No cost but high performance–An alternative open source solution for 3D‐visualizations in morphology. Issue 2 (3rd November 2022)

• Record Type: Journal Article
• Authors: Kalke, Paul; Helm, Conrad
• Is Part Of: Microscopy research and technique. Volume 86:Issue 2(2023)
• Page Start: 193
• Page End: 197
• Publication Date: 2022-11-03
• Subjects: Amira -- blender -- ImageJ -- MeshLab -- step‐by‐step guide -- workflow; Electron microscopy -- Technique -- Periodicals; Microscopy -- Periodicals; Microscopy -- Technique -- Periodicals; 502.825
• DOI: 10.1002/jemt.24250
• Languages: English
• ISSNs: 1059-910X

Abstract

Abstract: 3D‐visualization has become common courtesy in science and also found its way into teaching in schools and universities. Nevertheless, the way to high performance 3D‐visualization and analyses remains difficult and is often also a matter of budget. Due to the obvious advantages of presenting morphological and anatomical datasets with the help of 3D‐figures, all in one software solutions usually come along with high rental and maintenance fees. For that reason, it is more than overdue to establish and use open source software solutions with all their obvious advantages ‐ as other disciplines already do. Here we provide a modular, highly adaptive and freely available software pipeline for high performance 3D‐visualizations of (not only) morphological datasets by combining features of ImageJ, MeshLab and Blender, without any additional costs. Exemplarily using serial‐block face SEM data as well as serial AZAN‐stained histological sections, the herein presented step‐by‐step protocol allows for a fast and efficient analysis, visualization and animation of large, anatomical datasets. Regardless which type of serial, morphological datasets needs to be analyzed, our open source guide provides an easy to handle and promptly adaptable solution. Therefore, our pipeline for 3D‐visualization represents a valuable alternative to conventional, commercial packages. Research Highlights: We provide a highly modular and easy to learn open source solution for multiple 3D‐visualizations. The step‐by‐step‐guide make it easy to start, and advanced users can replace software, add others and such build your own individual software pipeline. Abstract : Summary of our modular open source solution for high performance 3D‐visualization.