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Category Archives: neuroscience
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
A clearing method for large human FFPE tissue blocks
During the lockdown in 2020, I was forced to stop my own experiments in the lab. This is when I turned to computational and analysis side-projects that since then have become quite central to my own work and approach to … Continue reading
Posted in Data analysis, Imaging, Microscopy, neuroscience
Tagged Dopamin, FFPE, Human brain, Light-sheet microscopy, Microscopy, Neuropathology, Pathology, Substantia nigra
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Hippocampal neuron and astrocyte responses to noradrenaline and natural arousal
Over the past few years, I worked with Sian Duss, a very skilled and talented PhD student in the lab of Johannes Bohacek, to dissect the role of noradrenaline release in the hippocampus. I’m very excited that the manuscript describing … 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 II)
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
Posted in Calcium Imaging, closed-loop, Imaging, neuroscience, Reviews
Tagged brain, Calcium Imaging, electrophysiology, Microscopy, neuroscience
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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
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
Posted in Calcium Imaging, Imaging, Microscopy, neuroscience
Tagged Calcium Imaging, Microscopy, photons, Scanning, technology
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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 Calcium Imaging, Microscopy, neuroscience, science
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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 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 Calcium Imaging, Microscopy
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A blog about neurophysiology 