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

Personal	Projects	Publications	Teaching

2019

Journal

Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation doi>

M. Jordão, R. Sankowski, S. Brendecke, S. Sagar, G. Locatelli, Y. Tai, T. Tay, E. Schramm, S. Armbruster, N. Hagemeyer, O. Groß, Dominic Mai, Özgün Çiçek, Thorsten Falk, M. Kerschensteiner, D. Grün, M. Prinz

Science, 363(6425): eaat7554, Jan 2019

U-Net – Deep Learning for Cell Counting, Detection, and Morphometry Paper

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, 2019

Conference

ISOO_DL^V2 - Semantic Instance Segmentation of Touching and Overlapping Objects Paper

doi>

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 Paper

paper-ISBI18_ISOO_final_030118_IEEE_CR.pdf

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 Paper

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 Paper

Schmidt2013VariationalAttenuationCorrectionInTwo-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) Paper

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 Paper

CoupledBSplinesForPointCloudAxisFitting.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 Paper

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 Paper

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

Robust Identification of Locally Planar Objects Represented by 2D Point Clouds under Affine Distortions Paper

Dominic Mai, Thorsten Schmidt, Hans Burkhardt

Pattern Recognition (Proc. DAGM), Springer, LNCS: 91--100, 2010

3D Object Detection Using a Fast Voxel-Wise Local Spherical Fourier Tensor Transformation Paper

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

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 Paper

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

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

Thorsten Schmidt

Albert-Ludwigs-Universität Freiburg, 2005