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.

Atlas of the shallow-water benthic habitats of Majuro Atoll, Republic of the Marshall Islands

Digital maps of the shallow (<~30m deep) coral reef ecosystems of Majuro Atoll, Republic of the Marshall Islands, were created through visual interpretation of remote sensing imagery acquired between 2004 and 2006. Reef ecosystem features were digitized directly into a Geographic Information System. Benthic features were categorized according to a classification scheme with attributes including zone (location such as lagoon or forereef, etc.), structure (bottom type such as sand or patch reef, etc.) and percent hard bottom. This atlas consists of 27 detailed maps displaying reef zone and structure of coral ecosystems around Majuro. Adjacent maps in the atlas overlap slightly to ensure complete coverage. Maps and associated products can be used to support science and management activities on Majuro reef ecosystems including inventory, monitoring, conservation, and sustainable development applications. Maps are not to be used for navigation.

Atlas of the shallow-water benthic habitats of American Samoa, Guam, and the Commonwealth of the Northern Mariana Islands

The National Oceanic and Atmospheric Administration (NOAA) National Ocean Service (NOS) initiated a coral reef research program in 1999 to map, assess, inventory, and monitor U.S. coral reef ecosystems (Monaco et al. 2001). These activities were implemented in response to requirements outlined in the Mapping Implementation Plan developed by the Mapping and Information Synthesis Working Group (MISWG) of the Coral Reef Task Force (CRTF) (MISWG 1999). As part of the MISWG of the CRTF, NOS' Biogeography Branch has been charged with the development and implementation of a plan to produce comprehensive digital coral-reef ecosystem maps for all U.S. States, Territories, and Commonwealths within five to seven years. Joint activities between Federal agencies are particularly important to map, research, monitor, manage, and restore coral reef ecosystems. In response to the Executive Order 13089 and the Coral Reef Conservation Act of 2000, NOS is conducting research to digitally map biotic resources and coordinate a long-term monitoring program that can detect and predict change in U.S. coral reefs, and their associated habitats and biological communities. Most U.S. coral reef resources have not been digitally mapped at a scale or resolution sufficient for assessment, monitoring, and/or research to support resource management. Thus, a large portion of NOS' coral reef research activities has focused on mapping of U.S. coral reef ecosystems. The map products will provide the fundamental spatial organizing framework to implement and integrate research programs and provide the capability to effectively communicate information and results to coral reef ecosystem managers. Although the NOS coral program is relatively young, it has had tremendous success in advancing towards the goal to protect, conserve, and enhance the health of U.S. coral reef ecosystems. One objective of the program was to create benthic habitat maps to support coral reef research to enable development of products that support management needs and questions. Therefore this product was developed in collaboration with many U.S. Pacific Territory partners. An initial step in producing benthic habitat maps was the development of a habitat classification scheme. The purpose of this document is to outline the benthic habitat classification scheme and protocols used to map American Samoa, Guam and the Commonwealth of the Northern Mariana Islands. Thirty-two distinct benthic habitat types (i.e., four major and 14 detailed geomorphological structure classes; eight major and 18 detailed biological cover types) within eleven zones were mapped directly into a geographic information system (GIS) using visual interpretation of orthorectified IKONOS satellite imagery. Benthic features were mapped that covered an area of 263 square kilometers. In all, 281 square kilometers of unconsolidated sediment, 122 square kilometers of submerged vegetation, and 82.3 square kilometers of coral reef and colonized hardbottom were mapped.

Research and compilation of the Geomorphologic Atlas of the People's Republic of China (1:1,000,000)

National Natural Science Foundation of China [40871177, 40830529]

Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas.

Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest due to the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome, and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3-D computerized tomography (CT) images of intact rat brains implanted with metal electrode bundles to a Magnetic Resonance Imaging Histology (MRH) Atlas. Our method allows accurate visualization of each electrode bundle's trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by "re-slicing" the images along different planes of view. Further, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience.

