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Category Archives: neuroscience
How to compute ΔF/F from calcium imaging data
Many neuroscientists use calcium imaging to record the activity from neurons (or other cells in the brain). The video below was recorded by Sian Duss and me in hippocampal CA1 pyramidal cells in mice. To make calcium imaging traces comparable … Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, Microscopy, neuroscience
Tagged Calcium Imaging, Data analysis
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Online spike inference with GCaMP8
Calcium imaging is used to record the activity of neurons in living animals. Often, these activity patterns are analyzed after the experiments to investigate how the brain works. Alternatively, it is also possible to extract the activity patterns in real … Continue reading
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
How to use Google Scholar as a neuroscientist
Google Scholar is a search engine for scientific publications. There are alternatives like PubMed (not a search engine but a database, often used in the medical field), Semantic Scholar (also a database, but with richer annotations), Citation Gecko (to discover … Continue reading
Posted in neuroscience, Review, Reviews, writing
Tagged Literature search, neuroscience, science
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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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A resource paper for building two-photon microscopes
The article discusses the challenges in learning to build microscopes, highlighting a manuscript by Schottdorf et al. that offers practical assembly instructions and rationale based on years of successful use. It emphasizes useful insights, such as design suggestions, performance compromises, and comprehensive documentation on GitHub, making it a valuable resource for researchers. Continue reading
Posted in Calcium Imaging, Imaging, Microscopy, neuroscience
Tagged Calcium Imaging, Microscopy, neuroscience, papers, photons, Scanning, science
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How to do science according to Ardem Patapoutian
Ardem Patapoutian is a neuroscientist who works on the molecular basis of sensation via mechanosensitive ion channels. In 2021, he was one of the recipients of the Nobel prize, at a relatively young age. He has since used his influence … Continue reading
Posted in neuroscience, Uncategorized
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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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A blog about neurophysiology 