19,256 research outputs found
Advanced optical imaging in living embryos
Developmental biology investigations have evolved from static studies of embryo anatomy and into dynamic studies of the genetic and cellular mechanisms responsible for shaping the embryo anatomy. With the advancement of fluorescent protein fusions, the ability to visualize and comprehend how thousands to millions of cells interact with one another to form tissues and organs in three dimensions (xyz) over time (t) is just beginning to be realized and exploited. In this review, we explore recent advances utilizing confocal and multi-photon time-lapse microscopy to capture gene expression, cell behavior, and embryo development. From choosing the appropriate fluorophore, to labeling strategy, to experimental set-up, and data pipeline handling, this review covers the various aspects related to acquiring and analyzing multi-dimensional data sets. These innovative techniques in multi-dimensional imaging and analysis can be applied across a number of fields in time and space including protein dynamics to cell biology to morphogenesis
Multispectral fingerprinting for improved in vivo cell dynamics analysis
Background:
Tracing cell dynamics in the embryo becomes tremendously difficult when cell trajectories cross in space and time and tissue density obscure individual cell borders. Here, we used the chick neural crest (NC) as a model to test multicolor cell labeling and multispectral confocal imaging strategies to overcome these roadblocks.
Results:
We found that multicolor nuclear cell labeling and multispectral imaging led to improved resolution of in vivo NC cell identification by providing a unique spectral identity for each cell. NC cell spectral identity allowed for more accurate cell tracking and was consistent during short term time-lapse imaging sessions. Computer model simulations predicted significantly better object counting for increasing cell densities in 3-color compared to 1-color nuclear cell labeling. To better resolve cell contacts, we show that a combination of 2-color membrane and 1-color nuclear cell labeling dramatically improved the semi-automated analysis of NC cell interactions, yet preserved the ability to track cell movements. We also found channel versus lambda scanning of multicolor labeled embryos significantly reduced the time and effort of image acquisition and analysis of large 3D volume data sets.
Conclusions:
Our results reveal that multicolor cell labeling and multispectral imaging provide a cellular fingerprint that may uniquely determine a cell's position within the embryo. Together, these methods offer a spectral toolbox to resolve in vivo cell dynamics in unprecedented detail
Analyzing library collections with starfield visualizations
This paper presents a qualitative and formative study of the uses of a starfield-based visualization interface for analysis of library collections. The evaluation process has produced feedback that suggests ways to significantly improve starfield interfaces and the interaction process to improve their learnability and usability. The study also gave us clear indication of additional potential uses of starfield visualizations that can be exploited by further functionality and interface development.
We report on resulting implications for the design and use of starfield visualizations that will impact their graphical interface features, their use for managing data quality and their potential for various forms of visual data mining. Although the current implementation and analysis focuses on the collection of a physical library, the most important contributions of our work will be in digital libraries, in which volume, complexity and dynamism of collections are increasing dramatically and tools are needed for visualization and analysis
Chlamydial infection from outside to inside
Chlamydia are obligate intracellular bacteria, characterized by a unique biphasic developmental cycle. Specific interactions with the host cell are crucial for the bacteria's survival and amplification because of the reduced chlamydial genome. At the start of infection, pathogen-host interactions are set in place in order for Chlamydia to enter the host cell and reach the nutrient-rich peri-Golgi region. Once intracellular localization is established, interactions with organelles and pathways of the host cell enable the necessary hijacking of host-derived nutrients. Detailed information on the aforementioned processes will increase our understanding on the intracellular pathogenesis of chlamydiae and hence might lead to new strategies to battle chlamydial infection. This review summarizes how chlamydiae generate their intracellular niche in the host cell, acquire host-derived nutrients in order to enable their growth and finally exit the host cell in order to infect new cells. Moreover, the evolution in the development of molecular genetic tools, necessary for studying the chlamydial infection biology in more depth, is discussed in great detail
Experiences with starfield visualizations for analysis of library collections
This paper presents a qualitative and formative study of the uses of a starfield-based visualization interface for analysis of library collections. The evaluation process has produced feedback that suggests ways to significantly improve starfield interfaces and the interaction process to improve their learnability and usability. The study also gave us clear indication of additional potential uses of starfield visualizations that can be exploited by further functionality and interface development. We report on resulting implications for the design and use of starfield visualizations that will impact their graphical interface features, their use for managing data quality and their potential for various forms of visual data mining. Although the current implementation and analysis focuses on the collection of a physical library, the most important contributions of our work will be in digital libraries, in which volume, complexity and dynamism of collections are increasing dramatically and tools are needed for visualization and analysis
Adaptive foveated single-pixel imaging with dynamic super-sampling
As an alternative to conventional multi-pixel cameras, single-pixel cameras
enable images to be recorded using a single detector that measures the
correlations between the scene and a set of patterns. However, to fully sample
a scene in this way requires at least the same number of correlation
measurements as there are pixels in the reconstructed image. Therefore
single-pixel imaging systems typically exhibit low frame-rates. To mitigate
this, a range of compressive sensing techniques have been developed which rely
on a priori knowledge of the scene to reconstruct images from an under-sampled
set of measurements. In this work we take a different approach and adopt a
strategy inspired by the foveated vision systems found in the animal kingdom -
a framework that exploits the spatio-temporal redundancy present in many
dynamic scenes. In our single-pixel imaging system a high-resolution foveal
region follows motion within the scene, but unlike a simple zoom, every frame
delivers new spatial information from across the entire field-of-view. Using
this approach we demonstrate a four-fold reduction in the time taken to record
the detail of rapidly evolving features, whilst simultaneously accumulating
detail of more slowly evolving regions over several consecutive frames. This
tiered super-sampling technique enables the reconstruction of video streams in
which both the resolution and the effective exposure-time spatially vary and
adapt dynamically in response to the evolution of the scene. The methods
described here can complement existing compressive sensing approaches and may
be applied to enhance a variety of computational imagers that rely on
sequential correlation measurements.Comment: 13 pages, 5 figure
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