Publications of Nico Scherf

Ruthig, P., Müller, G. F., Fink, M., Scherf, N., Morawski, M., & Schönwiesner, M. (2025). Hemispheric asymmetry of intracortical myelin orientation in the mouse auditory cortex. European Journal of Neuroscience, 61. doi:10.1111/ejn.16675

Williams, E., Kienast, M., Medawar, E., Reinelt, J., Merola, A., Klopfenstein, S. A. I., … Niehaus, S. (2023). A standardized clinical data harmonization pipeline for scalable AI application deployment (FHIR-DHP): Validation and usability study. JMIR Medical Informatics (JMI), 11. doi:10.2196/43847

Maiello, L., Ball, L., Micali, M., Iannuzzi, F., Scherf, N., Hoffmann, R.-T., … Huhle, R. (2022). Automatic lung segmentation and quantification of aeration in computed tomography of the chest using 3D transfer learning. Frontiers in Physiology, 12. doi:10.3389/fphys.2021.725865

Hoffmann, H., Baldow, C., Zerjatke, T., Gottschalk, A., Wagner, S., Karg, E., … Scherf, N. (2021). How to predict relapse in leukemia using time series data: A comparative in silico study. PLoS One, 16. doi:10.1371/journal.pone.0256585

Waschke, J., Hlawitschka, M., Anlas, K., Trivedi, V., Roeder, I., Huisken, J., & Scherf, N. (2021). linus: Conveniently explore, share, and present large-scale biological trajectory data in a web browser. PLoS Computational Biology, 17. doi:10.1371/journal.pcbi.1009503

Braune, M., Scherf, N., Heine, C., Sygnecka, K., Pillaiyar, T., Parravicini, C., … Franke, H. (2021). Involvement of GPR17 in neuronal fibre outgrowth. International Journal of Molecular Sciences, 22. doi:10.3390/ijms222111683

Zoraghi, M., Scherf, N., Jäger, C., Sack, I., Hirsch, S., Hetzer, S., & Weiskopf, N. (2021). 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. doi:10.3389/fnins.2021.722366

Wagner, S., Thierbach, K., Zerjatke, T., Glauche, I., Roeder, I., & Scherf, N. (2021). TraCurate: Efficiently curating cell tracks. SoftwareX, 13. doi:10.1016/j.softx.2021.100656

Kloenne, M., Niehaus, S., Lampe, L., Merola, A., Reinelt, J., Roeder, I., & Scherf, N. (2020). Domain-specific cues improve robustness of deep learning-based segmentation of CT volumes. Scientific Reports, 10. doi:10.1038/s41598-020-67544-y

Shah, G., Thierbach, K., Schmid, B., Waschke, J., Reade, A., Hlawitschka, M., … Huisken, J. (2019). Multi-scale imaging and analysis identify pan-embryo cell dynamics of germlayer formation in zebrafish. Nature Communications, 10. doi:10.1038/s41467-019-13625-0

Burek, P., Scherf, N., & Herre, H. (2019). Ontology patterns for the representation of quality changes of cells in time. Journal of Biomedical Semantics, 10. doi:10.1186/s13326-019-0206-4

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

Morawski, M., Kirilina, E., Scherf, N., Jäger, C., Reimann, K., Trampel, R., … Weiskopf, N. (2018). Developing 3D microscopy with CLARITY on human brain tissue: Towards a tool for informing and validating MRI-based histology. NeuroImage, 182, 417–428.

Weber, M., Scherf, N., Meyer, A. M., Panáková, D., Kohl, P., & Huisken, J. (2017). Cell-accurate optical mapping across the entire developing heart. ELife, 6. doi:10.7554/eLife.28307.001

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

Scherf, N., & Huisken, J. (2015). The smart and gentle microscope. Nature Biotechnology, 33, 815–818.

Heine, C., Sygnecka, K., Scherf, N., Grohmann, M., Bräsigk, A., & Franke, H. (2015). P2Y1 receptor mediated neuronal fibre outgrowth in organotypic brain slice co-cultures. Neuropharmacology, 93, 252–266.

Niederberger, T., Failmezger, H., Uskat, D., Poron, D., Glauche, I., Scherf, N., … Tresch, A. (2015). Factor graph analysis of live cell–imaging data reveals mechanisms of cell fate decisions. Bioinformatics, 31, 1816–1823.

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

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