Image Processing Software for 3D Light Microscopy

these microscopes to be used to study a wide range of physiological parameters in fi xed and living cells, tissue sections, and even live animals [1–4]. But it is the avail-ability of 3D image analysis software which runs on low-cost personal computers that makes 3D and 4D image-based research practical. This review examines some of the software tools and techniques that are available to process, analyze, and display these images. Most 3D imaging software can be divided into fi ve functional modules: image acquisition, processing, ren-dering, segmentation, and measurement ( fi g. 1). The soft-ware will include one or more of these functional mod-ules. Commercial software often consists of a base pro-gram, with additional modules that can be purchased as needed. Some programs can be customized by the user to perform additional tasks. Image Acquisition Image acquisition programs, which control micro-scopes and associated imaging hardware, are used to col-lect and store stacks of parallel planar (2D) images in fi les. These 3D fi les are then passed to other programs to be processed, displayed, and analyzed. Unfortunately, there is no standard fi le format for 3D images, so some micro-scope manufacturers have created their own formats, while others use TIFF or variants of TIFF. Key Word