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Category Archives: Imaging
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
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
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
A blog about neurophysiology 