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Category Archives: Microscopy
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
All-optical entirely passive laser scanning with MHz rates
Is it possible to let a laser beam scan over an angle without moving any mechanical parts to deflect the beam? It is. One strategy is to use a very short-pulsed laser beam: A short pulse width means a finite … Continue reading
Whole-cell patch clamp, part 2: Line-frequency pick-up via the perfusion system
With the experience of more than one year of patching (although you might say that this is not a lot), I’m now used to problems that I can solve after some time, but without being able to tell what the problem has … Continue reading
Matlab code for control of a resonant scanning microscope
For control of resonant scanning 2P microscopes, my host lab uses a software that I have written in Matlab. Due to some coincidences, the software is based on Scanimage 4.2, a version developed few years ago for an interface with a Thorlabs scope and Thorlabs … Continue reading
Preamplifier bandwidth & two ways of counting photons
For two-photon point scanning microscopy, the excitation laser is typically pulsing at a repetition rate of 80 MHz, that is one pulse each 12.5 ns. To avoid aliasing, it was suggested to synchronize the sampling clock to laser pulses. For this, it is important … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy
Tagged Calcium Imaging, laser scanning microscopy, Microscopy, Scanning
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Whole-cell patch clamp, part 1: introductory reading
Ever since I my interested in neuroscience become more serious, I was fascinated by the patch clamp technique, especially applied for the whole cell. Calcium imaging or multi-channel electrophysiology (recent review) is the way to go in order to get an idea what … Continue reading
Posted in electrophysiology, Microscopy, zebrafish
Tagged Calcium Imaging, electrophysiology, patch clamp, zebrafish
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Neuroscience on Youtube
Recently, I’ve been to the Basel ICON conference, where the recent Nobel laureate Eric Betzig gave an impressive talk on microscopy techniques (including lattice light sheet, SIM and expansion microscopy). Some days ago, I found a similar talk by Eric … Continue reading
Posted in Data analysis, Microscopy, Network analysis
Tagged Data analysis, theoretical neuroscience
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Large field of view microscopes for mouse brain imaging
For typical confocal or two-photon microscopes that maintain (sub)cellular resolution, a high-magnification objective is needed (typically 16x, 20x or 25x). This in turn limits the field of view (FOV) to ⌀ 1.0-1.5 mm. For imaging in the mouse brain cortex, which is … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy
Tagged Calcium Imaging, laser scanning microscopy, Microscopy
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A blog about neurophysiology 