2021 | |
Hoffmann H, Baldow C, Zerjatke T, Gottschalk A, Wagner S, Karg E, Niehaus S, Roeder I, Glauche I, Scherf N
How to predict relapse in leukemia using time series data: A comparative in silico study. PloS one 16 (2021) e0256585, DOI Link |
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Wagner S, Thierbach K, Zerjatke T, Glauche I, Roeder I, Scherf N
TraCurate: Efficiently curating cell tracks SoftwareX 13 (2021) 100656, DOI Link |
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Waschke J, Hlawitschka M, Anlas K, Trivedi V, Roeder I, Huisken J, Scherf N
linus: Conveniently explore, share, and present large-scale biological trajectory data in a web browser. PLoS computational biology 17 (2021) e1009503, DOI Link |
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Zoraghi M, Scherf N, Jaeger C, Sack I, Hirsch S, Hetzer S, Weiskopf N
Simulating Local Deformations in the Human Cortex Due to Blood Flow-Induced Changes in Mechanical Tissue Properties: Impact on Functional Magnetic Resonance Imaging. Frontiers in neuroscience 15 (2021) 722366, DOI Link |
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2020 | |
Kloenne M, Niehaus S, Lampe L, Merola A, Reinelt J, Roeder I, Scherf N
Domain-specific cues improve robustness of deep learning-based segmentation of CT volumes. Scientific reports 10 (2020) 10712, DOI Link |
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2019 | |
Seurig S, de Back W, Scherf N, Röder I
Automating pollen counting using deep learning Allergo Journal Sep 2019 (2019) |
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Burek P, Scherf N, Herre H
Ontology patterns for the representation of quality changes of cells in time Journal of Biomedical Semantics 10 (2019), DOI Link |
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Burek P, Scherf N, Herre H
A pattern-based approach to a cell tracking ontology Procedia Computer Science 159 (2019) 784-793, DOI Link |
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Shah G, Thierbach K, Schmid B, Waschke J, Reade A, Hlawitschka M, Roeder I, Scherf N, Huiken J
Multi-scale imaging and analysis identify pan-embryo cell dynamics of germlayer formation in zebrafish Nature Communications 10 (2019), DOI Link |
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2018 | |
Thierbach K, Bazin P, De Back W, Gavriilidis F, Kirilina E, Jaeger C, Morawski M, Geyer S, Weiskopf N, Scherf N
Combining Deep Learning and Active Contours Opens The Way to Robust, Automated Analysis of Brain Cytoarchitectonics (2018), DOI Link |
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2017 | |
MacLean AL, Smith MA, Liepe J, Sim A, Khorshed R, Rashidi NM, Scherf N, Krinner A, Roeder I, Lo Celso C, Stumpf MPH
Single Cell Phenotyping Reveals Heterogeneity Among Hematopoietic Stem Cells Following Infection Stem Cells 35 (2017) 2292–2304, DOI Link |
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2016 | |
Thierbach K, Shah G, Glauche I, Huisken J, Roeder I, Scherf N
Biology-inspired visualization of morphogenetic motion in the zebrafish endoderm In: IEEE: Conference Proceedings : 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI) (2016), ISBN: 978-1-4799-2349-6 |
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2015 | |
Scherf N, Huisken J
The smart and gentle microscope. Nature biotechnology 33 (2015) 815-8, DOI Link |
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Niederberger T, Failmezger H, Uskat D, Poron D, Glauche I, Scherf N, Roeder I, Schroeder T, Tresch A
Factor graph analysis of live cell imaging data reveals mechanisms of cell fate decisions. Bioinformatics (Oxford, England) (2015), DOI Link |
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2014 | |
Scherf N
Panta Rhei: Analysing the patterns of cellular organisation from time-lapse microscopy data PhD thesis (2014) Technische Universität DResden |
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Bach E, Zerjatke T, Herklotz M, Scherf N, Niederwieser D, Roeder I, Pompe T, Cross M, Glauche I
