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Thorsten Falk

PhD

3D Image Analysis Lab
Department of Computer Science
University of Freiburg
Germany


Contact:
Georges-Köhler-Allee, building 052, 2nd floor, room 01-42
79110 Freiburg

Phone: +49 761 203 8274
E-Mail: falk AT cs.uni-freiburg


Thorsten Falk
Personal Projects Publications Teaching
2019
Journal
U-Net – Deep Learning for Cell Counting, Detection, and Morphometry   Paperpaper-U-Net.pdf doi> Project
Thorsten Falk, Dominic Mai, Robert Bensch, Özgün Çiçek, Ahmed Abdulkadir, Yassine Marrakchi, Anton Böhm, J. Deubner, Z. Jäckel, K. Seiwald, A. Dovzhenko, O. Tietz, C. Dal Bosco, S. Walsh, D. Saltukoglu, T. Tay, M. Prinz, K. Palme, M. Simons, I. Diester, Thomas Brox, Olaf Ronneberger
Nature Methods, 16: 67--70, Jan 2019

Conference
ISOO_DL^V2 - Semantic Instance Segmentation of Touching and Overlapping Objects   Paperpaper.pdf
Anton Böhm, Maxim Tatarchenko, Thorsten Falk
IEEE International Symposium on Biomedical Imaging (ISBI), 2019
 
2018

Conference
ISOO_DL: Instance segmentation of overlapping biological objects using deep learning   doi>
Anton Böhm, A. Ücker, T. Jäger, Olaf Ronneberger, Thorsten Falk
15th International Symposium on Biomedical Imaging (ISBI), IEEE: 1225--1229, 2018
 
2017
Journal
A 3D digital atlas of the Nicotiana tabacum root tip and its use to investigate changes in the root apical meristem induced by the Agrobacterium 6b oncogene   doi>
T. Pasternak, T. Haser, Thorsten Falk, Olaf Ronneberger, K. Palme, L. Otten
The Plant Journal, 92(1): 31--42, Aug 2017
 
2016

Others
From voxels to models: towards quantification in 3-D confocal microscopy   PaperDissertation_ThorstenFalk_2016.pdf doi>
Thorsten Falk
PhD thesis from Albert-Ludwigs-Universität Freiburg, 2016

2014
Journal
The iRoCS Toolbox – 3D Analysis of the Plant Root Apical Meristem at Cellular Resolution   doi> Code/data
Thorsten Schmidt, T. Pasternak, Kun Liu, T. Blein, D. Aubry-Hivet, A. Dovzhenko, J. Dürr, W. Teale, F. Ditengou, Hans Burkhardt, Olaf Ronneberger, K. Palme
The Plant Journal, 77(5): 806--814, Mar 2014
Rotation-Invariant HOG Descriptors using Fourier Analysis in Polar and Spherical Coordinates   doi> Code/data
Kun Liu, Henrik Skibbe, Thorsten Schmidt, T. Blein, K. Palme, Thomas Brox, Olaf Ronneberger
International Journal of Computer Vision, 106(3): 342-364, 2014
 
2013
Journal
Variational attenuation correction in two-view confocal microscopy   PaperSchmidt2013VariationalAttenuationCorrectionInTwo-ViewConfocalMicroscopy.pdf doi>
Thorsten Schmidt, J. Dürr, Margret Keuper, T. Blein, K. Palme, Olaf Ronneberger
BMC Bioinformatics, 14(1): 366, Dec 2013

Conference
Joint 3D Cell Segmentation and Classification in the Arabidopsis Root using Energy Minimization and Shape Priors   doi>
Kun Liu, Thorsten Schmidt, T. Blein, J. Dürr, K. Palme, Olaf Ronneberger
IEEE International Symposium on Biomedical Imaging (ISBI): 422--425, 2013
Blind deconvolution of widefield fluorescence microscopic data by regularization of the optical transfer function (OTF)   Paperdeconv.pdf
Margret Keuper, Thorsten Schmidt, Maja Temerinac-Ott, J. Padeken, P. Heun, Olaf Ronneberger, Thomas Brox
IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2013
Variational Attenuation Correction of Two-View Confocal Microscopic Recordings   doi>
Thorsten Schmidt, J. Dürr, Margret Keuper, T. Blein, K. Palme, Olaf Ronneberger
IEEE 10th International Symposium on Biomedical Imaging (ISBI): 169--172, 2013
 
