Publications of Nico Scherf

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 (11), e1009503 (2021)

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, 722366 (2021)

Wagner, S.; Thierbach, K.; Zerjatke, T.; Glauche, I.; Roeder, I.; Scherf, N.: TraCurate: Efficiently curating cell tracks. SoftwareX 13, 100656 (2021)

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), 10712 (2020)

Shah, G.; Thierbach, K.; Schmid, B.; Waschke, J.; Reade, A.; Hlawitschka, M.; Roeder, I.; Scherf, N.; Huisken, J.: Multi-scale imaging and analysis identify pan-embryo cell dynamics of germlayer formation in zebrafish. Nature Communications 10, 5753 (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)

Burek, P.; Scherf, N.; Herre, H.: A pattern-based approach to a cell tracking ontology. Procedia Computer Science 159, pp. 784 - 793 (2019)

Morawski, M.; Kirilina, E.; Scherf, N.; Jäger, C.; Reimann, K.; Trampel, R.; Gavriilidis, F.; Geyer, S.; Biedermann, B.; Arendt, T. et al.; Weiskopf, N.: Developing 3D microscopy with CLARITY on human brain tissue: Towards a tool for informing and validating MRI-based histology. NeuroImage 182, pp. 417 - 428 (2018)

Weber, M.; Scherf, N.; Meyer, A. M.; Panáková, D.; Kohl, P.; Huisken, J.: Cell-accurate optical mapping across the entire developing heart. eLife 6, e28307 (2017)

Bensch, R.; Scherf, N.; Huisken, J.; Brox, T.; Ronneberger, O.: Spatiotemporal deformable prototypes for motion anomaly detection. International Journal of Computer Vision 122, pp. 502 - 523 (2017)

Scherf, N.; Huisken, J.: The smart and gentle microscope. Nature Biotechnology 33, pp. 815 - 818 (2015)

Heine, C.; Sygnecka, K.; Scherf, N.; Grohmann, M.; Bräsigk, A.; Franke, H.: P2Y1 receptor mediated neuronal fibre outgrowth in organotypic brain slice co-cultures. Neuropharmacology 93, pp. 252 - 266 (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 31 (11), pp. 1816 - 1823 (2015)

Sygnecka, K.; Heider, A.; Scherf, N.; Alt, R.; Franke, H.; Heine, C.: Mesenchymal stem cells support neuronal fiber growth in an organotypic brain slice co-culture model. Stem Cells and Development 24 (7), pp. 824 - 835 (2015)

Sygnecka, K.; Heine, C.; Scherf, N.; Fasold, M.; Binder, H.; Scheller, C.; Franke, H.: Nimodipine enhances neurite outgrowth in dopaminergic brain slice co‐cultures. International Journal of Developmental Neuroscience 40 (1), pp. 1 - 11 (2015)

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), pp. 826 - 837.e17 (2014)

Rashidi, N. M.; Scott, M. K.; Scherf, N.; Krinner, A.; Kalchschmidt, J. S.; Gounaris, K.; Selkirk, M. E.; Roeder, I.; Lo Celso, C.: In vivo time-lapse imaging shows diverse niche engagement by quiescent and naturally activated hematopoietic stem cells. Blood 124 (1), pp. 79 - 83 (2014)

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. Neurosignals 21 (3-4), pp. 197 - 212 (2013)

Weber, M.; Scherf, N.; Kahl, T.; Braumann, U.-D.; Scheibe, P.; Kuska, J.-P.; Bayer, R.; Büttner, A.; Franke, H.: Quantitative analysis of astrogliosis in drug-dependent humans. Brain Research 1500, pp. 72 - 87 (2013)

Schmid, B.; Shah, G.; Scherf, N.; Weber, M.; Thierbach, K.; Campos, C. P.; Roeder, I.; Aanstad, P.; Huisken, J.: High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics. Nature Communications 4, 2207 (2013)