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Tag Archives: zebrafish
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
Fast scanning, triplet states and photon yield
In point-scanning microscopy like two-photon or confocal microscopy, a focused laser beam is scanned across the field of view and thereby sequentially recovers an image of the object. In this blog post, I will discuss the idea that scanning faster … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy, Neuronal activity
Tagged Calcium Imaging, Microscopy, photons, Scanning, zebrafish
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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
Posted in Calcium Imaging, electrophysiology, Imaging, Neuronal activity, zebrafish
Tagged electrophysiology, Microscopy, photons, zebrafish
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Whole-cell patch clamp, part 4: look and feel
In previous blog posts, I have been discussing some aspects of whole-cell patch clamp recordings ([1], [2], [3], [4]). Today, I will show some instructive videos that I recorded during experiments. I’m hoping that they will convey the look and feel … Continue reading
Posted in Calcium Imaging, electrophysiology, Imaging, Microscopy, Neuronal activity, zebrafish
Tagged electrophysiology, Microscopy, photons, zebrafish
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Precise synaptic balance of excitation and inhibition
The main paper of my PhD just got published: Rupprecht and Friedrich, Precise Synaptic Balance in the Zebrafish Homolog of Olfactory Cortex, Neuron (2018). (PDF) You might like it if you are also interested in Classical balanced networks Things you … Continue reading
Open access 3D electron microscopy datasets of brains
One of the coolest technical developments in neuroscience during the last decade has been driven by 3D electron microscopy (3D EM). This allowed to cut large junks of small brains (or small junks of big brains) into 8-50 nm thick … Continue reading
Posted in Data analysis, machine learning, Microscopy, Network analysis, zebrafish
Tagged Data analysis, Microscopy, Network analysis, zebrafish
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Whole-cell patch clamp, part 3: Limitations of quantitative whole-cell voltage clamp
Before I first dived into experimental neuroscience, I imagined whole-cell voltage clamp recordings to be the holy grail of precision. Directly listening to the currents that take place inside of a living neuron! How beautiful and precise, compared to poor-resolution techniques like fMRI or … Continue reading
Posted in Data analysis, electrophysiology, Neuronal activity, zebrafish
Tagged Data analysis, electrophysiology, zebrafish
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The crow as an animal model for neuroscience
Close to my apartment in the outskirts of Basel, green fields and some small woods lie basically in front of my house door. This is also where some flocks of crows gather around, partly searching the fields for food, partly … Continue reading
Posted in electrophysiology, Imaging, Neuronal activity, Uncategorized
Tagged consciousness, electrophysiology, zebrafish
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Whole-cell patch clamp, part 1: introductory reading
Ever since I my interested in neuroscience become more serious, I was fascinated by the patch clamp technique, especially applied for the whole cell. Calcium imaging or multi-channel electrophysiology (recent review) is the way to go in order to get an idea what … Continue reading
Posted in electrophysiology, Microscopy, zebrafish
Tagged Calcium Imaging, electrophysiology, patch clamp, zebrafish
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The larval zebrafish, and the adult zebrafish
Zebrafish are often used as a model organism for in vivo brain imaging, because they are transparent. Or at least that is what many people think who do not work with zebrafish. In reality, most people use zebrafish larvae for in vivo … Continue reading
Posted in Calcium Imaging, Neuronal activity, zebrafish
Tagged Calcium Imaging, zebrafish
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A blog about neurophysiology 