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Johannes Stegmaier
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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
9252018
An objective comparison of cell-tracking algorithms
V Ulman, M Maška, KEG Magnusson, O Ronneberger, C Haubold, ...
Nature methods 14 (12), 1141-1152, 2017
5612017
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
3882019
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
1922016
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
1242018
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
1062014
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
812020
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
682019
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
642015
Denoising diffusion probabilistic models for 3D medical image generation
F Khader, G Müller-Franzes, S Tayebi Arasteh, T Han, C Haarburger, ...
Scientific Reports 13 (1), 7303, 2023
532023
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
522016
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
412022
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
412017
Medical diffusion: Denoising diffusion probabilistic models for 3d medical image generation
F Khader, G Mueller-Franzes, ST Arasteh, T Han, C Haarburger, ...
arXiv preprint arXiv:2211.03364, 2022
392022
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
352020
Ventral striatal islands of Calleja neurons control grooming in mice
YF Zhang, L Vargas Cifuentes, KN Wright, JP Bhattarai, J Mohrhardt, ...
Nature neuroscience 24 (12), 1699-1710, 2021
302021
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
302018
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
272019
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
272017
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
272016
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