ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms

Abstract

Visual understanding is a key aspect when studying electron tomography data-sets, aside quantitative assessments such as registration of high-resolution structures. We here present the free software tool ProViz (Protein Visualization) for visualisation and template matching in electron tomograms of biological samples. The ProViz software contains methods and tools which we have developed, adapted and computationally optimised for easy and intuitive visualisation and analysis of electron tomograms with low signal-to-noise ratio. ProViz complements existing software in the application field and serves as an easy and convenient tool for a first assessment and screening of the tomograms. It provides enhancements in three areas: (1) improved visualisation that makes connections as well as intensity differences between and within objects or structures easier to see and interpret, (2) interactive transfer function editing with direct visual result feedback using both piecewise linear functions and Gaussian function elements, (3) computationally optimised template matching and tools to visually assess and interactively explore the correlation results. The visualisation capabilities and features of ProViz are demonstrated on various biological volume data-sets: bacterial filament structures in vitro, a desmosome and the transmembrane cadherin connections therein in situ, and liposomes filled with doxorubicin in solution. The explorative template matching is demonstrated on a synthetic IgG data-set.

Keywords:

• Electron tomography
• direct volume rendering
• image registration
• connected component filtering
• visualisation and analysis software

Acknowledgements

We thank Daniel Evestedt and Huy Nguyen from SenseGraphics for their project participation and development of the GLSL volume rendering shader. We also thank Prof. Gunilla Borgefors, Prof. Ulf Skoglund, Docent Lars Norlén and Docent Lars-Göran Öfverstedt for valuable input and advice.

Notes

No potential conflict of interest was reported by the authors.

1 Available for download at http://www.cb.uu.se/research/proviz. The software is free and primarily open-source.

Additional information

Funding

This work has partially been done within the ProViz project funded through the Visualization Program by the Knowledge Foundation, Vårdal Foundation, the Foundation for Strategic Research, VINNOVA, and Invest in Sweden Agency.