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Category Archives: Imaging
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
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
How deconvolution of calcium data degrades with noise
How does the noisiness of the recorded calcium data affect the performance of spiking-inferring deconvolution algorithms? I cannot offer a rigorous treatment of this question (Update August 2020: Now I have treated this question rigorously.) , but some intuitive examples. … Continue reading
A convolutional network to deconvolve calcium traces, living in an embedding space of statistical properties
As mentioned before (here and here), the spikefinder competition was set up earlier this year to compare algorithms that infer spiking probabilities from calcium imaging data. Together with Stephan Gerhard, a PostDoc in our lab, I submitted an algorithm based on convolutional networks. Looking … Continue reading
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 consciousness, electrophysiology, zebrafish
2 Comments
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
10 Comments
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
7 Comments
A blog about neurophysiology 