CeLaVi: an interactive cell lineage visualization tool

Recent innovations in genetics and imaging are providing the means to reconstruct cell lineages, either by tracking cell divisions using live microscopy, or by deducing the history of cells using molecular recorders. A cell lineage on its own, however, is simply a description of cell divisions as branching events. A major goal of current research is to integrate this description of cell relationships with information about the spatial distribution and identities of the cells those divisions produce. Visualizing, interpreting and exploring these complex data in an intuitive manner requires the development of new tools. Here we present CeLaVi, a web-based visualization tool that allows users to navigate and interact with a representation of cell lineages, whilst simultaneously visualizing the spatial distribution, identities and properties of cells. CeLaVi's principal functions include the ability to explore and manipulate the cell lineage tree; to visualise the spatial distribution of cell clones at different depths of the tree; to colour cells in the 3D viewer based on lineage relationships; to visualise various cell qualities on the 3D viewer (e.g. gene expression, cell type) and to annotate selected cells/clones. All these capabilities are demonstrated with four different example data sets. CeLaVi is available at http://www.celavi.pro

Voronoi diagrams as a visualization technique for spatial autocorrelation in point data sets

This thesis explores a new way of visualizing spatial autocorrelation in a GIS environment. It explores some relationships between spatial autocorrelation models, spatial interaction models and weighted Voronoi diagrams. Since the weighted Voronoi diagram is equivalent to a form of spatial interaction models, any GIS with the ability to generate a gravity model can be utilized to perform this new technique of exploratory spatial data analysis. This thesis demonstrates how the cross product form of‘ spatial autocorrelation models like the Geary and the Moran statistics is equivalent to the form of a multiplicatively weighted distance utilized in the definition of weighted Voronoi diagrams. A transformation of the multiplicatively weighted distance into a representation of the Geary or the Moran statistic can be used to generate different weighted Voronoi diagrams. Since such a representation incorporates the spatial variation of data points and the spatial variation of the attribute values assigned to the data points, it provides a more appropriate visual representation than do existing representations that only operate on the spatial distribution of the data points. Data sets with a known degree of spatial autocorrelation are created with a simultaneous autoregressive model. The behaviour of the visual representations of the Geary and the Moran statistics for spatial autocorrelation varying from a high positive to a high negative degree is examined

Visualizing the dynamics of London's bicycle hire scheme

Visualizing flows between origins and destinations can be straightforward when dealing with small numbers of journeys or simple geographies. Representing flows as lines embedded in geographic space has commonly been used to map transport flows, especially when geographic patterns are important as they are when characterising cities or managing transportation. However, for larger numbers of flows, this approach requires careful design to avoid problems of occlusion, salience bias and information overload. Driven by the requirements identified by users and managers of the London Bicycle Hire scheme we present three methods of representation of bicycle hire use and travel patterns. Flow maps with curved flow symbols are used to show overviews in flow structures. Gridded views of docking station location that preserve geographic relationships are used to explore docking station status over space and time in a graphically efficient manner. Origin-Destination maps that visualise the OD matrix directly while maintaining geographic context are used to provide visual details on demand. We use these approaches to identify changes in travel behaviour over space and time, to aid station rebalancing and to provide a framework for incorporating travel modelling and simulation

The State-of-the-Art of Set Visualization

Sets comprise a generic data model that has been used in a variety of data analysis problems. Such problems involve analysing and visualizing set relations between multiple sets defined over the same collection of elements. However, visualizing sets is a non-trivial problem due to the large number of possible relations between them. We provide a systematic overview of state-of-the-art techniques for visualizing different kinds of set relations. We classify these techniques into six main categories according to the visual representations they use and the tasks they support. We compare the categories to provide guidance for choosing an appropriate technique for a given problem. Finally, we identify challenges in this area that need further research and propose possible directions to address these challenges. Further resources on set visualization are available at http://www.setviz.net

Stacking-based visualization of trajectory attribute data

Visualizing trajectory attribute data is challenging because it involves showing the trajectories in their spatio-temporal context as well as the attribute values associated with the individual points of trajectories. Previous work on trajectory visualization addresses selected aspects of this problem, but not all of them. We present a novel approach to visualizing trajectory attribute data. Our solution covers space, time, and attribute values. Based on an analysis of relevant visualization tasks, we designed the visualization solution around the principle of stacking trajectory bands. The core of our approach is a hybrid 2D/3D display. A 2D map serves as a reference for the spatial context, and the trajectories are visualized as stacked 3D trajectory bands along which attribute values are encoded by color. Time is integrated through appropriate ordering of bands and through a dynamic query mechanism that feeds temporally aggregated information to a circular time display. An additional 2D time graph shows temporal information in full detail by stacking 2D trajectory bands. Our solution is equipped with analytical and interactive mechanisms for selecting and ordering of trajectories, and adjusting the color mapping, as well as coordinated highlighting and dedicated 3D navigation. We demonstrate the usefulness of our novel visualization by three examples related to radiation surveillance, traffic analysis, and maritime navigation. User feedback obtained in a small experiment indicates that our hybrid 2D/3D solution can be operated quite well

Interactive tag maps and tag clouds for the multiscale exploration of large spatio-temporal datasets

'Tag clouds' and 'tag maps' are introduced to represent geographically referenced text. In combination, these aspatial and spatial views are used to explore a large structured spatio-temporal data set by providing overviews and filtering by text and geography. Prototypes are implemented using freely available technologies including Google Earth and Yahoo! 's Tag Map applet. The interactive tag map and tag cloud techniques and the rapid prototyping method used are informally evaluated through successes and limitations encountered. Preliminary evaluation suggests that the techniques may be useful for generating insights when visualizing large data sets containing geo-referenced text strings. The rapid prototyping approach enabled the technique to be developed and evaluated, leading to geovisualization through which a number of ideas were generated. Limitations of this approach are reflected upon. Tag placement, generalisation and prominence at different scales are issues which have come to light in this study that warrant further work