Elucidating functional heterogeneity in hematopoietic progenitor cells: a combined experimental and modeling approach. Experimental hematology 42 (2014) 826-37.e1-17, DOI Link |
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Rashidi NM, Scott MK, Scherf N, Krinner A, Kalchschmidt JS, Gounaris K, Selkirk ME, Roeder I, Lo Celso C
In vivo time-lapse imaging of mouse bone marrow reveals differential niche engagement by quiescent and naturally activated hematopoietic stem cells. Blood (2014), DOI Link |
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2013 | |
Scherf N, Ludborzs C, Thierbach K, Glauche I, Roeder I
A Fluid Registration Approach to Cell Tracking Current Medical Imaging Reviews 9 (2013) 102-12 |
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Scherf N, Zerjatke T, Klemm K, Glauche I, Roeder I
Beyond Genealogies: Mutual information of causal paths to analyse single cell tracking data In: IEEE: 10th International Symposium on Biomedical Imaging: From Nano to Macro, San Francisco, CA, USA, April 7-11, 2013 (2013), ISBN: 978-1-4673-6454-6/13 |
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Scherf N, Kunze M, Thierbach K, Zerjatke T, Burek P, Herre H, Glauche I, Roeder I
Assisting the Machine Paradigms for Human-Machine Interaction in Single Cell Tracking In: Hans-Peter Meinzer, Thomas Martin Deserno, Heinz Handels, Thomas Tolxdorff (eds.): Bildverarbeitung für die Medizin 2013 Springer (2013), ISBN: 978-3-642-36479-2 (Print) 978-3-642-36480-8 (Online) |
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Heine C, Sygnecka K, Scherf N, Berndt A, Egerland U, Hage T, Franke H
Phosphodiesterase 2 inhibitors promote axonal outgrowth in organotypic slice co-cultures. Neuro-Signals 21 (2013) 197-212, DOI Link |
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Schmid B, Shah G, Scherf N, Weber M, Thierbach K, Campos CP, Roeder I, Aanstad P, Huisken J
High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics. Nature communications 4 (2013) 2207, DOI Link |
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2012 | |
Scherf N, Herberg M, Thierbach K, Zerjatke T, Kalkan T, Humphreys P, Smith A, Glauche I, Roeder I
Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions. Bioinformatics (Oxford, England) 28 (2012) i556-i561, DOI Link |
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Scherf N, Ludborzs Ch, Kuska JP, Braumann UD, Scheibe P, Pompe T, Glauche I, Roeder I
FluidTracks - Combining Nonlinear Image Registration and Active Contours for Cell Tracking In: Tolxdorff, Th.; Deserno, Th.M.; Handels, H.; Meinzer, H.-P. (Hrsg.): Proc. Bildverarbeitung für die Medizin 2012 Springer (2012), ISBN: 978-3-643-28502-8 |
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Scherf N, Franke K, Glauche I, Kurth I, Bornhäuser M, Werner C, Pompe T, Roeder I
On the symmetry of siblings: automated single-cell tracking to quantify the behavior of hematopoietic stem cells in a biomimetic setup. Experimental hematology 40 (2012) 119-130.e9, DOI Link |
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2010 | |
Burek P, Herre H, Roeder I, Glauche I, Scherf N, Loeffler M
Towards a Cellular Genealogy Ontology In: H. Herre, R. Hoehndorf, J. Kelso, S. Schulz (eds.): 2nd Workshop of the GI-Fachgruppe "Ontologien in Biomedizin und Lebenswissenschaften (OBML)", 09-10. September 2010 in Mannheim, Germany Universität Leipzig (2010), ISBN: ISSN 1610-7233 |
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2008 | |
Scherf N, Roeder I, Glauche I
Correlation patterns of cellular genealogies In: Miika Ahdesmäki, Korbinian Strimmer, Nicole Radde, Jörg Rahnenführer, Konstantin Klemm, Harri Lähdesmäki, Olli Yli-Harja (eds.): Proccedings of the Fifth International Workshop on Computational Systems Biology (WCSB), June 11-13 2008, Leipzig, Germany Tampere International Center for Signal Processing (2008), ISBN: 978-952-15-1988-8 |