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Category Archives: Calcium Imaging
Open PhD position in my research group
Are you a finishing Master’s student with a quantitative background and are interested in neuroscience? This is your opportunity. Project: You will be supervised by Dr. Peter Rupprecht and Prof. Fritjof Helmchen at the Brain Research Institute, University of Zurich. … Continue reading
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
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
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
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 