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.

Tecnología cloud para el hogar digital

El mundo tecnológico está cambiando hacia la optimización en la gestión de recursos gracias a la poderosa influencia de tecnologías como la virtualización y la computación en la nube (Cloud Computing). En esta memoria se realiza un acercamiento a las mismas, desde las causas que las motivaron hasta sus últimas tendencias, pasando por la identificación de sus principales características, ventajas e inconvenientes. Por otro lado, el Hogar Digital es ya una realidad para la mayoría de los seres humanos. En él se dispone de acceso a múltiples tipos de redes de telecomunicaciones (3G, 4G, WI-FI, ADSL…) con más o menos capacidad pero que permiten conexiones a internet desde cualquier parte, en todo momento, y con prácticamente cualquier dispositivo (ordenadores personales, smartphones, tabletas, televisores…). Esto es aprovechado por las empresas para ofrecer todo tipo de servicios. Algunos de estos servicios están basados en el cloud computing sobre todo ofreciendo almacenamiento en la nube a aquellos dispositivos con capacidad reducida, como son los smarthphones y las tabletas. Ese espacio de almacenamiento normalmente está en los servidores bajo el control de grandes compañías. Guardar documentos, videos, fotos privadas sin tener la certeza de que estos no son consultados por alguien sin consentimiento, puede despertar en el usuario cierto recelo. Para estos usuarios que desean control sobre su intimidad, se ofrece la posibilidad de que sea el propio usuario el que monte sus propios servidores y su propio servicio cloud para compartir su información privada sólo con sus familiares y amigos o con cualquiera al que le dé permiso. Durante el proyecto se han comparado diversas soluciones, la mayoría de código abierto y de libre distribución, que permiten desplegar como mínimo un servicio de almacenamiento accesible a través de Internet. Algunas de ellas lo complementan con servicios de streaming tanto de música como de videos, compartición y sincronización de documentos entre múltiples dispositivos, calendarios, copias de respaldo (backups), virtualización de escritorios, versionado de ficheros, chats, etc. El proyecto finaliza con una demostración de cómo utilizar dispositivos de un hogar digital interactuando con un servidor Cloud, en el que previamente se ha instalado y configurado una de las soluciones comparadas. Este servidor quedará empaquetado en una máquina virtual para que sea fácilmente transportable e utilizable. ABSTRACT. The technological world is changing towards optimizing resource management thanks to the powerful influence of technologies such as Virtualization and Cloud Computing. This document presents a closer approach to them, from the causes that have motivated to their last trends, as well as showing their main features, advantages and disadvantages. In addition, the Digital Home is a reality for most humans. It provides access to multiple types of telecommunication networks (3G, 4G, WI-FI, ADSL...) with more or less capacity, allowing Internet connections from anywhere, at any time, and with virtually any device (computer personal smartphones, tablets, televisions...).This is used by companies to provide all kinds of services. Some of these services offer storage on the cloud to devices with limited capacity, such as smartphones and tablets. That is normally storage space on servers under the control of important companies. Saving private documents, videos, photos, without being sure that they are not viewed by anyone without consent, can wake up suspicions in some users. For those users who want control over their privacy, it offers the possibility that it is the user himself to mount his own server and its own cloud service to share private information only with family and friends or with anyone with consent. During the project I have compared different solutions, most open source and with GNU licenses, for deploying one storage facility accessible via the Internet. Some supplement include streaming services of music , videos or photos, sharing and syncing documents across multiple devices, calendars, backups, desktop virtualization, file versioning, chats... The project ends with a demonstration of how to use our digital home devices interacting with a cloud server where one of the solutions compared is installed and configured. This server will be packaged in a virtual machine to be easily transportable and usable.

Secure transmission of information by digital chaotic signals

Protecting signals is one of the main tasks in information transmission. A large number of different methods have been employed since many centuries ago. Most of them have been based on the use of certain signal added to the original one. When the composed signal is received, if the added signal is known, the initial information may be obtained. The main problem is the type of masking signal employed. One possibility is the use of chaotic signals, but they have a first strong limitation: the need to synchronize emitter and receiver. Optical communications systems, based on chaotic signals, have been proposed in a large number of papers. Moreover, because most of the communication systems are digital and conventional chaos generators are analogue, a conversion analogue-digital is needed. In this paper we will report a new system where the digital chaos is obtained from an optically programmable logic structure. This structure has been employed by the authors in optical computing and some previous results in chaotic signals have been reported. The main advantage of this new system is that an analogue-digital conversion is not needed. Previous works by the authors employed Self-Electrooptical Effect Devices but in this case more conventional structures, as semiconductor laser amplifiers, have been employed. The way to analyze the characteristics of digital chaotic signals will be reported as well as the method to synchronize the chaos generators located in the emitter and in the receiver.

El Entorno Aumentado: Imperativo informacional para una ecología digital de lo arquitectónico

