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Category Archives: Data analysis
Detecting single spikes from calcium imaging
There are two mutually exclusive holy grails of calcium imaging: First, recording from the highest number of neurons simultaneously. Second, detecting spike patterns with single-spike precision. This blog post focuses on the latter. Many studies have claimed to demonstrate single-spike … Continue reading
Non-linearity of calcium indicators: history-dependence of spike reporting
Calcium indicators are used to report the calcium concentration inside single cells. In neurons, calcium imaging can be used as a readout of neuronal activity (action potentials). However, some calcium indicators like GCaMP transform the calcium concentration of a cell … Continue reading
Annual report of my intuition about the brain (2024)
The brain is a complex system that cannot be understood by a strictly structured approach. Knowledge must grow organically, and a systematic approach can sometimes hinder understanding. In formal education, this truth is often hidden because curricula and instructors provide the structuring of knowledge already. But when it comes to acquiring new knowledge and insight, rather than merely processing and assembling pre-existing knowledge, this systematic approach must be continuously interrupted and re-invented to enable real progress. Continue reading
Posted in Data analysis, Neuronal activity, neuroscience, Reviews
Tagged brain, neuroscience, research, science, theoretical neuroscience, writing
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Spike inference with GCaMP8: new pretrained models available
Calcium imaging is only an indirect readout of neuronal activity via fluorescence signals. To estimate the true underlying firing rates of these neurons, methods for “spike inference” have been developed. They are useful to denoise calcium imaging data and make … Continue reading
A collaborative review on error signals in predictive processing
Predictive processing is one of the most influential ideas from computational neuroscience for the experimental neurosciences. However, definitions of predictive processing vary broadly, to the extent that “predictive coding” is used sometimes in a very narrow sense (there are specific … Continue reading
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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Two random but interesting papers on neurophysiology with behavior
Bagur, Bourg et al. (2022) from the Bathellier Lab in Paris make the interesting finding that the auditory code is represented as temporal sequences of neuronal activity in early auditory processing stages and as spatial patterns in auditory cortex. I … Continue reading
A blog about neurophysiology 