Registration of Histologic Colour Images of Different Staining. - Ulf-Dietrich Braumann; Jens Einenkel; Lars-Christian Horn; Jens-Peer Kuska; Markus Löffler; Nico Scherf; Nicolas Wentzensen (Bildverarbeitung für die Medizin, 2006)

Image Registration of Differently Stained Histological Sections. - Jens-Peer Kuska; Ulf-Dietrich Braumann; Nico Scherf; Markus Löffler; Jens Einenkel; Michael Höckel; Lars-Christian Horn; Nicolas Wentzensen; Magnus von Knebel Doeberitz (ICIP, 2006)

Segmentation of Axonal Fibres in Tissue Slices. - Nico Scherf; Jens-Peer Kuska; Claudia Heine; Ulf-Dietrich Braumann; Heike Franke (Bildverarbeitung für die Medizin, 2008)

Spatio-temporal Analysis of Unstained Cells In-vitro. - Nico Scherf; Jens-Peer Kuska; Ulf-Dietrich Braumann; Katja Franke; Tilo Pompe; Ingo Röder (Bildverarbeitung für die Medizin, 2009)

FluidTracks - Combining Nonlinear Image Registration and Active Contours for Cell Tracking. - Nico Scherf; Christian Ludborzs; Konstantin Thierbach; Jens-Peer Kuska; Ulf-Dietrich Braumann; Patrick Scheibe; Tilo Pompe; Ingmar Glauche; Ingo Roeder (Bildverarbeitung für die Medizin, 2012)

Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions. - Nico Scherf; Maria Herberg; Konstantin Thierbach; Thomas Zerjatke; Tuzer Kalkan; Peter Humphreys; Austin Smith; Ingmar Glauche; Ingo Roeder (Bioinform., 2012)

Assisting the Machine Paradigms for Human-Machine Interaction in Single Cell Tracking. - Nico Scherf; Michael Kunze; Konstantin Thierbach; Thomas Zerjatke; Patryk Burek; Heinrich Herre; Ingmar Glauche; Ingo Roeder (Bildverarbeitung für die Medizin, 2013)

Beyond genealogies: Mutual information of causal paths to analyse single cell tracking data. - Nico Scherf; Thomas Zerjatke; K. Klemm; Ingmar Glauche; Ingo Roeder (ISBI, 2013)

Panta Rhei: analysing the patterns of cellular organisation from time-lapse microscopy data. - Nico Scherf (2013)

The benchmark data SET CeTReS.B-MI for in vitro mitosis detection. - Tim Becker; W. Kanje; Daniel H. Rapoport; Konstantin Thierbach; Nico Scherf; Ingo Roeder; Amir Madany Mamlouk (ISBI, 2014)

Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions. - Theresa Niederberger; Henrik Failmezger; Diana Uskat; Don Poron; Ingmar Glauche; Nico Scherf; Ingo Roeder; Timm Schroeder; Achim Tresch (Bioinform., 2015)

Biology-inspired visualization of morphogenetic motion in the zebrafish endoderm. - Konstantin Thierbach; Gopi Shah; Ingmar Glauche; Jan Huisken; Ingo Roeder; Nico Scherf (ISBI, 2016)

Spatiotemporal Deformable Prototypes for Motion Anomaly Detection. - Robert Bensch; Nico Scherf; Jan Huisken; Thomas Brox; Olaf Ronneberger (Int. J. Comput. Vis., 2017)

Combining Deep Learning and Active Contours Opens The Way to Robust, Automated Analysis of Brain Cytoarchitectonics. - Konstantin Thierbach; Pierre-Louis Bazin; Walter de Back; Filippos Gavriilidis; Evgeniya Kirilina; Carsten Jäger; Markus Morawski; Stefan Geyer; Nikolaus Weiskopf; Nico Scherf (MLMI@MICCAI, 2018)

Developing 3D microscopy with CLARITY on human brain tissue: Towards a tool for informing and validating MRI-based histology. - Markus Morawski; Evgeniya Kirilina; Nico Scherf; Carsten Jäger; Katja Reimann; Robert Trampel; Filippos Gavriilidis; Stefan Geyer; Bernd Biedermann; Thomas Arendt; Nikolaus Weiskopf (NeuroImage, 2018)

Foundations of the Cell Tracking Ontology. - Patryk Burek; Nico Scherf; Heinrich Herre (JOWO, 2019)

A pattern-based approach to a cell tracking ontology. - Patryk Burek; Nico Scherf; Heinrich Herre (KES, 2019)

Ontology patterns for the representation of quality changes of cells in time. - Patryk Burek; Nico Scherf; Heinrich Herre (J. Biomed. Semant., 2019)

Convolutional neural network stacking for medical image segmentation in CT scans. - Marie Kloenne; Sebastian Niehaus; Leonie Lampe; Alberto Merola; Janis Reinelt; Nico Scherf (CoRR, 2019)

On the Formal Representation and Annotation of Cellular Genealogies. - Patryk Burek; Nico Scherf; Heinrich Herre (EKAW, 2020)

On the Ontological Foundations of Cellular Development. - Patryk Burek; Heinrich Herre; Nico Scherf (JOWO, 2020)

A comparative study of semi- and self-supervised semantic segmentation of biomedical microscopy data. - Nastassya Horlava; Alisa Mironenko; Sebastian Niehaus; Sebastian Wagner; Ingo Roeder; Nico Scherf (CoRR, 2020)

Quality control for more reliable integration of deep learning-based image segmentation into medical workflows. - Elena Williams; Sebastian Niehaus; Janis Reinelt; Alberto Merola; Paul Glad Mihai; Ingo Roeder; Nico Scherf; Maria del C. Valdés Hernández (CoRR, 2021)

linus: Conveniently explore, share, and present large-scale biological trajectory data in a web browser. - Johannes Waschke; Mario Hlawitschka; Kerim Anlas; Vikas Trivedi; Ingo Roeder; Jan Huisken; Nico Scherf (PLoS Comput. Biol., 2021)

Open Problem: Active Representation Learning. - Nikola Milosevic; Gesine Müller; Jan Huisken; Nico Scherf (CoRR, 2024)

Revealing the learning process in reinforcement learning agents through attention-oriented metrics. - Charlotte Beylier; Simon M. Hofmann; Nico Scherf (CoRR, 2024)

Embedding Safety into RL: A New Take on Trust Region Methods. - Nikola Milosevic; Johannes Müller; Nico Scherf (CoRR, 2024)

Fair Distributed Machine Learning with Imbalanced Data as a Stackelberg Evolutionary Game. - Sebastian Niehaus; Ingo Roeder; Nico Scherf (CoRR, 2024)

Exploring Geometric Representational Alignment through Ollivier-Ricci Curvature and Ricci Flow. - Nahid Torbati; Michael Gaebler; Simon M. Hofmann; Nico Scherf (CoRR, 2025)

Central Path Proximal Policy Optimization. - Nikola Milosevic; Johannes Müller; Nico Scherf (CoRR, 2025)

Multimodal Recurrent Ensembles for Predicting Brain Responses to Naturalistic Movies (Algonauts 2025). - Semih Eren; Deniz Küçükahmetler; Nico Scherf (CoRR, 2025)