Esta tesis se suma a los intentos teóricos de clarificar la impronta del dominio digital en lo arquitectónico. Propone una cartografía crítica para reconstruir el proceso de tal convergencia considerando aquellos acontecimientos reveladores que lo han pautado. La integración de la extensión digital propia las tecnologías de la información y la comunicación en el contexto tradicional arquitectónico ha supuesto el advenimiento de un ecosistema artificial complejo. A esta realidad o proceso concurrente se la denomina el Entorno Aumentado. La línea principal de investigación explora el desarrollo de la interacción hombre-máquina, en sendas trayectorias sincrónicas convergentes. El análisis se aborda por tanto desde la consideración de esa naturaleza dual, atendiendo simultáneamente a la humanización del dominio digital o cómo la computación se adapta a la condición natural de ser humano, y a la digitalización del ser humano o cómo éste asume el imperativo digital. El análisis resulta vertebrado desde la condición panóptica del punto de observación del acontecimiento: la cuarta pared, entendida como pantalla y punto de inflexión que estructura la convergencia de los entornos físico y digital. La reflexión acometida sobre la construcción del Entorno Aumentado procura la verificación de la tesis, que es central en esta investigación: la multiplicación dimensional del lugar físico mediante su extensión con un campo informacional procedente del dominio digital, y sus efectos en la construcción de la nueva ecología digital propia del Entorno Aumentado. Esta circunstancia se produce tras la eclosión de la Revolución Digital en la segunda mitad del siglo XX, el consecuente incremento de la interacción entre los entornos digital y físico, y el alcance de un nivel superior de comunicación en los procesos arquitectónicos. Los síntomas del Entorno Aumentado se hacen notar en nuestra contemporaneidad; en ese sentido, la tesis alcanza un diagnóstico del cambio. La fractura y obsolescencia del límite espacio-temporal establecido por las dicotomías históricas privado-público, casa-ciudad, trabajo-ocio,…etc., o la vigencia del proyecto procedimental son algunas de sus consecuencias en el modo de abordar la disciplina arquitectónica. Abstract This dissertation aims to complete the theoretical attempts to clarify the digital domain imprint on the architectural realm. It constructs a critical cartography to reconstruct the process of such convergence, considering those principal events who have scheduled it. The integration of TIC’s digital extension through the traditional architectural context has meant the advent of an artificial complex ecosystem. This reality or concurrent process is called The Augmented Environment. The key research attempt explores man-machine interaction process in both synchronous converging trajectories. The analysis therefore addresses from the consideration of this dual nature, focusing simultaneously in humanizing digital domain process or how the computer fits the natural condition of human beings, and in digitalizing human beings or how it affords the digital imperative. The analysis is structured from the panoptic condition of the event scope: the fourth wall as screen that structures the convergence of physical and digital environments. The examination of The Augmented Environment’s assembly pretends the verification of the central point of this research: the dimensional multiplication of physical space by extending informational fields from the digital domain, and its effects on the construction of the Augmented Environment new digital ecology. This circumstance occurs after the arrival of the Digital Revolution in the second half of the twentieth century, with the consequent increase in the interaction between digital and physical environments, and the reach of a higher level of communication in architectural processes. The Augmented Environment signs are alive nowadays; in that sense, the thesis reaches a diagnostic of the changes. The fracture and obsolescence of the time-space limit established by historic dichotomies as private-public, home-city, working-leisure...etc., or the validity of the procedural design are some of its consequences on the architectural discipline.

Importance of canopy porosity into vineyard and the relationship with the grape maturity. Digital estimation method

In warm and dry climates, the use of porous systems should be required in order to allow a better leaf distribution inside the plant, causing more space in the clusters area and enhancing determined physiological processes so in the leaf (photosynthesis, v entilation, transpiration) as in berry (growth and maturation). Plant geometry indexes, yield and must composition have been studied in three different systems: sprawl with 12 shoots/m (S1); sprawl system with 18 shoots/m (S2) and vertical positioned syste m or VSP with 12 shoots/m (VSP1). Total leaf area increases as the crop load does, whoever surface area depends on to two factors: crop load and the training system (VSP vs. sprawl), which can provide differences in leaf exposure efficiencies. The main objective of this study was to validate digital photography measurements used to compare porosity differences among treatments and, as they affect plant microclimate and, therefore, yield and berry quality. Also, all previous studied indexes (LAI, SA, SFEr) tended to overestimate the relationship between exposed leaf surface and porosity of each treatment, but the use of digital method proved to be an effective tool in order to assess canopy porosity. Results showed that not positioned and free systems (sprawl) scored between 25- 50% more porosity in the clusters area than the fixed vertical system (VSP), which resulted in a better plant microclimate for test conditions, mainly by improving the exposure of internal clusters and internal canopy ventilation. On the other hand, higher crop load treatment (S2) showed a real increase in yield (16%) without any relevant change into must composition, even improving total anthocyanin content into berry during ripening

Importance of canopy porosity into vineyard and the relationship with the grape maturity. Digital estimation method

In warm and dry climates, the use of porous systems should be required in order to allow a better leaf distribution inside the plant, causing more space in the clusters area and enhancing determined physiological processes so in the leaf (photosynthesis, ventilation, transpiration) as in berry (growth and maturation). Plant geometry indexes, yield and must composition have been studied in three different systems: sprawl with 12 shoots/m (S1); sprawl system with 18 shoots/m (S2) and vertical positioned system or VSP with 12 shoots/m (VSP1). Total leaf area increases as the crop load does, whoever surface area depends on to two factors: crop load and the training system (VSP vs . sprawl), which can provide differences in leaf exposure efficiencies. The main objective of this study was to validate digital photography measurements used to compare porosity differences among treatments and, as they affect plant microclimate and, therefore, yield and berry quality. Also, all previous studied indexes (LAI, SA, SFEr) tended to overestimate the relationship between exposed leaf surface and porosity of each treatment, but the use of digital method proved to be an effective tool in order to assess canopy porosity. Results showed that not positioned and free systems (sprawl) scored between 25 - 50% more porosity in the clusters area than the fixed vertical system (VSP), which resulted in a better plant microclimate for test conditions, mainly by improving the exposure of internal clusters and internal canopy ventilation. On the other hand, higher crop load treatment (S2) showed a real increase in yield (16%) without any relevant change into must composition, even improving total anthocyanin content into berry during ripening

A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis

A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.