D-CAT: Density and Clustering Annotation Tool for three dimensional electron microscopic volumes

M N Lebbink; L H P Hekking; W J C Geerts; J A Post

doi:10.1016/j.jsb.2011.11.030

D-CAT: Density and Clustering Annotation Tool for three dimensional electron microscopic volumes

J Struct Biol. 2012 Feb;177(2):571-7. doi: 10.1016/j.jsb.2011.11.030. Epub 2011 Dec 7.

Authors

M N Lebbink¹, L H P Hekking, W J C Geerts, J A Post

Affiliation

¹ Biomolecular Imaging, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

PMID: 22173221
DOI: 10.1016/j.jsb.2011.11.030

Abstract

Three dimensional (3D) electron microscopy techniques have become valuable tools for investigating cellular architecture and the processes that govern it. A vast amount of information is available in every 3D tomogram but the options for presenting this information in a clear and visually appealing way are limited. To address this, we developed D-CAT; a MatLab-application to accurately visualize the distribution of membrane proteins and/or membrane-bound structures. Presence (density) and distribution (clustering, depletion) are presented as color-coded areas on membranes. By using IMOD models both as input and output format, we ensure that the application fits within workflows common in the field of 3D electron microscopy.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Membrane / ultrastructure
Cluster Analysis
Computer Simulation
Data Interpretation, Statistical
Dendritic Cells / ultrastructure
Electron Microscope Tomography / methods*
Humans
Imaging, Three-Dimensional
Membrane Proteins / ultrastructure
Software*

Substances

Membrane Proteins