Image analysis and computational methods

Understanding plant development requires extracting quantitative information from imaging data. This project develops and applies computational methods for plant image analysis, including cellular-resolution reconstruction of organs such as the root apical meristem, rotation-invariant image descriptors and correction of signal attenuation in confocal microscopy, providing the quantitative basis for studying growth and morphogenesis.

This work is part of the root system architecture project.

Thomas Blein, Jasmin Duerr, Taras Pasternak, Thomas Haser, Thorsten Falk, Kun Liu, Franck A. Ditengou, Olaf Ronneberger, Klaus Palme
bioRxiv, January 2018
Light dynamically regulates growth rate and cellular organisation of the Arabidopsis root meristem
Kun Liu, Henrik Skibbe, Thorsten Schmidt, Thomas Blein, Klaus Palme, Thomas Brox, Olaf Ronneberger
International Journal of Computer Vision, Volume 106, Issue 3, June 2014, 342--364
DOI
Rotation-invariant HOG descriptors using Fourier analysis in polar and spherical coordinates
Thorsten Schmidt, Taras Pasternak, Kun Liu, Thomas Blein, Dorothée Aubry-Hivet, Alexander Dovzhenko, Jasmin Duerr, William Teale, Franck A. Ditengou, Hans Burkhardt, Olaf Ronneberger, Klaus Palme
The Plant journal : for cell and molecular biology, Volume 77, Issue 5, March 2014, 806—814
The iRoCS Toolbox--3D analysis of the plant root apical meristem at cellular resolution
Thorsten Schmidt, Jasmin Dürr, Margret Keuper, Thomas Blein, Klaus Palme, Olaf Ronneberger
BMC bioinformatics, Volume 14, December 2013, 366