Soft Part 3D visualization by serial sectioning and computer reconstruction

Abstract

Recent increases in performance of personal computer hard- and software enabled a variety of 3D graphical applications, such as surface visualizations of biological specimens. This indirectly recalled an old morphological method back to life, the investigation of soft part anatomy by light microscopical serial section analysis. A practical guide covering all procession steps beginning with anesthetization leading to the fi nal goal, 3D visualization of specimens, is provided. Most useful for 3D procession—of particularly small specimens—are ribbon-forming serial resin (= “semithin”) sections. A reliable method for achievement of ribbon formation is described in detail for the fi rst time. Contact cement is applied only to the cutting surface of the block, which represents a modifi cation of an old protocol. Details on the materials and tools, such as embedding media (epoxy resins) and knives (Ralph glass or special diamond knife) used and general handling for the entire procedure are given and critically evaluated. 3D procession is explained for the software AMIRA®. The major processing steps, from section image capturing until refi ning of surfaces, are explained. Based on the experience of the author, practical aids that cannot be found in the user’s guide of the software or elsewhere for facilitating the process are given. These include preliminary calculation of resolution, calibration and strategies for facilitating the process and improvement of results. The interpolate function is emphasized as most useful for completion of segmentation and also correction works. Visualization examples are followed by an estimate of work expenditure for graphical processes involved