Category Archives: electrophysiology

Annual report of my intuition about the brain (2022)

How does the brain work and how can we understand it? To view this big question from a broad perspective at the end of each year, I’m reporting some of the thoughts about the brain that marked me most during … Continue reading

Posted in electrophysiology, Network analysis, Neuronal activity, Review, Reviews | Tagged , , | 6 Comments

Ambizione fellowship and an open PhD position

I’m glad to share that I am going to start my own junior research group at the University of Zurich in March 2023! As an Ambizione fellow, I will receive funding for my own salary, some equipment, consumables and a … Continue reading

Posted in Calcium Imaging, Data analysis, electrophysiology, machine learning, Microscopy, Neuronal activity | Tagged , , , , , , , | Leave a comment

Video introduction to CASCADE

A video with tutorial on CASCADE, a supervised method to infer spike rates from calcium imaging data. Continue reading

Posted in Calcium Imaging, Data analysis, electrophysiology, Imaging, machine learning, Microscopy, Neuronal activity | Tagged , , , , | Leave a comment

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

Posted in Calcium Imaging, Data analysis, electrophysiology, Imaging, machine learning, Microscopy, Neuronal activity | Tagged , , , , | Leave a comment

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

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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

Posted in Calcium Imaging, Data analysis, electrophysiology, machine learning, Microscopy, Neuronal activity, zebrafish | Tagged , , , , | Leave a comment

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

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

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 , , , | 4 Comments