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Author Archives: P.T.R. Rupprecht
Neuro Methods
One of the most important unseen developments in neuroscience during the years 2010-2020 was the creation of online community spaces for open exchange about methods. One of these places was Science Twitter, which was used as an exchange platform for … Continue reading
Posted in Calcium Imaging, Data analysis, electrophysiology, Links, Microscopy, neuroscience
Tagged Calcium Imaging, electrophysiology, Microscopy
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Astigmatism in a microscopy point spread function
To assess the resolution of your microscope, measuring the point spread function (PSF) is one of the most basic and reliable methods. The PSF essentially shows how large the image of a very small, often sub-diffractive object will be. See … Continue reading
What happens inside your brain when you form a memory?
Kurzgesagt is a Youtube channel that breaks down science topics for a broad audience. They have great videos, both in terms of narrative, animation, and scientific accuracy. A few days ago, the channel dropped a video that addresses a neuroscientific … Continue reading
Posted in hippocampus, Locus coeruleus, neuroscience, Reviews
Tagged Kurzgesagt, Memory, Neuronal ensembles, neuroscience, Plasticity, Replay, Reviews, science, theoretical neuroscience, Youtube
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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
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
Posted in Astrocytes, Calcium Imaging, hippocampus, Imaging, Locus coeruleus, neuroscience
Tagged Astrocytes, Calcium Imaging, hippocampus, Interneurons, Locus coeruleus, Microscopy, neuroscience, science
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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
A blog about neurophysiology 