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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
Detecting single spikes from calcium imaging – March 21, 2025
Hodgkin-Huxley model in current clamp and voltage clamp – December 9, 2020
Simultaneous calcium imaging and extracellular recording from the same neuron – September 22, 2020
Discrepancies between calcium imaging and extracellular ephys recordings – September 14, 2020
The cell-attached soundtrack of calcium imaging – July 30, 2019
Whole-cell patch clamp, part 4: look and feel – October 27, 2018
Blue light-induced artifacts in glass pipette-based recording electrodes – August 27, 2018
Whole-cell patch clamp, part 3: Limitations of quantitative whole-cell voltage clamp – May 9, 2017
Whole-cell patch clamp, part 2: Line-frequency pick-up via the perfusion system – May 5, 2017
Whole-cell patch clamp, part 1: introductory reading – September 4, 2016
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Microscopy
Protocols to check the performance of your multiphoton microscope – March 18, 2025
A resource paper for building two-photon microscopes – September 28, 2024
Why your two-photon images are noisier than you expect – April 24, 2024
Improving the resonant scanner’s sync signal using a phase locked loop (PLL) – October 20, 2023
Interesting papers on online motion correction for calcium imaging – September 4, 2023
“Laser Scanners” by William Benner – November 15, 2022
Simple geometrical optics to understand and design point-scanning microscopes – May 28, 2022
Fast scanning, triplet states and photon yield – July 22, 2021
Heating up the objective for two-photon imaging – May 1, 2021
Interview with Bruno Pichler – September 25, 2020
Alignment tools – August 19, 2020
A practical guide for adaptive optics – November 21, 2019
Photon yield and pulse dispersion – March 13, 2019
Alvarez lenses and other strangely shaped optical elements – September 27, 2018
Springtime for two-photon microscopy – April 25, 2018
Can two-photon scanning be too fast? – December 4, 2017
All-optical entirely passive laser scanning with MHz rates – August 30, 2017
Matlab code for control of a resonant scanning microscope – December 1, 2016
Preamplifier bandwidth & two ways of counting photons – September 20, 2016
Fast z-scanning using a voice coil motor – April 6, 2016
Modulating laser intensity on multiple timescales (x, y and z) – March 25, 2016
Undistort/unwarp images for resonant scanning microscopy – February 16, 2016
Point spread functions – December 14, 2015
EODs for kHz imaging – August 29, 2015
A pockels cell with a broken crystal – August 27, 2015
Gain and photons per pixel – March 2, 2015
The excitation PSF in 2P point scanning – January 27, 2015
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Calcium imaging
How to compute ΔF/F from calcium imaging data – April 2, 2025
Accurately computing noise levels for calcium imaging data – April 25, 2025
Non-linearity of calcium indicators: history-dependence of spike reporting – March 14, 2025
Protocols to check the performance of your multiphoton microscope – March 18, 2025
Detecting single spikes from calcium imaging – March 21, 2025
Online spike inference with GCaMP8 – March 24, 2025
Spike inference with GCaMP8: new pretrained models available – August 22, 2024
Why your two-photon images are noisier than you expect – April 24, 2024
Interesting papers on online motion correction for calcium imaging – September 4, 2023
Self-supervised denoising of calcium imaging data – August 23, 2022
Video introduction to CASCADE – August 2, 2022
Large-scale calcium imaging & noise levels – October 4, 2021
5 reasons why to use Cascade for spike inference – August 9, 2021
Online spike rate inference with Cascade – May 13, 2021
Temporal dispersion of spike rates from deconvolved calcium imaging data – February 23, 2021
Simultaneous calcium imaging and extracellular recording from the same neuron – September 22, 2020
Discrepancies between calcium imaging and extracellular ephys recordings – September 14, 2020
Review: An artificial ground truth for calcium imaging – September 2, 2019
The cell-attached soundtrack of calcium imaging – July 30, 2019
How well do CNNs for spike detection generalize to unseen datasets? – June 23, 2018
How deconvolution of calcium data degrades with noise – August 22, 2017
A convolutional network to deconvolve calcium traces – August 1, 2017
Large field of view microscopes for mouse brain imaging – June 30, 2016
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Paper discussions
Interesting papers on the role of cell organelles in neuronal dendrites for calcium signaling – August 11, 2025
Interesting papers on VIP interneurons in cortex and hippocampus – June 23, 2025
Protocols to check the performance of your multiphoton microscope – March 18, 2025
