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Category Archives: Imaging
5 reasons why to use Cascade for spike inference
Our paper on A database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging is out now in Nature Neuroscience. It consists of a large and diverse ground truth database with simultaneous calcium imaging and juxtacellular recordings … Continue reading
Fast scanning, triplet states and photon yield
In point-scanning microscopy like two-photon or confocal microscopy, a focused laser beam is scanned across the field of view and thereby sequentially recovers an image of the object. In this blog post, I will discuss the idea that scanning faster … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy, Neuronal activity
Tagged Calcium Imaging, Microscopy, photons, Scanning, zebrafish
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Heating up the objective for two-photon imaging
To image neurons in vivo with a large field of view, a large objective is necessary. This big piece of metal and glass is in indirect contact with the brain surface, with only water and maybe a cover slip in … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy
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Interview with Bruno Pichler
Bruno Pichler studied medicine, obtained a PhD in neuroscience, worked in the labs of Arthur Konnerth, Tom Mrsic-Flogel and Troy Margrie, and was R&D manager at Scientifica, before founding his own company, INSS, “to provide the international neuroscience community with … Continue reading
Posted in Calcium Imaging, Data analysis, Imaging, Microscopy
Tagged interview, Microscopy, Two-photon
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Discrepancies between calcium imaging and extracellular ephys recordings
To record the activity from a population of neurons, calcium imaging and extracellular recordings with small electrodes are the two most widely used methods that are still able to disentangle the contributions from single units. Here, I would like to … Continue reading
Alignment tools
This blog posts covers some tools and techniques that I’m typically using to align two-photon microscopes. If you’re an expert, you will probably find nothing new, but if you haven’t been doing this for years, this might offer you some … Continue reading
Posted in Imaging, Microscopy
Tagged Alignment, laser scanning microscopy, Microscopy, Optics, Two-photon
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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
