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Category Archives: Imaging
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
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
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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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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A blog about neurophysiology 