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Tag Archives: Data analysis
Subcellular calcium and voltage imaging of pyramidal neurons in mouse hippocampus
Dendrites are the tree-like arborizations of neurons through which they receive input from other neurons. This compartmentalized anatomy has given rise to the idea that individual dendrites process information independently from each other and from the soma. This idea has … Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, Microscopy, Neuronal activity, neuroscience, Reviews
Tagged Data analysis, Calcium Imaging, Microscopy, Scanning
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CascadeTorch: a PyTorch version of Cascade for spike inference
I’m glad to share a PyTorch-based implementation of spike inference from calcium imaging data: CascadeTorch, now available on GitHub. The original Cascade repository remains fully supported. This post explains why I re-implemented Cascade in Torch, and what this means for … Continue reading
Annual report of my intuition about the brain (2025, part III)
How does the brain work, and how can we understand it? To approach this big question from a broad perspective, I want to report on some ideas about the brain that marked me most over the past twelve months and that, on the … Continue reading
Annual report of my intuition about the brain (2025, part I)
How does the brain work, and how can we understand it? To approach this big question from a broad perspective, I want to report on some ideas about the brain that marked me most over the past twelve months and that, on the … Continue reading
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 Data analysis, Microscopy
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Interesting papers on VIP interneurons in cortex and hippocampus
Interneurons are inhibitory neurons in the brain that are thought to shape the computations performed by principal cells. The effects of inhibition can be rather diverse, depending on which neurons – or which parts of a neuron (dendrites, soma, or … Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, Neuronal activity, neuroscience, Reviews
Tagged Calcium Imaging, Data analysis
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Accurately computing noise levels for calcium imaging data
It is fascinating how much data quality can vary between different calcium imaging data sets. In this blog post, I will discuss a metric to quantify and compare data quality and in particular shot noise between calcium imaging datasets. This … Continue reading
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
A blog about neurophysiology 