AFM/CLSM data visualization and comparison using an open-source toolkit.

There is a vast difference in the traditional presentation of AFM data and confocal data. AFM data are presented as surface contours while confocal data are usually visualized using either surface- or volume-rendering techniques. Finding a common meaningful visualization platform is not an easy task. AFM and CLSM technologies are complementary and are more frequently being used to image common biological systems. In order to provide a presentation method that would assist us in evaluating cellular morphology, we propose a simple visualization strategy that is comparative, intuitive, and operates within an open-source environment of ImageJ, SurfaceJ, and VolumeJ applications. In order to find some common ground for AFM-CLSM image comparison, we have developed a plug-in for ImageJ, which allows us to import proprietary image data sets into this application. We propose to represent both AFM and CLSM image data sets as shaded elevation maps with color-coded height. This simple technique utilizes the open source VolumeJ and SurfaceJ plug-ins. To provide an example of this visualization technique, we evaluated the three-dimensional architecture of living chick dorsal root ganglia and sympathetic ganglia measured independently with AFM and CLSM. Copyright 2004 Wiley-Liss, Inc.