Visualisation of confocal microscope data

Written by Paul Bourke
March 2000

Confocal microscope data from Swinburne University
School of Biophysical Sciences and Electrical Engineering.


The following documents a visualisation exercise, namely to interactively explore 3D voxel based data from a confocal microscope. The software that came with the microscope provided the ability to view semi transparent rendered images but their generation was slow and the depth cues weren't strong. The goal then was to create interactive 3D models and present them in an existing 3D stereo pair projection environment.


The following illustrates the images as they are saved from the confocal microscope software. It saves a multilayer, 16bit tiff file. Selected slices from that file are presented below for the dataset being demonstrated here. The original images are 512 pixels square while the examples below are presented at 200 pixels square. The original file consisted of 18 layers, as is typical of this sort of acquisition the sampling in one direction (18) is much less than the sampling in the other directions (512).

Subsampling voxel space

The first stage in processing the images was to subsample in the image plane by a factor of 8. It turns out that in this application the in-plane dimensions are greatly oversampled and a factor of 8 is not unreasonable to smooth out the noise in the in-plane data. It also conveniently brings the voxel cube into more appropriate/manageable dimensions of 64x64x18.

Marching cubes

The marching cubes algorithm is applied to the voxel space to derive isocontour levels. Two examples are shown below, in the left example the resulting triangular facets are shown in wire frame. In the right hand image is the same data and view shown as a shaded model. The normal at each vertex is derived by averaging the normals of the faces that share the vertex.

Isolevel: 200

Isolevel: 200

The noise that one sees in the top right image makes the 2D views very hard to interpret but it adds a visually powerful 3D stereo effect and even makes the geometry of the rest of the structure clearer. These models have around 15,000 triangular facets, at this level they can easily be rotated interactively (around 20 frames per second) by the low performance end of the OpenGL card market.

Multiple isosurfaces

The following image on the right shows multiple isolevel surfaces each made semi transparent. While the structure isn't so clear from this image, it is very clear when it can be interactively inspected in stereo (the extra contour levels only added another 10,1000 facets to the model).

Isolevel: 200

Isolevel: 120,160,200