Research

About me #

I completed my BSc and MSc degrees in computer science at TU Darmstadt in Germany, including two semesters as a visiting graduate student with the computer science department of the University of British Columbia in Vancouver, Canada.

I received my PhD from TU Darmstadt (supervised by Stefan Roth) mainly for work on image restoration, in particular developing methods to remove noise and camera shake from photographs. While working on my PhD, I did an internship at Microsoft Research in Cambridge, United Kingdom.

I then was a Postdoc with the Myers Lab at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) / Center for Systems Biology Dresden (CSBD) in Germany, where I worked on image restoration and image segmentation in the context of microscopy. During my time there, I also collaborated with Carsten Rother’s group at TU Dresden and Siân Culley from University College London, United Kingdom.

I’m no longer affiliated with a research institution since 2020, but I’m occasionally still active as an independent researcher in collaboration with Martin Weigert from EPFL in Lausanne, Switzerland.

Here’s my Google scholar profile and academic CV. For research-related inquiries, please contact me via research AT uweschmidt DOT org.

Publications #

Martin Weigert and Uwe Schmidt. Nuclei Instance Segmentation and Classification in Histopathology Images with StarDist. In Proc. of the IEEE International Symposium on Biomedical Imaging Challenges (ISBIC), Kolkata, India, March 2022.

Paper Paper at IEEE Xplore Paper at arXiv

Yuhan Wang, Mark Eddison, Greg Fleishman, Martin Weigert, Shengjin Xu, Tim Wang, Konrad Rokicki, Cristian Goina, Fredrick E. Henry, Andrew L. Lemire, Uwe Schmidt, Hui Yang, Karel Svoboda, Eugene W. Myers, Stephan Saalfeld, Wyatt Korff, Scott M. Sternson, and Paul W. Tillberg. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization. Cell 184.26 (2021).

Paper at Cell (open access)

Debayan Saha, Uwe Schmidt, Qinrong Zhang, Aurelien Barbotin, Qi Hu, Na Ji, Martin J. Booth, Martin Weigert, and Eugene W. Myers. Practical sensorless aberration estimation for 3D microscopy with deep learning. Optics Express 28.20 (2020).

Paper at Optics Express (open access) arXiv preprint

Gautam Dey, Siân Culley, Scott Curran, Uwe Schmidt, Ricardo Henriques, Wanda Kukulski, and Buzz Baum. Closed mitosis requires local disassembly of the nuclear envelope. Nature 585 (2020).

Paper at Nature bioRxiv preprint

Andre Arashiro Pulschen, Delyan R. Mutavchiev, Siân Culley, Kim Nadine Sebastian, Jacques Roubinet, Marc Roubinet, Gabriel Tarrason Risa, Marleen van Wolferen, Chantal Roubinet, Uwe Schmidt, Gautam Dey, Sonja-Verena Albers, Ricardo Henriques, and Buzz Baum. Live Imaging of a Hyperthermophilic Archaeon Reveals Distinct Roles for Two ESCRT-III Homologs in Ensuring a Robust and Symmetric Division. Current Biology 30.14 (2020).

Paper at Current Biology (open access)

Sarah Schmell, Falk Zakrzewski, Walter de Back, Martin Weigert, Uwe Schmidt, Torsten Wenke, Silke Zeugner, Robert Mantey, Christian Sperling, Ingo Roeder, Pia Hoenscheid, Daniela Aust, and Gustavo Baretton. An interpretable automated detection system for FISH-based HER2 oncogene amplification testing in histo-pathological routine images of breast and gastric cancer diagnostics. Short paper at Medical Imaging with Deep Learning (MIDL), Montréal, Canada, July 2020.

Paper, reviews, videos at MIDL (open access)

Coleman Broaddus, Alexander Krull, Martin Weigert, Uwe Schmidt, and Gene Myers. Removing Structured Noise with Self-Supervised Blind-Spot Networks. In Proc. of the IEEE 17th International Symposium on Biomedical Imaging (ISBI), Iowa City, Iowa, April 2020. Best Paper Award Finalist.

Paper

Martin Weigert, Uwe Schmidt, Robert Haase, Ko Sugawara, and Gene Myers. Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy. In Proc. of the IEEE Winter Conference on Applications of Computer Vision (WACV), Snowmass, Colorado, March 2020.

Paper Poster Conference video Python code

Robert Haase, Loic A. Royer, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug, and Eugene W. Myers. CLIJ: GPU-accelerated image processing for everyone. Nature Methods 17.01 (2020): 5–6.

Paper at Nature Methods Project website

Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, and Eugene W. Myers. Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy. Nature Methods 15.12 (2018): 1090–1097.

Paper at Nature Methods bioRxiv preprint Project website Python code

Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers. Cell Detection with Star-convex Polygons. In International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Granada, Spain, September 2018.

Paper Poster Python code

Jakob Kruse, Carsten Rother, and Uwe Schmidt. Learning to Push the Limits of Efficient FFT-based Image Deconvolution. In Proc. of the IEEE International Conference on Computer Vision (ICCV), Venice, Italy, October 2017. Spotlight presentation.

Paper Supplemental material Poster Conference video Python code

Uwe Schmidt, Jeremy Jancsary, Sebastian Nowozin, Stefan Roth, and Carsten Rother. Cascades of Regression Tree Fields for Image Restoration. IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI) 38.4 (2016): 677–689.

Paper at TPAMI (open access) arXiv preprint

Uwe Schmidt and Stefan Roth. Shrinkage Fields for Effective Image Restoration. In Proc. of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Columbus, Ohio, June 2014. Oral presentation.

Paper Supplemental material Slides Conference video Teaser video MATLAB code

Uwe Schmidt, Carsten Rother, Sebastian Nowozin, Jeremy Jancsary, and Stefan Roth. Discriminative Non-blind Deblurring. In Proc. of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Portland, Oregon, June 2013. Oral presentation. Best Student Paper Award.

Paper Slides Poster C++ code

Thorsten Franzel, Uwe Schmidt, and Stefan Roth. Object Detection in Multi-View X-Ray Images. In Joint Pattern Recognition Symposium (34th DAGM, 36th OAGM), Graz, Austria, August 2012. Oral presentation.

Paper

Uwe Schmidt and Stefan Roth. Learning Rotation-Aware Features: From Invariant Priors to Equivariant Descriptors. In Proc. of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Providence, Rhode Island, June 2012. Oral presentation.

Paper Supplemental material Slides Conference video MATLAB code

Uwe Schmidt, Kevin Schelten, and Stefan Roth. Bayesian Deblurring with Integrated Noise Estimation. In Proc. of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Colorado Springs, Colorado, June 2011.

Paper Poster MATLAB code

Uwe Schmidt, Qi Gao, and Stefan Roth. A Generative Perspective on MRFs in Low-Level Vision. In Proc. of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), San Francisco, California, June 2010. Oral presentation.

Paper Supplemental material Slides Poster Conference video MATLAB code

Jussi Kangasharju, Uwe Schmidt, Dirk Bradler, and Julian Schröder-Bernhardi. ChunkSim: Simulating Peer-to-Peer Content Distribution. In Communications and Networking Simulation Symposium, 2007.

Theses #

PhD thesis. Half-quadratic Inference and Learning for Natural Images.
Supervisor: Stefan Roth

MSc thesis. Learning and Evaluating Markov Random Fields for Natural Images.
Supervisor: Stefan Roth

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