Category Archives: Microscopy

Astrocytes hiding in a hippocampal CA3 EM dataset

Few things in neuroscience are more beautiful than the ultrastructure of individual neurons. Zhihao Zheng and his colleagues from the Tank/Seung labs have now published a 3D electron microscopy dataset from hippocampal CA3. All neurons in this volume were automatically … Continue reading

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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 , , | Leave a comment

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

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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 , , , | Leave a comment

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

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

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

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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

Posted in Data analysis, fMRI, Imaging, machine learning, Microscopy, Network analysis, Neuronal activity, neuroscience, Reviews | Tagged , , , , | 4 Comments

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

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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