All blog posts

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This is a thematically organized list of all blog posts. Please check out the chronologically ordered list as well.

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Electrophysiology

The cell-attached soundtrack of calcium imaging – July
Whole-cell patch clamp, part 4: look and feel
Blue light-induced artifacts in glass pipette-based recording electrodes
Whole-cell patch clamp, part 3: Limitations of quantitative whole-cell voltage clamp
Whole-cell patch clamp, part 2: Line-frequency pick-up via the perfusion system
Whole-cell patch clamp, part 1: introductory reading

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Microscopy

A practical guide for adaptive optics
Photon yield and pulse dispersion
Alvarez lenses and other strangely shaped optical elements
Springtime for two-photon microscopy
Can two-photon scanning be too fast?
All-optical entirely passive laser scanning with MHz rates
Matlab code for control of a resonant scanning microscope
Preamplifier bandwidth & two ways of counting photons
Fast z-scanning using a voice coil motor
Modulating laser intensity on multiple timescales (x, y and z)
Undistort/unwarp images for resonant scanning microscopy
Point spread functions
EODs for kHz imaging
A pockels cell with a broken crystal
Gain and photons per pixel
The excitation PSF in 2P point scanning

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Calcium imaging

Review: An artificial ground truth for calcium imaging – September
The cell-attached soundtrack of calcium imaging – July
How well do CNNs for spike detection generalize to unseen datasets?
How deconvolution of calcium data degrades with noise
A convolutional network to deconvolve calcium traces
Large field of view microscopes for mouse brain imaging

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Paper discussions

Post-publication review:┬áSomato-dendritic coupling of L5 neurons in V1 – July
Post-publication review: Precise excitation-inhibition balance controls gain and timing in the hippocampus – June
Precise synaptic balance of excitation and inhibition
Genetically encoded voltage sensors
Some interesting 2-photon microscopy papers

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Neuroscientific questions

Annual report of my intuition about the brain (2019)
Annual report of my intuition about the brain
Entanglement of temporal and spatial scales in the brain, but not in the mind
The crow as an animal model for neuroscience
Aphantasia
Finding the engram
A neuronal network of pointers
The unsolved problems of neuroscience
Odd opinions in neurobiology

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Data analysis

The power of correlation functions
Spatial visualization of temporal components for neuronal activity imaging
A simple non-graphical user interface in Matlab: keyboard callback functions
Beyond correlation analysis: Dynamic causal modeling (DCM)
Beyond correlation analysis: Transfer entropy
Beyond correlation analysis: Granger causality
Beyond correlation analysis: incremental mutual information
Beyond correlation analysis: mutual information
Beyond correlation analysis
Beyond correlation analysis

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Deep learning

Layer-wise decorrelation in deep-layered artificial neuronal networks
Understanding style transfer
The basis of feature spaces in deep networks
The most interesting machine learning AMAs on Reddit
Deep learning, part IV (2): Compressing the dynamic range in raw audio signals
Deep learning, part IV: Deep dreams of music, based on dilated causal convolutions
Deep learning, part III: understanding the black box
Deep learning, part II : frameworks & software
Deep learning, part I

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Various other topics

Open access 3D electron microscopy datasets of brains
A list of cognitive biases
A short report from a Cold Spring Harbor lab course
The spikefinder dataset
Spike detection competition
Weblogs on circuit and cellular neuroscience
The larval zebrafish, and the adult zebrafish
Neuroscience on Youtube
Reglo ICC serial port control via Matlab
Colormaps (without colorspace theory)
Neuroengineering blogs