ortofotografías, estéreo- modelos, estereo- ortofotografías) así como su integración en autocad para un tratamiento interactivo. En la aplicación de la fotogrametría a la disciplina arquitectónica, se considera de interés estructurar aplicaciones con carácter integrador que, con mayores capacidades de interactuación y a partir de información veraz y rigurosa, permitan completar o elaborar documentos de interés proyectual, ABSTRACT This doctoral thesis explains the developments carried out, and finally patented with intellectual property rights, for the integration of the new photogrammetric technology documentation and terrestrial scanner databases in the preparation, documentation and implementation processes of restoration projects and architectural renovation. The technological advances in metric control, as well as the digital image techniques and photogrammetric developments, can together bring a significant improvement to the projecting process, and, under the direct control and supervision of those in charge of the project, can allow new data extraction processes to be applied in order to easily generate the most appropriate metric information and documentation. The principles and, therefore, the basis for the design of this tool are that the developments have indeed produced the widespread use of the CAD system (as a drawing instrument) and the use of digital images as a documentation tool. The tool to be designed is therefore based on digital images (rectify images, orthophotos, stereomodels, stereo-orthophotos) as well as its integration in Autocad for interactive processing. In the application of photogrammetry to the architectural discipline, what interests us is to structure applications of an integrative nature which, with a greater capacity for interaction and from accurate and thorough information, enable the completion or elaboration of documents that are of interest to the project.

Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy

Investigating cell dynamics during early zebrafish embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second- and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebrafish embryos from 1- to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebrafish embryogenesis.