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(1) 2020, 10712, DOI Link
2019
Burek P, Scherf N, Herre H
Ontology patterns for the representation of quality changes of cells in time
Journal of Biomedical Semantics 10(16) 2019, DOI Link
Burek P, Scherf N, Herre H
A pattern-based approach to a cell tracking ontology
Procedia Computer Science 159, 2019, 784-793, DOI Link
Seurig S, de Back W, Scherf N, Röder I
Automating pollen counting using deep learning
Allergo Journal Sep 2019, 2019
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(5753) 2019, DOI Link
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
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(11) 2017, 2292–2304, DOI Link
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)
, 978-1-4799-2349-6
2015
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
Scherf N, Huisken J
The smart and gentle microscope.
Nature biotechnology 33(8) 2015, 815-8, DOI Link
2014
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
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(9) 2014, 826-37.e1-17, DOI Link
Scherf N
Panta Rhei: Analysing the patterns of cellular organisation from time-lapse microscopy data
PhD thesis (2014) Technische Universität DResden
2013
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 , 978-3-642-36479-2 (Print) 978-3-642-36480-8 (Online)
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
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
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(3-4) 2013, 197-212, DOI Link
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
, 978-1-4673-6454-6/13
2012
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(2) 2012, 119-130.e9, DOI Link
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(18) 2012, i556-i561, DOI Link
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 , 978-3-643-28502-8
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 , ISSN 1610-7233
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 41, 978-952-15-1988-8