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Category Archives: electrophysiology
5 reasons why to use Cascade for spike inference
Our paper on A database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging is out now in Nature Neuroscience. It consists of a large and diverse ground truth database with simultaneous calcium imaging and juxtacellular recordings … Continue reading
Hodgkin-Huxley model in current clamp and voltage clamp
As a short modeling session for an electrophysiology course at the University of Zurich, I made a tutorial for students to play around with the Hodgkin-Huxley equations in a Colab Notebook / Python, which does not require them to install … Continue reading
Posted in electrophysiology, Neuronal activity
Tagged action potential, electrophysiology, Python
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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
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
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
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
Posted in Calcium Imaging, electrophysiology, Imaging, Neuronal activity, zebrafish
Tagged electrophysiology, Microscopy, photons, zebrafish
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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 Dendrites, electrophysiology, photons, theoretical neuroscience
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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
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 Data analysis, electrophysiology, Matlab, Microscopy, Python
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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
