Stages of academic/
professional
career | | 2022 - present Interim Professor (W3) at the Institute of
Imaging and Computer Vision, RWTH Aachen University,
Germany
2018 - present Junior Professorship (W1) for Biomedical
Image Processing, RWTH Aachen University, Germany
2016 - 2017 Postdoc, California Institute of Technology,
Pasadena (CA), USA (3 months)
2016 - 2017 Postdoc, Karlsruhe Institute of Technology,
Germany
2014 Short Term Scholar at Janelia Research Campus,
Ashburn (VA), USA (5 months)
2012 - 2016 PhD student, Karlsruhe Institute of Technology,
Germany
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Supervision of Researchers in Early Career Phases
L. Fieten, “Intraoperative Patient-to-Image Registration with Sparse and Highly Uncertain Data
in Computer-Assisted Surgery”, PhD Thesis, RWTH Aachen University, 2023. E. Mededovic, “Automatic Detection and Tracking of Rodents in Large-Scale Video
Recordings”, PhD Thesis, RWTH Aachen University, (working title, ongoing work since 4/2023). E. Jin, “Automatic Anomaly Detection in Industrial and Biological Image Data”, PhD Thesis,
RWTH Aachen University, (working title, ongoing work since 3/2023). A. Amrutkar,“Elucidating Olfactory Traits and Their Multisensory Associations”, PhD Thesis,
RWTH Aachen University, (working title, ongoing work since 12/2021). A. Jose, “Context-Aware Cell Tracking in 3D+t Microscopy Image Data”, Postdoc, RWTH
Aachen University, (working title, ongoing work since 11/2021). Y. Wu, “Computer Vision Approaches for Retina Implants and Ophthalmological Image
Processing”, PhD Thesis, RWTH Aachen University, (working title, ongoing work since
07/2021). F. Khader, “Automatic Segmentation in Large-Scale Medical Image Data”, PhD Thesis, RWTH
Aachen University, (working title, ongoing work since 10/2020). I. Laube, “Automatic Spatiotemporal Alignment of Large-Scale 3D+T Point Clouds”, PhD Thesis,
RWTH Aachen University, (working title, ongoing work since 6/2020). B. Schott, “Interactive and Quantitative Knowledge-Discovery in Large-Scale 3D Tracking Data”,
PhD Thesis, Karlsruhe Institute of Technology, 2018. D. Eschweiler, “Development, Implementation and Validation of New Machine Learning-based
Algorithms for Large-Scale 3D+T Microscopy Image Analysis”, PhD Thesis, RWTH Aachen
University, (working title, ongoing work since 6/2018). |
Scientific Results Category A - D. Bähr, D. Eschweiler, A. Bhattacharyya, D. Moreno-Andrés, W. Antonin, J. Stegmaier, “CellCycleGAN: Spatiotemporal Microscopy Image Synthesis of Cell Populations using Statistical Shape Models and Conditional GANs”, IEEE International Symposium on Biomedical Imaging, Nice (France), April 13-16, 2021.
- D. Eschweiler, M. Rethwisch, M. Jarchow, S. Koppers, J. Stegmaier, “3D Fluorescence Microscopy Data Synthesis for Segmentation and Benchmarking”, PLOS ONE, 12(16), e0260509, 2021.
- Y.-F. Zhang, L. V. Cifuentes, K. N. Wright, J. P. Bhattarai, J. Mohrhardt, D. Fleck, E. Janke, C. Jiang, S. L. Cranfill, N. Goldstein, M. Schreck, A. H. Moberly, Y. Yu, B. R. Arenkiel, J. N. Betley, W. Luo, J. Stegmaier, D. W. Wesson, M. Spehr, M. V. Fuccillo, M. Ma, “Ventral Striatal Islands of Calleja Neurons Control Grooming in Mice”, Nature Neuroscience, 24(12), pp. 1699–1710, 2021.
- M. Takamiya, J. Stegmaier, A. Y. Kobitski, B. Schott, B. Weger, D. Margariti, A. R. Cereceda Delgado, V. Gourain, T. Scherr, L. Yang, S. Sorge, J. C. Otte, V. Hartmann, J. v. Wezel, R. Stotzka, T. Reinhard, G. Schlunck, T. Dickmeis, S. Rastegar, R. Mikut, G. U. Nienhaus, U. Strähle, “Pax6 Organizes the Anterior Eye Segment by Guiding Two Distinct Neural Crest Waves”, PLOS Genetics, 16, e1008774, 2020.
- B. Schott, M. Traub, C. Schlagenhauf, M. Takamiya, T. Antritter, A. Barschat, K. Löffler, D. Blessing, J. C. Otte, A. Kobitski, G. U. Nienhaus, U. Strähle, R. Mikut, J. Stegmaier, “EmbryoMiner: A New Framework for Interactive Knowledge Discovery in Large-Scale Cell Tracking Data of Developing Embryos”, PLOS Computational Biology, 14(4), e1006128, 2018.
- V. Ulman, M. Maška, K. Magnusson, O. Ronneberger, C. Haubold, N. Harder, P. Matu- la, P. Matula, D. Svoboda, M. Radojevic, I. Smal, K. Rohr, J. Jaldén, H. Blau, O. Dzyu- bachyk, B. Lelieveldt, P. Xiao, Y. Li, S. Cho, A. Dufour, J. Olivo-Marin, C. Reyes-Aldasoro, J. Solis-Lemus, R. Bensch, T. Brox, J. Stegmaier, R. Mikut, S. Wolf, F. Hamprecht, T. Esteves, P. Quelhas, Ö. Demirel, L. Malmström, F. Jug, P. Tomančák, E. Meijering, A. Muñoz-Barrutia, M. Kozubek, C. Ortiz-de-Solórzano, “An Objective Comparison of Cell Tracking Algorithms”, Nature Methods, 14, pp. 1141–1152, 2017.
- A. Bartschat, E. Hübner, M. Reischl, R. Mikut, J. Stegmaier, “XPIWIT - An XML Pipeline Wrapper for the Insight Toolkit”, Bioinformatics, 32(2), pp. 315–317, 2016.
- J. Stegmaier, F. Amat, B. Lemon, K. McDole, Y. Wan, G. Teodoro, R. Mikut, P. J. Keller, “Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos”, Developmental Cell, 36(2), pp. 225–240, 2016.
- J. Stegmaier, J. Arz, B. Schott, J. C. Otte, A. Kobitski, G. U. Nienhaus, U. Strähle, P. Sanders, R. Mikut, “Generating Semi-Synthetic Validation Benchmarks for Embryomics”, IEEE International Symposium on Biomedical Imaging, Prague (Czech Republic), April 13-16, 2016.
- J. Stegmaier, J. C. Otte, A. Kobitski, A. Bartschat, A. Garcia, G. U. Nienhaus, U. Strähle, R. Mikut, “Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks”, PLOS ONE, 9(2), e90036, 2014.
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