| Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust HMT Choi, M Schwarzkopf, ME Fornace, A Acharya, G Artavanis, ... Development 145 (12), dev165753, 2018 | 710 | 2018 |
| An objective comparison of cell-tracking algorithms V Ulman, M Maška, KEG Magnusson, O Ronneberger, C Haubold, ... Nature methods 14 (12), 1141-1152, 2017 | 503 | 2017 |
| A multi-organ nucleus segmentation challenge N Kumar, R Verma, D Anand, Y Zhou, OF Onder, E Tsougenis, H Chen, ... IEEE transactions on medical imaging 39 (5), 1380-1391, 2019 | 289 | 2019 |
| Real-time three-dimensional cell segmentation in large-scale microscopy data of developing embryos J Stegmaier, F Amat, WC Lemon, K McDole, Y Wan, G Teodoro, R Mikut, ... Developmental cell 36 (2), 225-240, 2016 | 180 | 2016 |
| Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates B Mattes, Y Dang, G Greicius, LT Kaufmann, B Prunsche, J Rosenbauer, ... Elife 7, e36953, 2018 | 113 | 2018 |
| Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks J Stegmaier, JC Otte, A Kobitski, A Bartschat, A Garcia, GU Nienhaus, ... PloS one 9 (2), e90036, 2014 | 101 | 2014 |
| Automated high-throughput heartbeat quantification in medaka and zebrafish embryos under physiological conditions J Gierten, C Pylatiuk, OT Hammouda, C Schock, J Stegmaier, J Wittbrodt, ... Scientific Reports 10 (1), 2046, 2020 | 71 | 2020 |
| CNN-based preprocessing to optimize watershed-based cell segmentation in 3D confocal microscopy images D Eschweiler, TV Spina, RC Choudhury, E Meyerowitz, A Cunha, ... 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019 …, 2019 | 58 | 2019 |
| An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution AY Kobitski, JC Otte, M Takamiya, B Schäfer, J Mertes, J Stegmaier, ... Scientific reports 5 (1), 8601, 2015 | 58 | 2015 |
| XPIWIT—an XML pipeline wrapper for the Insight Toolkit A Bartschat, E Hübner, M Reischl, R Mikut, J Stegmaier Bioinformatics 32 (2), 315-317, 2016 | 46 | 2016 |
| The MATLAB toolbox SciXMiner: User's manual and programmer's guide R Mikut, A Bartschat, W Doneit, JÁG Ordiano, B Schott, J Stegmaier, ... arXiv preprint arXiv:1704.03298, 2017 | 40 | 2017 |
| Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves M Takamiya, J Stegmaier, AY Kobitski, B Schott, BD Weger, D Margariti, ... PLoS Genetics 16 (6), e1008774, 2020 | 32 | 2020 |
| Microfluidic chips for life sciences—A comparison of low entry manufacturing technologies M Grösche, AE Zoheir, J Stegmaier, R Mikut, D Mager, JG Korvink, ... Small 15 (35), 1901956, 2019 | 25 | 2019 |
| EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos B Schott, M Traub, C Schlagenhauf, M Takamiya, T Antritter, A Bartschat, ... PLOS Computational Biology 14 (4), e1006128, 2018 | 25 | 2018 |
| Tracking of indels by decomposition is a simple and effective method to assess efficiency of guide RNAs in zebrafish C Etard, S Joshi, J Stegmaier, R Mikut, U Strähle Zebrafish 14 (6), 586-588, 2017 | 25 | 2017 |
| Generating semi-synthetic validation benchmarks for embryomics J Stegmaier, J Arz, B Schott, JC Otte, A Kobitski, GU Nienhaus, U Strahle, ... 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), 684-688, 2016 | 25 | 2016 |
| Cell segmentation in 3D confocal images using supervoxel merge-forests with CNN-based hypothesis selection J Stegmaier, TV Spina, AX Falcao, A Bartschat, R Mikut, E Meyerowitz, ... 2018 IEEE 15th International symposium on biomedical imaging (ISBI 2018 …, 2018 | 24 | 2018 |
| Zebrafish biosensor for toxicant induced muscle hyperactivity M Shahid, M Takamiya, J Stegmaier, V Middel, M Gradl, N Klüver, R Mikut, ... Scientific Reports 6 (1), 23768, 2016 | 23 | 2016 |
| Information fusion of image analysis, video object tracking, and data mining of biological images using the open source MATLAB toolbox Gait-CAD J Stegmaier, R Alshut, M Reischl, R Mikut Biomedical Engineering/Biomedizinische Technik 57 (SI-1-Track-B …, 2012 | 23 | 2012 |
| Using positional information to provide context for biological image analysis with MorphoGraphX 2.0 S Strauss, A Runions, B Lane, D Eschweiler, N Bajpai, N Trozzi, ... Elife 11, e72601, 2022 | 22 | 2022 |
