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Category Archives: Microscopy
Four interesting papers on astrocyte physiology
A review of four interesting recent papers on astrocyte neuroscience: (1) Norepinephrine Signals Through Astrocytes To Modulate Synapses (2) A spatial threshold for calcium surge (3) Network-level encoding of local neurotransmitters in cortical astrocytes, and (4) Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, Microscopy, Neuronal activity, neuroscience, Reviews, zebrafish
Tagged Calcium Imaging, Data analysis, Microscopy, zebrafish
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There is no recipe for discoveries
There is no recipe for discoveries, and there is no cookbook on how to publish a paper. But at least there are typical events and routes that are often encountered. Here, I’d like to share the trajectory of a study … Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, machine learning, Microscopy, neuroscience, Review
Tagged Calcium Imaging, Data analysis, Microscopy
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Why your two-photon images are noisier than you expect
A gallery of calcium imaging recordings of neurons and astrocytes with single noisy frames on the left and averaged beautiful noise-free images on the right side. Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, Microscopy, Neuronal activity, neuroscience, zebrafish
Tagged Calcium Imaging, Data analysis, Microscopy, photons, Scanning, zebrafish
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Useful pieces from Twitter
Twitter used to be (and still is to some extent) a source of useful information for neuroscientists about technical details, clarifications of research findings and open discussions that cannot be obtained so easily otherwise. Here is a list of some … Continue reading
Posted in Data analysis, electrophysiology, Links, machine learning, Microscopy
Tagged Data analysis, electrophysiology, Microscopy
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Improving the resonant scanner’s sync signal using a phase locked loop (PLL)
Calcium imaging with two-photon point scanning is the technique to chronically record from identified neurons in the living brain of animals. The central piece of two-photon point scanning microscopes is a scan engine. This can be a complex optical device … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy, neuroscience
Tagged Microscopy, photons, Scanning
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Interesting papers on recent neuroscience methods
Find below three interesting methods papers relevant for neuroscience. All three of them are, in my opinion, worth a quick read. Acoustic cameras to localize ultrasound vocalization of mice Sterling et al. (2023) from the lab of Bernhard Englitz addressed … Continue reading
Posted in Data analysis, Imaging, Microscopy, neuroscience, Reviews
Tagged Data analysis, Microscopy, photons
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Interesting papers on online motion correction for calcium imaging
In a living animal, the brain is moving up and down in the skull. This brain motion can be due to breathing, heartbeat, tongue movements, but also due to changes of posture or running. For each brain region and posture, … Continue reading
Posted in Calcium Imaging, Data analysis, Imaging, machine learning, Microscopy, Neuronal activity, neuroscience
Tagged Calcium Imaging, Data analysis, Microscopy, photons, Scanning
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“Laser Scanners” by William Benner
William Benner is a scanner enthusiast and the president of the company Pangolin. His company sells equipment mostly for laser shows but also for other applications. Some years ago, he wrote a book on “Laser Scanners”, which is available through … Continue reading
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
Self-supervised denoising of calcium imaging data
This blog post is about algorithms based on deep networks to denoise raw calcium imaging movies. More specifically, I will write about the difficulties to interprete their outputs, and on how to address these limitations in future work. I will … Continue reading
A blog about neurophysiology 