I’m also on Google Scholar. My PhD thesis can be found online as a pdf.
Rupprecht P, Carta S, Hoffmann A, Echizen M, Blot A, Kwan AC, Dan Y, Hofer SB, Kitamura K, Helmchen F*, and Friedrich RW*. A database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging. Nature Neuroscience (2021)
In this large effort, we collected a database of almost 300 neurons with simultaneous calcium imaging and juxtacellular recordings of action potentials, across 8 calcium indicators and 9 brain regions in 2 species, with a total of almost 500,000 action potentials. I used this database to train a powerful algorithm based on deep networks to recover spike rates from calcium recordings, which generalized very well to unseen data. The algorithm uses its knowledge about the spike-calcium relationship and therefore is able to both recover spike rates at an improved temporal resolution and to suppress noise. Many more details and insights are in the paper, which could be a very interesting read to anybody interested in calcium imaging. Essential parts of this study are an easy-to-use Github repository that includes both code and the ground truth datasets, and a Colab Notebook that can be applied to your data, without installation or parameter tuning.
Schoenfeld G*, Carta S*, Rupprecht P, Ayaz A, Helmchen F. In vivo calcium imaging of CA3 pyramidal neuron populations in adult mouse hippocampus. eNeuro (2021)
This study was led by Gwendolin Schoenfeld, and I joined this project only at a later stage for data analysis, interpretation of results and writing. Two findings that I would like to highlight: First, despite reports that tuning of CA3 neurons is unstable across days, we found that patterns of co-activity remained stable across days; co-activity therefore might be conserved across days, while tuning is less so. Second, using simultaneous calcium imaging and juxtacellular recordings, we found a supra-linearity of calcium, hinting at the involvement of calcium spikes, a potential learning-related signal. We have performed these difficult juxtacellular experiments together with calcium imaging in anesthetized animals, but it would be really interesting to repeat this in awake animals.
Huang KH, Rupprecht P, Frank T, Kawakami K, Bouwmeester T, Friedrich RW. A virtual reality system to analyze neural activity and behavior in adult zebrafish. Nature Methods (2020)
In this study, Kuo-Hua Huang developed a method to head-fixate adult zebrafish, made them interact with a virtual reality and imaged neuronal acitivty through the skull – all at the same time. I was mainly involved in the technical parts of the study and in the writing of the manuscript. Specifically, I helped to install a resonant scanning microscope system and to synchronize it via the control software (ScanimgeB) with the virtual reality. In addition, this was the first time when my and Stephan Gerhard’s algorithm for calcium signal deconvolution (Elephant) was really crucial, namely to reveal fast, swim-triggered dynamics of neuronal activity that are masked by the slow transients of calcium indicators. Overall, this is a really cool study and I’m proud to have contributed to this work. (Read-only PDF)
Rupprecht P, Friedrich RW. Precise synaptic balance in the zebrafish homolog of olfactory cortex. Neuron (2018)
This is the main paper from my PhD thesis. Having developed methods to record and analyze calcium population data during the first part, I switched to whole-cell voltage clamp recordings in single neurons during the second part of my PhD. I was less interested in the coarse description of neuronal population activity, but rather in the mechanisms underlying the firing of single neurons. This work tries to understand how the biophysical properties of single neurons constrain or enable computational properties of the underlying circuit. Therefore, this experimental study directly connects to questions arising from theoretical neuroscience; in general, I think that intracellular electrophysiology in the intact brain might be the best tool to test theoretical circuit models due to its high precision. The picture to the left shows a single neuron that is slowly filled with a dye by the micropipette after break-in. (PDF, SI)
Berens P, Freeman J, Deneux T, Chenkov N, McColgan T, Speiser A, Macke JH, Turaga S, Mineault P, Rupprecht P, Gerhard S, Friedrich RW, Friedrich J, Paninski L, Pachitariu M, Harris KD, Bolte B, Machado TA, Ringach D, Reimer J, Froudarakis E, Euler E, Roman-Roson M, Theis L, Tolias AS, Bethge M. Community-based benchmarking improves spike inference from two-photon calcium imaging data. PLoS Computational Biology (2018)
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.
Jacobson GJ, Rupprecht P, Friedrich RW. Experience-dependent plasticity of odor representations in the telencephalon of zebrafish. Current Biology (2017)
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 RW. Remote z-scanning with a macroscopic voice coil motor for fast 3D multiphoton laser scanning microscopy. Biomedical Optics Express (2016)
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.
Rupprecht P, Prevedel R, Groessl F, Haubensak WE, Vaziri A. Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience. Biomedical Optics Express (2015)
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.
Rupprecht P*, Golé L*, Rieu JP, Vézy C, Ferrigno R, Mertani HC, Rivière C. A tapered channel microfluidic device for comprehensive cell adhesion analysis, using measurements of detachment kinetics and shear stress-dependent motion. Biomicrofluidics (2012)
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.