Complex Biosystems Inc.

xScheme Viewer

Graphic objects supported by ViewPort viewer. Ordered by complexity, 2D; two-dimensional object, 3D: three-dimensional object, Surface: when referring to graphic object displayed on a surface, e.g. curves or symbols on a surface.

Graphic objects	Description
Symbols	Circles, squares, diamonds, cross, ...etc. in 2D and 3D
Curves	Single or array of curves displayed with different patterns in 2D or 3D
Histograms	One axis histogram
Vector fields	Layout in 2D, 3D, or on surfaces
Stream lines	Patterns as used in fluid dynamics. Support 2D, 3D or on surfaces
Images	Displayed as tiles, stack of images, or stack of images on planes perpendicular to arbitrary axes. Multiple stacks can be displayed at the same time
Surface models	Arrays of triangles, quadrilaterals, or polygons, including material properties, and texture, displayed in a scene where lighting is controled by the user
Meshes	2D: triangular and quadrilaterals. 3D: tetrahedral and hexahedral. Surface: triangular or quadrilateral
Volume rendering	Light reflected/transmitted by volume data (like a gas) to which material properties been assigned. Algorithms are based on overlaid textures or ray tracing methods. Data can be displayed on planes positioned along excursion axes
Field data	Scalar: color coded field on a surface model. Vector: vector field on a surface model. Both can be combined

Screenshot of one of an application designed with our viewer. This application is used in heart model reconstruction.

The Figure on the right is a screenshot of an application designed with our viewer. The application is used in heart model reconstruction. The left winow shows the basic layout of the viewer with control buttons. The two graphic windows are two panoramas included in this particular application. The one in the background display a sequence of images collected with an electro scanning microscope. The panorama on the right shows the same slices stacked at spatial locations where they were collected.

Operations like edge dected are performed on the slices and they results are mapped on the stacke. This data is subsequently used to fit parametric surfaces (shown in dark and light blue) to the contour data. All the underlying operations are performed interactively. The resulting surfaces are used to mesh the heart and model electric conduction.

Basic processes included with the viewer. Note that stack of images differs from volume data in the sense that operations are performed slices by slices in a stack, and in 3D for volume data.

Processes	Description
	image, stack of images, or volume data
Contrast enhancement	Application of gradient operator to enhance contrast
Segmentation	Class data according to their texture properties
Edge detection	Automatic: contour extraction with the sobel algorithm. Assisted: Contour extraction based on active controus algorithms. Applies only to images and stack of images.
Convolution	Convolve an image with a pre-determined pattern. Applies only to images and stack of images.
Filtering	Fourier transform based filtering. Applies only to images and stack of images.
Gradient	Extract 2D intensity gradient vectors
Mask	Apply local operations based on weights in a mask
Surface extraction	Extract triangulated surface crossing a pre-determined gray level. Based on a modified marching cube algorithm. Applies only to volume data.
	Surface models
Contour	Extract contours based on elements connectivity
Length	Calculate contour length by summing segments length
Area	Calculate area by summing elementary polygonal areas
	Vector fields in 2D, 3D, or on surfaces.
Divergence	Calculate the divergence of a vector field and color code the result
Rotational	Calculate the rotational of a vector field and color code the result
Trajectories	Track the trajectories of a set of initial points displaced along a path tangent to the vector field
	Mesh, 2D, 3D, or surfaces
Structure	Display mesh edges in a domain with elements surface redenred in a manner to visualize the mesh structure
Jacobian	Calculate the Jacobian of each mesh element and color code the result
Area/Volume	Calculate elementary area/volume of mesh elements and color code the information
Orthogonality	For quadrilateral and hexahedral meshes metric on mesh orthogonality and color code the infrmation
Property	Detect mesh elements not meeting some cirteria, e.g. Jacobian, rate of spatial change in area/volume.

A panorama illustrating some of the multiple graphic objects supported by the viewer and how they can be combined in a scene.

The above panorama is a close up on the image stack and surfaces fitted to the border of the slices. It is a step in the reconstruction of a heart model. In this case were are interested to reconstruct a detailed geometry, and to see simulatneously cardiac fiber orientation and to do so in convoluted regions of the heart geometry.

Here a geometric reconstruction based on the frontiers delineated from the slices, and also based on CT slices (data not shown) allow the operator to inspect this geometry. The epicradium (dark blue) and left ventricle (light blue) are displayed as surface models. The left ventricle is semi-transparent in order to see the fiber structure.

cross sections of the heart stained for myofibrils and imaged at different height with a laser scanning confocal microscope are show in green. The slices are displayed as textures in 3D. The image intensity moulates the texture. The operator can follow how fiber orientation changes across the heart and can do so ine relation to specific features of the geometry.

Since our viewer support all viewing modalities required by this task, an application like this one can be readily created with the builder