Category Archives: Neuronal activity

Whole-cell patch clamp, part 3: Limitations of quantitative whole-cell voltage clamp

Before I first dived into experimental neuroscience, I imagined whole-cell voltage clamp recordings to be the holy grail of precision. Directly listening to the currents that take place inside of a living neuron! How beautiful and precise, compared to poor-resolution techniques like fMRI or … Continue reading

Posted in Data analysis, electrophysiology, Neuronal activity, zebrafish | Tagged , , | 3 Comments

The crow as an animal model for neuroscience

Close to my apartment in the outskirts of Basel, green fields and some small woods lie basically in front of my house door. This is also where some flocks of crows gather around, partly searching the fields for food, partly … Continue reading

Posted in electrophysiology, Imaging, Neuronal activity, Uncategorized | Tagged , , | Leave a comment

Weblogs on circuit and cellular neuroscience

A couple of days ago, I discovered a list of neuroblog feeds managed by Neurocritic, covering almost 200 blogs in total. Out of those, I picked the blogs most relevant for circuit and cellular neuroscience. This excludes most blogs on cognitive neuroscience and … Continue reading

Posted in Links, Neuronal activity | Tagged , | 1 Comment

The zebrafish, and the other zebrafish

Zebrafish are often used as a model organism for in vivo brain imaging, because they are transparent. Or at least that is what many people think who do not work with zebrafish. In reality, most people use zebrafish larvae for in vivo … Continue reading

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Spatial visualization of temporal components for neuronal activity imaging

The standard analysis workflow for neuronal activity imaging based on calcium signals is to 1) draw ROIs around putative neurons, 2) extract the average fluorescence time trace of this ROI, 3) work with this timetrace for subsequent analysis (principal components, … Continue reading

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Fast z-scanning using a voice coil motor

We just published a paper on fast remote z-scanning using a voice coil motor. For 2P calcium imaging. It’s a nice paper with some interesting technical details. The starting point was the remote z-scanning scheme used by Botcherby et al. (2012) from … Continue reading

Posted in Calcium Imaging, Imaging, Microscopy, Neuronal activity | Tagged , , , | 2 Comments

Beyond correlation analysis

There are many papers out that use calcium imaging of a lot (tens to thousands) of neurons in animal brains. When I first encountered these kind of publications (roughly a year ago), it took me some hours to become familiar … Continue reading

Posted in Calcium Imaging, Data analysis, Neuronal activity | 2 Comments