Author Archives: P.T.R. Rupprecht

Simultaneous calcium imaging and extracellular recording from the same neuron

Calcium imaging is a powerful method to record from many neurons simultaneously. But what do the recorded signals really mean? This question can only be properly addressed by experiments which record both calcium signals and action potentials from the same … Continue reading

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Discrepancies between calcium imaging and extracellular ephys recordings

To record the activity from a population of neurons, calcium imaging and extracellular recordings with small electrodes are the two most widely used methods that are still able to disentangle the contributions from single units. Here, I would like to … Continue reading

Posted in Calcium Imaging, Data analysis, electrophysiology, Imaging, Network analysis, Neuronal activity, Reviews | Tagged , | 1 Comment

Alignment tools

This blog posts covers some tools and techniques that I’m typically using to align two-photon microscopes. If you’re an expert, you will probably find nothing new, but if you haven’t been doing this for years, this might offer you some … Continue reading

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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 , , , , , , , | 8 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

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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 , , , | 3 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