Neuroinformatics�Analysis of multiple spike trains

Kenneth D. Harris, UCL

What drives brain activity?

Sensory stimulus

(controlled by experimenter)

Internal state

Neurons you happen to be recording

Observable behavior

Cross-correlogram

Cortex: putative monosynaptic connections between putative excitatory (red) and FS inhibitory cells (Bartho et al J Neurophys 2004)

CA1: non-synaptic CCGs between putative excitatory cells (Harris et al Nature 2003)

Scaling for cross correlogram

Types of correlation

• Spontaneous correlation
• No controlled stimuli

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• Stimulus-dependent correlations (“signal correlation”)
• Stimulus drives both cells to fire, so they are correlated

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• Stimulus-independent correlations (“noise correlation”)
• Correlation between responses to repeated stimulus

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• Total correlation
• Stimuli present but don’t care whether they cause

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How to compute them

• Spontaneous correlation, total correlation
• straightforward

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• Stimulus-dependent correlation
• Correlate activity of cell 1 on repeat 1 with cell 2 on repeat 2
• Don’t correlate average responses across repeats (Why?)

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• Stimulus-independent correlation
• Correlate difference to mean response

Joint peristimulus time histogram (JPSTH)

https://www.med.upenn.edu/mulab/jpst.html

Conditional independence

• There are no correlations between cells other than those imposed by the stimulus

Cell

Repeat

Cell

Repeat

Looks conditionally

independent

Not conditionally

independent

Peer-prediction

• When you have lots of cells: predict 1 cell from the activity of the others

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• Can you predict it better than you could from the stimulus?

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• If so, suggests not conditionally independent

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Peer prediction for hippocampal place cells

Harris et al Nature 2003

Timescale of peer prediction

Harris et al Nature 2003

Spontaneous activity in mouse V1

Stringer et al Science 2019

https://github.com/MouseLand/rastermap

Shared variance components analysis

Stringer et al Science 2019

What drives brain activity?

Sensory stimulus

(controlled by experimenter)

Internal state

Neurons you happen to be recording

Observable behavior

Multidimensional prediction from behavior video

Stringer et al Science 2019

Stimulus-independent activity is almost orthogonal to stimulus-related activity

Cross-validated PCA to find high-dimensional structure of stimulus-dependent correlations

Stringer et al Nature 2019

Power-law eigenspectra

Stringer et al Nature 2019

Power-law eigenspectra

Stringer et al Nature 2019