@article{OzelKulkarniHasanetal.2019, author = {Ozel, Mehmet Neset and Kulkarni, Abhishek and Hasan, Amr and Brummer, Josephine and Moldenhauer, Marian and Daumann, Ilsa-Maria and Wolfenberg, Heike and Dercksen, Vincent J. and Kiral, Ferdi Ridvan and Weiser, Martin and Prohaska, Steffen and von Kleist, Max and Hiesinger, Peter Robin}, title = {Serial synapse formation through filopodial competition for synaptic seeding factors}, volume = {50}, journal = {Developmental Cell}, number = {4}, doi = {10.1016/j.devcel.2019.06.014}, pages = {447 -- 461}, year = {2019}, abstract = {Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.}, language = {en} } @misc{OezelKulkarniHasanetal.2019, author = {{\"O}zel, M. Neset and Kulkarni, Abhishek and Hasan, Amr and Brummer, Josephine and Moldenhauer, Marian and Daumann, Ilsa-Maria and Wolfenberg, Heike and Dercksen, Vincent J. and Kiral, F. Ridvan and Weiser, Martin and Prohaska, Steffen and von Kleist, Max and Hiesinger, Peter Robin}, title = {Serial synapse formation through filopodial competition for synaptic seeding factors}, issn = {1438-0064}, doi = {10.1016/j.devcel.2019.06.014}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74397}, year = {2019}, abstract = {Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.}, language = {en} } @article{BrenceBrummerDercksenetal.2026, author = {Brence, Blaž and Brummer, Josephine and Dercksen, Vincent J. and {\"O}zel, Mehmet Neset and Kulkarni, Abhishek and Wolterhoff, Neele and Prohaska, Steffen and Hiesinger, Peter Robin and Baum, Daniel}, title = {Semi-automatic geometrical reconstruction and analysis of filopodia dynamics in 4D two-photon microscopy images}, volume = {27}, journal = {BMC Bioinformatics}, doi = {10.1186/s12859-026-06385-4}, year = {2026}, abstract = {Background: Filopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells. Results: To address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing. Conclusion: To facilitate simple application within Amira or other frameworks, we share the source code, which is available at https://github.com/zibamira/filopodia-tool.}, language = {en} }