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Open Access Methodology article

A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy

Patrick Happel12*, Kerstin Möller23, Ralf Kunz1 and Irmgard D Dietzel2

Author Affiliations

1 Central Unit for Ionbeams and Radionuclides (RUBION), Ruhr University of Bochum, D-44780 Bochum, Germany

2 Department of Molecular Neurobiochemistry, Ruhr University of Bochum, D-44780 Bochum, Germany

3 Department of Cardiovascular Physiology, University of Heidelberg, Heidelberg, Germany

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BMC Bioinformatics 2010, 11:323  doi:10.1186/1471-2105-11-323

Published: 15 June 2010



Cell volume determination plays a pivotal role in the investigation of the biophysical mechanisms underlying various cellular processes. Whereas light microscopy in principle enables one to obtain three dimensional data, the reconstruction of cell volume from z-stacks is a time consuming procedure. Thus, three dimensional topographic representations of cells are easier to obtain by scanning probe microscopical measurements.


We present a method of separating the cell soma volume of bipolar cells in adherent cell cultures from the contributions of the cell processes from data obtained by scanning ion conductance microscopy. Soma volume changes between successive scans obtained from the same cell can then be computed even if the cell is changing its position within the observed area. We demonstrate that the estimation of the cell volume on the basis of the width and the length of a cell may lead to erroneous determination of cell volume changes.


We provide a new algorithm to repeatedly determine single cell soma volume and thus to quantify cell volume changes during cell movements occuring over a time range of hours.