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Author Archives: P.T.R. Rupprecht
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
Protocols to check the performance of your multiphoton microscope
In an exceptionally useful paper, Lees et al. provide a set of protocols for checking the performance of your multiphoton microscope: Standardized measurements for monitoring and comparing multiphoton microscope systems (link to preprint). The paper covers the following procedures: Check … 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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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
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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On the night train to FENS in Vienna
The FENS is the biggest neuroscientific conference in Europe. It is 5 days long and is attended by 5’000-10’000 participants. This year, the conference took place in Austria’s capital, Vienna, roughly 600 km from my current workplace in Zürich. Of … Continue reading
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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
A blog about neurophysiology 