1. PointCloudXplore 2: Overview

PointCloudXplore (PCX) is a visualization tool to allow exploration of 3D and temporal gene expression data in PointCloud and VirtualEmbryo files. PCX is based on two simple but powerful basic principles. Multiple views allow the data to be viewed from different perspectives without being overwhelmed by the high dimensionality of the data. Each view emphasizes different data properties and the interplay between all views makes detailed data analysis possible. The second basic principle is called Brushing & Linking. Brushing refers to the fact that the user can select parts of the data according different data properties in all views. Selected data parts (i.e. the brush) are then highlighted visually in all data displays. In this way all views are linked together. Linking simply means that it is possible to identify visually which parts of one data display correspond to that of another one.

PCX displays data about gene expression in a series of different data views. These data views can be divided into two major classes. Physical Views and Abstract Views. Physical Views show the spatial relationships between different genes' expression patterns within the embryo. Abstract Views use a variety of ways to show the quantitative relationships between multiple genes expression in one or all cells of the embryo. The physical views are 3D view, orthogonal view, and unrolled view. The Abstract Views are 2D/3D scatter plots , 2D/3D parallel coordinates,  and the cell magnifier.

All Physical Views reside within one window, that by default is initially displayed on the left. Tabs on the window allow quick swapping between the different modes. Abstract Views reside within the second major PCX window, that by default is initially displayed on the right. The different Abstract Views are also selected by tabs. This second window also contains a tab with the Gene Selection Panel. This panel is used to select which genes' expression is to be displayed in the Physical Views as well to define gene expression surfaces . Additional control panels are used e.g. for the managment of brushes also refered to as Cell Selectors.