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Tag Archives: Microscopy
A practical guide for adaptive optics
There is no standard curriculum to learn practical procedures about microscopy: how to align a setup, how to identify misalignments, how to identify broken parts, where to buy components, how to check their performance, and much more. How to learn … Continue reading
Review: An artificial ground truth for calcium imaging
Selected paper: Charles, Song, Tank et al., Neural Anatomy and Optical Microscopy Simulation (NAOMi) for evaluating calcium imaging methods, bioRxiv (2019). What is the paper about? Calcium imaging is a central method to observe neuronal activity in the brain of … Continue reading
Posted in Calcium Imaging, Data analysis, Imaging, Microscopy, Neuronal activity, Reviews
Tagged Data analysis, Microscopy, photons, PSF, Scanning
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The cell-attached soundtrack of calcium imaging
Old-school electrophysiologists like to listen to the ephys signals during experiments. For example, this allows to precisely hear when the patch pipette approaches a target neuron. The technique is discussed in the Axon Guide: “Audio Monitor: Friend or Foe?”. The … Continue reading
Posted in Calcium Imaging, electrophysiology, Imaging, Neuronal activity, zebrafish
Tagged electrophysiology, Microscopy, photons, zebrafish
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Photon yield and pulse dispersion
This case report describes how a two-photon microscope was found to come with a fluorescence yield that was lower than expected; how the underlying cause was found out in a systematic manner; and how the problem was solved. All approaches and solutions are specific for the microscope under question. However, I hope that this report (1) will inspire other people who are troubleshooting or optimizing their microscopes, (2) will help other people better understand two-photon microscopes and the relevance of technical details. Continue reading
The power of correlation functions
During my physics studies, I got to know several mathematical tools that turned out to be extremely useful to describe the world and to analyze data, for example vector calculus, fourier analysis or differential equations. Another tool that I find … Continue reading
Posted in Calcium Imaging, Data analysis, electrophysiology
Tagged Data analysis, electrophysiology, Matlab, Microscopy, Python
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Whole-cell patch clamp, part 4: look and feel
In previous blog posts, I have been discussing some aspects of whole-cell patch clamp recordings ([1], [2], [3], [4]). Today, I will show some instructive videos that I recorded during experiments. I’m hoping that they will convey the look and feel … Continue reading
Posted in Calcium Imaging, electrophysiology, Imaging, Microscopy, Neuronal activity, zebrafish
Tagged electrophysiology, Microscopy, photons, zebrafish
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Alvarez lenses and other strangely shaped optical elements
In typical microscopes, lenses or mirrors are moved forth and back to change the position of their focus. Tunable lenses like the electro-tunable lens or the TAG lens, on the other hand, are deformed by an external force and thereby … Continue reading
Open access 3D electron microscopy datasets of brains
One of the coolest technical developments in neuroscience during the last decade has been driven by 3D electron microscopy (3D EM). This allowed to cut large junks of small brains (or small junks of big brains) into 8-50 nm thick … Continue reading
Posted in Data analysis, machine learning, Microscopy, Network analysis, zebrafish
Tagged Data analysis, Microscopy, Network analysis, zebrafish
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Springtime for two-photon microscopy
Today, the fields and forests around Basel are full of flowers that try to disseminate their pollen. Fixed pollen are, apart from sub-diffraction beads and the convallaria rhizome, one of the most commonly used test/reference samples for fluorescence microscopy. This … Continue reading
Can two-photon scanning be too fast?
The following back-of-the-envelope calculations do not lead to any useful result, but you might be interested in reading through them if you want to get a better understanding of what happens during two-photon excitation microscopy. The basic idea of two-photon microscopy … Continue reading
A blog about neurophysiology 