Publications

I’m also on Google Scholar.

SpikefinderBerens, P., Freeman, J., Deneux, T., Chenkov, N., McColgan, T., Speiser, A., Macke, J.H., Turaga, S., Mineault, P., Rupprecht, P., Gerhard, S., Friedrich, R.W., Friedrich, J., Paninski, L., Pachitariu, M., Harris, K.D., Bolte, B., Machado, T.A., Ringach, D., Reimer, J., Froudarakis, E., Euler, E., Roman-Roson, M., Theis, L., Tolias, A.S., Bethge, M. (2018). Community-based benchmarking improves spike inference from two-photon calcium imaging data. PLoS Computational Biology 14(5). This paper is the result of the spikefinder competition, with the goal to solve the (inverse) problem of spike inference for calcium imaging data. I participated in the competition, together with Stephan Gerhard, using an algorithm based on 1D convolutional networks and embedding spaces, which got us a first prize. More details are on this blog (link 1, link 2, link 3), in the paper itself and on Github.
nice-ob-recording-6if-kept-stack-1Jacobson, G.J., Rupprecht, P., Friedrich, R.W. (2017). Experience-dependent plasticity of odor representations in the telencephalon of zebrafish. Current Biology, 28, 1–14.
Most of the work and analysis in this paper was done by Gilad Jacobson. I joined the project when it came to recording the neuronal population activity of mitral cells in the olfactory bulb. Those cells are scattered in 3D, which makes it necessary to perform multi-plane calcium imaging to simultaneously record from a decent number of cells. I did these experiments, taking advantage of the voice coil-based remote z-scanning that I had developed before. Dynamics in the olfactory bulb are very rich and fascinating; mitral cells respond together with the large dendritic tuft (some 10 μms in diameter), which makes the visualization more fascinating than blinking somata alone (a small excerpt of a FOV is shown to the left).
Rupprecht, P., Prendergast, A., Wyart, C., & Friedrich, R. W. (2016). Remote z-scanning with a macroscopic voice coil motor for fast 3D multiphoton laser scanning microscopy. Biomedical optics express, 7(5), 1656-1671.
This is one of the side-projects of my PhD. It lead to a method for fast 3D scanning for two-photon imaging which I have been using since routinely for multi-plane calcium imaging, replacing the more expensive and fragile standard technique (piezo-attached objectives). The design is described elsewhere on this website (link). For me, who was rather new to electrical engineering, it was a great adventure to discover and apply the working principles of voice coil motors, starting with contacting vendors, over attempts to control the device, to the first use with imaging – when I realized that it would work.
tefo2Rupprecht, P., Prevedel, R., Groessl, F., Haubensak, W. E., & Vaziri, A. (2015). Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience. Biomedical optics express, 6(2), 353-368.
Robert Prevedel, now junior group leader at the EMBL, had developed a wide-field temporal focusing 2P microscope, published in Nature Methods. The main factor that was limiting the field of view was laser power. By replacing wide-field by line- or spiral-scanning, we could circumvent this limiting factor and increase the field of view and imaging speed. What I liked particularly about the paper is the use of the rolling shutter of the CMOS camera as a slit pinhole in order to reduce the impact of scattered light. The idea, based on a recent publication, was great; in reality, however, the technical specifications of existing cameras were not ideal for this method.
cancercellRupprecht*, P., Golé*, L., Rieu, J. P., Vézy, C., Ferrigno, R., Mertani, H. C., & Riviere, C. (2012). A tapered channel microfluidic device for comprehensive cell adhesion analysis, using measurements of detachment kinetics and shear stress-dependent motion. Biomicrofluidics, 6(1), 014107.
Together with Laurent Golé, a PhD student in the biophysics lab of Jean-Paul Rieu in Lyon, I developed a microfluidics device based on soft lithography with PDMS that can be loaded with cancer cells or amoeba. This allows to observe their migration or detachment behavior. Cancer cells do not only migrate in microfluidic channels, but also in blood vessels, e.g., when they are on their way to form metastases. The part of the paper that I like most is the analysis of possible errors for calculating physical stress based on laminar flow in a given boundary geometry. This analysis is not included in the main paper, but in the supplementary information.