Author Archives: P.T.R. Rupprecht

Matlab magic spells

Most neuroscientists who analyze their data themselves use either Matlab or Python or both – the use of R is much less common than in other fields of biology. I’ve been working with Matlab on a daily basis for >10 … Continue reading

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Annual report of my intuition about the brain (2019)

How does the brain work and how can we understand it? I want to make it a habit to report some of the thoughts about the brain that marked me most during the past twelve month at the end of … Continue reading

Posted in Calcium Imaging, Data analysis, electrophysiology, machine learning, Network analysis, Neuronal activity, Review | Tagged , , , , , , , | 7 Comments

A practical guide for adaptive optics

There is no standard curriculum to learn practical procedures about microscopy: how to align a setup, how to identify misalignments, how to identify broken parts, where to buy components, how to check their performance, and much more. How to learn … Continue reading

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Review: An artificial ground truth for calcium imaging

Selected paper: Charles, Song, Tank et al., Neural Anatomy and Optical Microscopy Simulation (NAOMi) for evaluating calcium imaging methods, bioRxiv (2019). What is the paper about? Calcium imaging is a central method to observe neuronal activity in the brain of … Continue reading

Posted in Calcium Imaging, Data analysis, Imaging, Microscopy, Neuronal activity, Reviews | Tagged , , , , | 2 Comments

The cell-attached soundtrack of calcium imaging

Old-school electrophysiologists like to listen to the ephys signals during experiments. For example, this allows to precisely hear when the patch pipette approaches a target neuron. The technique is discussed in the Axon Guide: “Audio Monitor: Friend or Foe?”. The … Continue reading

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Post-publication review: Somato-dendritic coupling of L5 neurons in V1

It requires more than a quick look at the abstract and the figures to fully understand a research paper and its limitations. One way to get there is to write a summary or critical review of a paper. In a contribution to … Continue reading

Posted in Calcium Imaging, electrophysiology, Microscopy, Reviews | Tagged , , , | 2 Comments

Post-publication review: “Precise excitation-inhibition balance controls gain and timing in the hippocampus”

It requires more than a quick look at the abstract and the figures to fully understand a research paper and its limitations. One way to go there is to write a summary or critical review of a paper. In a contribution to … Continue reading

Posted in electrophysiology, Neuronal activity, Reviews | Tagged , , , | 2 Comments

Photon yield and pulse dispersion

This case report describes how a two-photon microscope was found to come with a fluorescence yield that was lower than expected; how the underlying cause was found out in a systematic manner; and how the problem was solved. All approaches and solutions are specific for the microscope under question. However, I hope that this report (1) will inspire other people who are troubleshooting or optimizing their microscopes, (2) will help other people better understand two-photon microscopes and the relevance of technical details. Continue reading

Posted in Calcium Imaging, Imaging, Microscopy | Tagged , , , | 3 Comments

The power of correlation functions

During my physics studies, I got to know several mathematical tools that turned out to be extremely useful to describe the world and to analyze data, for example vector calculus, fourier analysis or differential equations. Another tool that I find … Continue reading

Posted in Calcium Imaging, Data analysis, electrophysiology | Tagged , , , , | 4 Comments

Annual report of my intuition about the brain

There are not many incentives for young neuroscientists to think aloud about big questions. Due to lack both of knowledge and authority, discussing very broad questions like how the brain works risks to be embarrassing at best. Still, I feel … Continue reading

Posted in Calcium Imaging, electrophysiology, machine learning, Neuronal activity | Tagged , , , , | 3 Comments