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Rotating the field of view to follow the biology
Microscopes are designed to image flat surfaces, unlike the curved structures typical for biology. Here, I would like to mention a piece of work where we demonstrate a method based on K-mirrors to overcome this lack of flexibility for two-photon … Continue reading
Posted in Calcium Imaging, hippocampus, Imaging, Microscopy, Neuronal activity, neuroscience
Tagged Calcium Imaging, Microscopy, Scanning, science, technology
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CascadeTorch: a PyTorch version of Cascade for spike inference
I’m glad to share a PyTorch-based implementation of spike inference from calcium imaging data: CascadeTorch, now available on GitHub. The original Cascade repository remains fully supported. This post explains why I re-implemented Cascade in Torch, and what this means for … Continue reading
Dirigo: a future Python alternative to Scanimage?
Over the last 20 years, many microscopes that are capable of resonant scanning two-photon microscopy have converged on using ScanImage, a powerful software package with many strengths but also two downsides: First, it is no longer open-source, and second, it … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy, neuroscience
Tagged Calcium Imaging, Microscopy, photons, Scanning, technology
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Online spike inference with GCaMP8
Calcium imaging is used to record the activity of neurons in living animals. Often, these activity patterns are analyzed after the experiments to investigate how the brain works. Alternatively, it is also possible to extract the activity patterns in real … Continue reading
Non-linearity of calcium indicators: history-dependence of spike reporting
Calcium indicators are used to report the calcium concentration inside single cells. In neurons, calcium imaging can be used as a readout of neuronal activity (action potentials). However, some calcium indicators like GCaMP transform the calcium concentration of a cell … Continue reading