Atlas sedimentológico de la plataforma continental peruana

Presenta un atlas sedimentológico compuesto por un texto explicativo y 19 cartas elaboradas en base a la información obtenida de 726 muestras de sedimento superficial de la plataforma continental peruana y del talud continental, extraídas entre 1976 y 1983 mediante una draga Van Veen de 0,10m2. Incluye la batimetría de la zona estudiada,la ubicación de los puntos de muestreo, la textura y granulometría del sedimento, así como el contenido tanto de carbonatos como de carbono orgánico. Las cartas son más detalladas para la plataforma que para el talud y muestran la predominancia de sedimentos arenosos en la mayor parte de la plataforma continental y del talud superior entre los 6°15' y 10°30' S, y la presencia de arcilla limosa cubriendo todo el talud continental y gran parte de la plataforma al sur de los 10°30' S. En cuanto al carbono orgánico y carbonatos se observa valores muy bajos ( <2% de carbono orgánico y <10% de carbonatos en sedimento) al norte de los 10"30'S y valores altos (>5%- 20% de carbono orgánico y hasta de 30%-50% de carbonatos) al sur de los 10°30'S.

Atles de les Illes Balears. 'Atlas de las Islas Baleares'.

Resumen tomado parcialmente del propio recurso

USGS Topographic Maps over a Hillshaded Digital Elevation Model

http://digitalcommons.colby.edu/atlasofmaine2005/1013/thumbnail.jpg

Atlas ambiental como subsídio aos estudos de sustentabilidade - a bacia do Araçuaí no Vale do Jequitinhonha - MG

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Desenvolvimento do protótipo de um atlas escolar interativo

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Establishment of Regional Herbarium Leads to More Than 200 New Flora Atlas Records for New York State

Loss of small herbaria is an unfortunate global trend, and initiation of new collections at small academic institutions is an increasingly rare occurrence. In 2006, a new herbarium was established at the State University of New York College at Plattsburgh. The PLAT herbarium has since grown to more than 7,000 specimens, many of them representative of the flora of northeastern New York (especially Clinton County). Previous to 2006, this region was without a recognized herbarium, the nearest in-state collections being more than 150 miles away. Although botanists have previously worked in the region, relatively few plant species were recorded for Clinton County by the New York Flora Atlas – a resource providing species distribution records based on specimens accessioned in herbarium collections. Given the dearth of available distribution data for Clinton County (including the eastern Adirondack Mountains and the western Lake Champlain valley), this project sought to provide records of previously unreported species by comparing NY Flora Atlas maps with current holdings. 203 species will now be added to the NY Flora Atlas for Clinton County, roughly half of those considered exotic. This exercise has amplified the importance of supporting and maintaining small regional herbaria as repositories of valuable biodiversity information. Likewise, this project also highlights the enduring value of training in floristics and taxonomy.

BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy

BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses.

