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Category Archives: Imaging
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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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
A blog about neurophysiology 