Category Archives: Microscopy

Dirigo: a future Python alternative to Scanimage?

Over the last 20 years, many microscopes that are capable of resonant scanning two-photon microscopy have converged on using ScanImage, a powerful software package with many strengths but also two downsides: First, it is no longer open-source, and second, it … Continue reading

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Interesting papers on astrocyte ultrastructure and function

Astrocytes are brain cells that are often completely overlooked and dismissed or, in the opposite extreme, presented as mysterious devices that somehow solve all problems of computational neuroscience. The truth is somewhere in the middle, but it is not clear yet where exactly. First of all, we still do not understand even the basic mechanistic rules by which individual astrocytes operate. For neurons, we have precise, often even mathematical ideas how they receive input via synapses, how they depolarize, and how depolarizations propagate to the soma and elicit action potentials. For astrocytes, this mechanistic book of rules is still missing – and this gap limits our ability to interpret experiments or build coherent theories. Continue reading

Posted in Astrocytes, Calcium Imaging, Data analysis, Microscopy, neuroscience, Reviews | Tagged , , , | Leave a comment

I never meant to study the brainstem

I was recently invited to contribute a guest post on Substack by Vijay Iyer – some years ago one of the main developers of ScanImage in the lab of Karel Svoboda, and more recently a strong advocate for ME/CFS awareness … Continue reading

Posted in Astrocytes, Brain machine interface, Calcium Imaging, hippocampus, Locus coeruleus, Microscopy, writing | Tagged , , , , , , , | Leave a comment

Displaying the hippocampus as EM image on the office wall

One of the most amazing methods in modern neuroscience is dense volumetric electron microscopy of the brain. I have mentioned some openly accessible datasets before (see my previous blog post), but many additional datasets have been released since then – … Continue reading

Posted in Data analysis, hippocampus, Imaging, Microscopy, Network analysis, neuroscience | Tagged , | 3 Comments

Interesting papers on the role of cell organelles of neuronal dendrites in calcium signaling

Researchers utilize calcium imaging to track neuronal activity in the brain, highlighting the role of calcium as a signaling molecule. Recent studies investigate intracellular calcium dynamics, particularly its coupling between organelles and its influence on synaptic plasticity in dendrites. Findings emphasize the necessity of in vivo methods for accurate insights into neuronal behavior. Continue reading

Posted in Calcium Imaging, Data analysis, hippocampus, Microscopy, neuroscience, Reviews | Tagged , | 2 Comments

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

Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, machine learning, Microscopy, Neuronal activity, neuroscience | Tagged , , , , , | Leave a comment

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

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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

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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

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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

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