2012
Journal
ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brains   doi>
Olaf Ronneberger, Kun Liu, M. Rath, D. Rueß, T. Mueller, Henrik Skibbe, Benjamin Drayer, Thorsten Schmidt, A. Filippi, R. Nitschke, Thomas Brox, Hans Burkhardt, W. Driever
Nature Methods, 9(7): 735-742, 2012
Fast rotation invariant 3D feature computation utilizing efficient local neighborhood operators   doi> Code/data
Henrik Skibbe, M. Reisert, Thorsten Schmidt, Thomas Brox, Olaf Ronneberger, Hans Burkhardt
IEEE Transactions on Pattern Analysis and Machine Intelligence, 34(8): 1563 - 1575 , 2012

Conference
Modeling of Sparsely Sampled Tubular Surfaces Using Coupled Curves   PaperCoupledBSplinesForPointCloudAxisFitting.pdf
Thorsten Schmidt, Margret Keuper, T. Pasternak, K. Palme, Olaf Ronneberger
Pattern Recognition (Proc. DAGM), Springer, LNCS, Vol.7476: 83--92, 2012
 
2011

Conference
Hierarchical Markov Random Fields for Mast Cell Segmentation in Electron Microscopic Recordings   PaperMastCells_paper.pdf
Margret Keuper, Thorsten Schmidt, M. Rodriguez-Franco, W. Schamel, Thomas Brox, Hans Burkhardt, Olaf Ronneberger
IEEE International Symposium on Biomedical Imaging (ISBI): 973 - 978, 2011
3D Rotation-Invariant Description from Tensor Operation on Spherical HOG Field   PaperBMVC2011_79_final.pdf doi>
Kun Liu, Henrik Skibbe, Thorsten Schmidt, T. Blein, K. Palme, Olaf Ronneberger
British Machine Vision Conference (BMVC), Aug 2011
 
2010
Journal
Inversin relays Frizzled-8 signals to promote proximal pronephros development   doi>
S. Lienkamp, A. Ganner, C. Boehlke, Thorsten Schmidt, S. Arnold, T. Schäfer, D. Romaker, J. Schuler, S. Hoff, C. Powelske, A. Eifler, C. Krönig, A. Bullerkotte, R. Nitschke, E. Kuehn, E. Kim, Hans Burkhardt, Thomas Brox, Olaf Ronneberger, J. Gloy, G. Walz
Proceedings of the National Academy of Sciences, 107(47): 20388-20393, 2010

Conference
3D Object Detection Using a Fast Voxel-Wise Local Spherical Fourier Tensor Transformation   Paper2010_Skibbe_DAGM.pdf doi>
H. Skibbe, M. Reisert, Thorsten Schmidt, K. Palme, Olaf Ronneberger, Hans Burkhardt
Pattern Recognition (Proc. DAGM), Springer Berlin / Heidelberg, LNCS, Vol.6376: 412-421, 2010
Robust Identification of Locally Planar Objects Represented by 2D Point Clouds under Affine Distortions   PaperDAGM2010.pdf
Dominic Mai, Thorsten Schmidt, Hans Burkhardt
Pattern Recognition (Proc. DAGM), Springer, LNCS: 91--100, 2010
3D Deformable Surfaces with Locally Self-Adjusting Parameters - A Robust Method to Determine Cell Nucleus Shapes  
Margret Keuper, Thorsten Schmidt, J. Padeken, P. Heun, K. Palme, Hans Burkhardt, Olaf Ronneberger
IEEE International Conference on Pattern Recognition (ICPR): 2254-2257, 2010
 
2008

Conference
Invariance via Group-Integration: A Feature Framework for 3D Biomedical Image Analysis  
J. Fehr, Olaf Ronneberger, J. Schulz, Thorsten Schmidt, M. Reisert, Hans Burkhardt
Proceedings of Computer Graphics and Imaging (CGIM): 276--285, 2008
 
2006

Conference
Fast Scalar and Vectorial Grayscale Based Invariant Features for 3D Cell Nuclei Localization and Classification   Paperschulz_dagm06.pdf doi>
J. Schulz, Thorsten Schmidt, Olaf Ronneberger, Hans Burkhardt, T. Pasternak, A. Dovzhenko, K. Palme
Pattern Recognition (Proc. DAGM), Springer, Vol.4174/2006: 182--191, 2006



Diploma thesis
Automatische Selektion von optimalen Kernfunktionen für Grauwertbasierte Invarianten   kernelselect.pdf
Thorsten Schmidt
Albert-Ludwigs-Universität Freiburg, 2006
 
Student research project
Entwicklung von Vorverarbeitungsverfahren(Enfaltung, etc.) für fluoreszenzmikroskopische 3D Volumendaten zur Verbesserung der Nachfolgenden Erkennung Mittels Grauwertbasierter Invarianten   deconvolution.pdf
Thorsten Schmidt
Albert-Ludwigs-Universität Freiburg, 2005