Markus Rempfler

Former doctoral candidate and scientific staff at the Image-Based Biomedical Modeling Group.

Research Interests

I am interested in developing methods for quantitative analysis of biomedical data at the intersection of fields such as machine learning, computer vision and optimization. My main focus lies on tasks that can be posed as inference of a graph, such as the estimation of vascular networks from image volumes or cell lineage forests from microscopy videos.

Teaching & Student Projects

Feel free to contact me for available projects.

Lectures at TUM:

• Engineering Informatics I - IN8011 WS 2016
• Blockkurs Imagine Neurooncology 2016: Machine Learning for Medical Image Segmentation
• Computational Physiology for Medical Image Computing - IN2319 2016

Code

• Contributor to andres::graph
• Network optimization with integer programming
• Efficient algorithms for moral lineage tracing

Publications

2019
	A. Sekuboyina, M. Rempfler, A. Valentinitsch, M. Loeffler, J. Kirschke, B. Menze Probabilistic Point Cloud Reconstructions for Vertebral Shape Analysis Proceedings of the 22th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Shenzen, China, October 2019. (bib)
2018
	A. Sekuboyina, M. Rempfler, J. Kukacka, G. Tetteh, A. Valentinitsch, J. Kirschke, B. Menze Btrfly Net: Vertebrae Labelling with Energy-based Adversarial Learning of Local Spine Prior Proceedings of the 21th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Granada, Spain, September 2018. (bib)
	M. Rempfler, V. Stierle, , S. Kumar, P. Paulitschke, B. Andres, B. Menze Tracing Cell Lineages in Videos of Lens-free Microscopy Medical Image Analysis Special Issue MICCAI 2017 (bib)
2017
	M. Rempfler, J.-H. Lange, F. Jug, C. Blasse, E. W. Myers, B. Menze, B. Andres Efficient Algorithms for Moral Lineage Tracing International Conference on Computer Vision (ICCV), Venice, Italy, October 2017 (bib)
	M. Rempfler, B. Andres, B. Menze Uncertainty Estimation in Vascular Networks Accepted to Proceedings of the MICCAI workshop on Graphs in Biomedical Image Analysis, Quebec, Canada, September 2017. (bib)
	M. Rempfler, S. Kumar, V. Stierle, P. Paulitschke, B. Andres, B. Menze Cell Lineage Tracing in Lens-free Microscopy Videos Accepted to Proceedings of the 20th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Quebec, Canada, September 2017. (bib)
2016
	M. Rempfler, B. Andres, B. Menze The minimum cost connected subgraph problem in medical image analysis Proceedings of the 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Athens, Greece, October 2016 (bib)
	P. Christ, M.E.A. Elshaer, F. Ettlinger, S. Tatavarty, M. Bickel, P. Bilic, M. Rempfler, M. Armbruster, M. Hofmann, M. D'Anastasi, W.H. Sommer, A. Ahmadi, B. Menze Automatic Liver and Lesion Segmentation in CT Using Cascaded Fully Convolutional Neural Networks and 3D Conditional Random Fields Proceedings of the 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Athens, Greece, October 2016 (bib)
	E. Alberts, M. Rempfler, G. Alber, D. Huber, J. Kirschke, C. Zimmer, B. Menze Uncertainty quantification in brain tumor segmentation using CRFs and random perturbation models IEEE International Symposium on Biomedical Imaging (ISBI), Prague, Czech Republic, April 2016 (bib)
	U. Sivalingam, M. Wels, M. Rempfler, S. Grosskopf, M. Suehling, B. Menze Inner and outer coronary vessel wall segmentation from CCTA using an active contour model with machine learning-based 3D voxel context-aware image force Medical Imaging 2016: Computer-Aided Diagnosis, San Diego, California, US, February 27, 2016. Proc. SPIE, vol. 9785 (bib)
2015
	V. Zografos, A. Valentinitsch, M. Rempfler, F. Tombari, B. Menze Hierarchical multi-organ segmentation without registration in 3D abdominal CT images MICCAI-MCV 2015, 2015, Munich, Germany (bib)
	M. Rempfler, M. Schneider, G. D. Ielacqua, X. Xiao, S. R. Stock, J. Klohs, G. Szekely, B. Andres, B. Menze Reconstructing cerebrovascular networks under local physiological constraints by integer programming Medical Image Analysis, Volume 25, Issue 1, Special Issue on MICCAI 2014 (bib)
	M. Rempfler, M. Schneider, G. D. Ielacqua, X. Xiao, S. R. Stock, J. Klohs, G. Szekely, B. Andres, B. Menze Rekonstruktion zerebraler Gefässnetzwerke aus in-vivo μMRA mittels physiologischem Vorwissen zur lokalen Gefässgeometrie Bildverarbeitung fuer die Medizin (BVM 2015), Luebeck, Germany, March 2015 (bib)
2014
	M. Rempfler, M. Schneider, G. D. Ielacqua, X. Xiao, S. R. Stock, J. Klohs, G. Szekely, B. Andres, B. Menze Extracting Vascular Networks under Physiological Constraints via Integer Programming Proceedings of the 17th Conference on Medical Image Computing and Computer Assisted Interventions - MICCAI, 2014, Boston, MA, USA (bib)