Hydrochemical Atlas of the Arctic Ocean

Introduction: Chemical composition of water determines its physical properties and character of processes proceeding in it: freezing temperature, volume of evaporation, density, color, transparency, filtration capacity, etc. Presence of chemical elements in water solution confers waters special physical properties exerting significant influence on their circulation, creates necessary conditions for development and inhabitance of flora and fauna, and imparts to the ocean waters some chemical features that radically differ them from the land waters (Alekin & Liakhin, 1984). Hydrochemical information helps to determine elements of water circulation, convection depth, makes it easier to distinguish water masses and gives additional knowledge of climatic variability of ocean conditions. Hydrochemical information is a necessary part of biological research. Water chemical composition can be the governing characteristics determining possibility and limits of use of marine objects, both stationary and moving in sea water. Subject of investigation of hydrochemistry is study of dynamics of chemical composition, i.e. processes of its formation and hydrochemical conditions of water bodies (Alekin & Liakhin 1984). The hydrochemical processes in the Arctic Ocean are the least known. Some information on these processes can be obtained in odd publications. A generalizing study of hydrochemical conditions in the Arctic Ocean based on expeditions conducted in the years 1948-1975 has been carried out by Rusanov et al. (1979). The "Atlas of the World Ocean: the Arctic Ocean" contains a special section "Hydrochemistry" (Gorshkov, 1980). Typical vertical profiles, transects and maps for different depths - 0, 100, 300, 500, 1000, 2000, 3000 m are given in this section for the following parameters: dissolved oxygen, phosphate, silicate, pH and alkaline-chlorine coefficient. The maps were constructed using the data of expeditions conducted in the years 1948-1975. The illustrations reflect main features of distribution of the hydrochemical elements for multi-year period and represent a static image of hydrochemical conditions. Distribution of the hydrochemical elements on the ocean surface is given for two seasons - winter and summer, for the other depths are given mean annual fields. Aim of the present Atlas is description of hydrochemical conditions in the Arctic Ocean on the basis of a greater body of hydrochemical information for the years 1948-2000 and using the up-to-date methods of analysis and electronic forms of presentation of hydrochemical information. The most wide-spread characteristics determined in water samples were used as hydrochemical indices. They are: dissolved oxygen, phosphate, silicate, pH, total alkalinity, nitrite and nitrate. An important characteristics of water salt composition - "salinity" has been considered in the Oceanographic Atlas of the Arctic Ocean (1997, 1998). Presentation of the hydrochemical characteristics in this Hydrochemical Atlas is wider if compared with that of the former Atlas (Gorshkov, 1980). Maps of climatic distribution of the hydrochemical elements were constructed for all the standard depths, and seasonal variability of the hydrochemical parameters is given not only for the surface, but also for the underlying standard depths up to 400 m and including. Statistical characteristics of the hydrochemical elements are given for the first time. Detailed accuracy estimates of initial data and map construction are also given in the Atlas. Calculated values of mean-root deviations, maximum and minimum values of the parameters demonstrate limits of their variability for the analyzed period of observations. Therefore, not only investigations of chemical statics are summarized in the Atlas, but also some elements of chemical dynamics are demonstrated. Digital arrays of the hydrochemical elements obtained in nodes of a regular grid are the new form of characteristics presentation in the Atlas. It should be mentioned that the same grid and the same boxes were used in the Atlas, as those that had been used by creation of the US-Russian climatic Oceanographic Atlas. It allows to combine hydrochemical and oceanographic information of these Atlases. The first block of the digital arrays contains climatic characteristics calculated using direct observational data. These climatic characteristics were not calculated in the regions without observations, and the information arrays for these regions have gaps. The other block of climatic information in a gridded form was obtained with the help of objective analysis of observational data. Procedure of the objective analysis allowed us to obtain climatic estimates of the hydrochemical characteristics for the whole water area of the Arctic Ocean including the regions not covered by observations. Data of the objective analysis can be widely used, in particular, in hydrobiological investigations and in modeling of hydrochemical conditions of the Arctic Ocean. Array of initial measurements is a separate block. It includes all the available materials of hydrochemical observations in the form, as they were presented in different sources. While keeping in mind that this array contains some amount of perverted information, the authors of the Atlas assumed it necessary to store this information in its primary form. Methods of data quality control can be developed in future in the process of hydrochemical information accumulation. It can be supposed that attitude can vary in future to the data that were rejected according to the procedure accepted in the Atlas. The hydrochemical Atlas of the Arctic Ocean is the first specialized and electronic generalization of hydrochemical observations in the Arctic Ocean and finishes the program of joint efforts of Russian and US specialists in preparation of a number of atlases for the Arctic. The published Oceanographic Atlas (1997, 1998), Atlas of Arctic Meteorology and Climate (2000), Ice Atlas of the Arctic Ocean prepared for publication and Hydrochemical Atlas of the Arctic Ocean represent a united series of fundamental generalizations of empirical knowledge of Arctic Ocean nature at climatic level. The Hydrochemical Atlas of the Arctic Ocean was elaborated in the result of joint efforts of the SRC of the RF AARI and IARC. Dr. Ye. Nikiforov was scientific supervisor of the Atlas, Dr. R. Colony was manager on behalf of the USA and Dr. L. Timokhov - on behalf of Russia.