A resource paper for building two-photon microscopes – September 28, 2024
Four interesting papers on astrocyte physiology – July 8, 2024
There is no recipe for discoveries – June 4, 2024
Three recent interesting papers on computational neuroscience – March 26, 2024
Two random but interesting papers on neurophysiology with behavior – October 15, 2023
Interesting papers on behavioral timescale synaptic plasticity (theory) – October 6, 2023
Interesting papers on behavioral timescale synaptic plasticity (experiments) – September 18, 2023
Interesting papers on recent neuroscience methods – September 12, 2023
Interesting papers on online motion correction for calcium imaging – September 4, 2023
Annual report of my intuition about the brain (2022) – December 31, 2022
Post-publication review: The geometry of robustness in spiking neural networks – October 9, 2022
Self-supervised denoising of calcium imaging data – August 23, 2022
Public peer review files – February 11, 2022
Post-publication review: Somato-dendritic coupling of L5 neurons in V1 – July 10, 2019
Post-publication review: Precise excitation-inhibition balance controls gain and timing in the hippocampus – June 19, 2019
Precise synaptic balance of excitation and inhibition – October 12, 2018
Finding the engram – August 27, 2015
Genetically encoded voltage sensors – August 16, 2014
Some interesting 2-photon microscopy papers – March 13, 2014
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Neuroscientific questions
Annual report of my intuition about the brain (2024) – January 8, 2025
A collaborative review on error signals in predictive processing – July 23, 2024
Annual report of my intuition about the brain (2022) – December 31, 2022
Annual report of my intuition about the brain (2021) – December 31, 2021
Annual report of my intuition about the brain (2020) – January 1, 2021
Annual report of my intuition about the brain (2019) – December 31, 2019
Annual report of my intuition about the brain – December 30, 2018
Entanglement of temporal and spatial scales in the brain, but not in the mind – September 15, 2018
The crow as an animal model for neuroscience – December 25, 2016
Aphantasia – November 14, 2015
Finding the engram – August 27, 2015
A neuronal network of pointers – June 18, 2015
The unsolved problems of neuroscience – March 28, 2015
Odd opinions in neurobiology – November 10, 2014
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Data analysis
How to compute ΔF/F from calcium imaging data – April 2, 2025
Accurately computing noise levels for calcium imaging data – April 25, 2025
Detecting single spikes from calcium imaging – March 21, 2025
Online spike inference with GCaMP8 – March 24, 2025
Spike inference with GCaMP8: new pretrained models available – August 22, 2024
Self-supervised denoising of calcium imaging data – August 23, 2022
Video introduction to CASCADE – August 2, 2022
5 reasons why to use Cascade for spike inference – August 9, 2021
Online spike rate inference with Cascade – May 13, 2021
Magic Matlab spells – April 24, 2020
The power of correlation functions – January 9, 2019
Spatial visualization of temporal components for neuronal activity imaging – May 3, 2016
A simple non-graphical user interface in Matlab: keyboard callback functions – June 24, 2015
Beyond correlation analysis: Dynamic causal modeling (DCM) – March 25, 2014
Beyond correlation analysis: Transfer entropy – March 19, 2014
Beyond correlation analysis: Granger causality – March 15, 2014
Beyond correlation analysis: incremental mutual information – March 12, 2014
Beyond correlation analysis: mutual information – February 15, 2014
Beyond correlation analysis – February 15, 2014
Beyond correlation analysis – February 8, 2014
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Deep learning
Spike inference with GCaMP8: new pretrained models available – August 22, 2024
Self-supervised denoising of calcium imaging data – August 23, 2022
Video introduction to CASCADE – August 2, 2022
5 reasons why to use Cascade for spike inference – August 9, 2021
Online spike rate inference with Cascade – May 13, 2021
Layer-wise decorrelation in deep-layered artificial neuronal networks – January 8, 2018
Understanding style transfer – December 5, 2017
The basis of feature spaces in deep networks – November 14, 2017
The most interesting machine learning AMAs on Reddit – August 22, 2017
Deep learning, part IV (2): Compressing the dynamic range in raw audio signals – October 5, 2016
Deep learning, part IV: Deep dreams of music, based on dilated causal convolutions – September 13, 2016
Deep learning, part III: understanding the black box – February 27, 2016
Deep learning, part II : frameworks & software – February 3, 2016
Deep learning, part I – January 27, 2016
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A blog about neurophysiology 