IsoSurf v1.5d Documentation

Program overview

The input data is first read, then thresholded at a user-defined value, resulting in a set of binary cross-sections. These cross-sections can optionally be filtered using a morphological opening and/or closing with a disc size appropriate to the sampling resolution. This operation ensures that the contours do not contain features which are smaller than the sampling resolution. If no morphological filtering is used, the original data values are used to define the location of the cross-section in each slice more accurately - this can result in smoother surfaces at very high resolution.

Having done this, each cross-section is transformed such that pixels in the image represent the minimum distance to the contour in that image (discussed further in a technical report). This improves both the interpolation of the surface and the smoothness of the surface display.

Surface triangulation is performed at a user-defined resolution, using regularised marching tetrahedra (described in a technical report). If this resolution is greater than the inter-plane spacing (the z resolution), then additional planes are interpolated using disc-guided interpolation (described in another technical report). For faster though less realistic results, shape-based interpolation can optionally be used instead of the previous technique. Obviously higher resolutions will lead to greater surface detail, but also greater numbers of triangles - and therefore longer processing times for visualisation.

The filtered cross-sections are also extracted and saved to a file as vectors which can be displayed in 3-D - this can be helpful in defining a sensible threshold for the input data.

As an extremely rough guide, triangles can be generated at about 4000 per second on typical modern hardware - plus several seconds for pre-processing (more if a very large filter is required due to a very low sampling resolution). This drops to 1000 or less triangles per second if the cross-sections also require interpolation - in this case the processing time is dependent on the complexity of the input data.