Computational Neuroscience: Neural Data Analyses - Psychology 496/596L
Readings and Resources

• Class1 Introduction to biophysical neurons and neural networks.
  - Readings
  (optional): Neuroscience Primer: Brain Facts
  (optional) Basic Information about the brain from the Society for Neuroscience
  
  
• Class2 Basic recording techniques: single and multi unit data. Generating your own data: surrogate datasets, NEURON simulations.
  - Readings:
  Johnson, 1996: Point Process models of single-neuron discharges
  (optional) Reinagel and Reid, 2002: Precise Firing Events Are Conserved across Neurons
  (optional) Berry and Meister 1998: Refractoriness and Neural Precision
  (optional) Userey et. al, 2003: Receptive Fields and Response Properties of Neurons in Layer 4 of Ferret Visual Cortex
  
  Part I: Single unit data analyses

• Class3 Spontaneous activity: Spike count, firing rate, CV, return maps, fano factor.
  - Readings:
  Pare et al, 1998: Impact of Spontaneous Synaptic Activity on the Resting Properties of Cat Neocortical Pyramidal Neurons In Vivo
  Holt et al, 1996: Comparison of Discharge Variability In Vitro and In Vivo in Cat Visual Cortex Neurons
  (optional): Siegel 1990: Non Linear Dynamical Systems Theory and Primary Visual Cortical Processing
  (optional): Teich et al 1996: Temporal Correlation in Cat Striate-Cortex Neural Spike Trains
  
  
• Class4 Stimulus driven activity: Histograms, spike triggered average, PSTH.
  - Readings:
  Kara et al, 2000: Low Response Variability in Simultaneously Recorded Retinal, Thalamic, and Cortical Neurons .
  Reich et al, 1997: Response Variability and Timing Precision of Neuronal Spike Trains In Vivo
  (optional): Gur et al, 1997: Response Variability of Neurons in Primary Visual Cortex (V1) of Alert Monkeys
  (optional): Lewen et al, 2001: Neural coding of naturalistic motion stimuli
  
  
• Class5 Reverse correlations, tuning curves, receptive fields, discriminability and ROC curves.
  - Readings:
  Ringach and Shapley, 2004: Reverse Correlation in neurophysiology
  Userey et al, 2003: Receptive fields and response properties of neurons in Layer 4 of ferret visual cortex
  (optional) Quiroga et al, 2005: Invariant visual representation by single neurons in the human brain
  
  
• Class6 Rhythms and oscillations, autocorrelation, field potentials, power spectra and spectrogram.
  -Readings:
  Gray and di Prisco 1997: Stimulus-Dependent Neuronal Oscillations and Local Synchronization in Striate Cortex of the Alert Cat
  Kocsis and Li 2004: In vivo contribution of h-channels in the septal pacemaker to theta rhythm generation
  (optional): Ghose and Freeman 1992: Oscillation discharges in the visual system: Does it have a functional role?
  
  
• Class7 Spike timing and spike patterns. Reliability, precision.
  -Readings:
  Fellous et al., 2004: Discovering Spike Patterns in Neuronal Responses
  Ikegaya et al, 2004: Synfire Chains and Cortical Songs: Temporal Modules of Cortical Activity
  (optional) Mokeichev et al, 2007: Stochastic Emergence of Repeating Cortical Motifs in Spontaneous Membrane Potential Fluctuations In Vivo.
  (optional) Ikegaya et al, 2008: Statistical Significance of Precisely Repeated Intracellular Synaptic Patterns
  
  
• Class8 Displaying single unit data and analyses. Q&A for Midterm 1
  
  Part II: Multi-unit data analyses
  
  
• Class9 Population vectors, cortical maps.
  -Readings:
  Miller et. al, 1991: Representation of Sensory Information in the Cricket Cereal Sensory System. I. Response Properties of the Primary Interneurons.
  Crowe et. al, 2005: Dynamics of Parietal Neural Activity during Spatial Cognitive Processing.
  (optional) Fortier et. al, 1989: Cerebellar Neuronal Activity Related to Whole-Arm Reaching Movements in the Monkey
  
  
• Class10 Dimension reduction: PCA and ICA.
  - Readings:
  Chapin and Nicolelis 1999: Principal component analysis of neuronal ensemble activity reveals multidimensional somatosensory representations.
  Matsumoto et al, 2005: Population Dynamics of Face-responsive Neurons in the Inferior Temporal Cortex
  
  
• Class12 Cross correlations, joint-PSTH, synchrony and coherence.
  - Readings:
  Aersten et al, 1989: Dynamics of Neural Firing Correlation: Modulation of 'effective connectivity'
  Fries et al, 2001: Modulation of oscillatory neuronal synchronization by selesctive visual attention.
  (optional) Kimpo et al, 2003: Propagation of correlated activity through multiple stages of a neural circuit.
  
  
• Class13 Introduction to information theory. Measures of information (Shannon Vs Fisher).
  - Readings:
  Hastopoulos et al., 1998: Information about movement direction obtained from synchronous activity of motor cortical neurons.
  Dean et al. 2005: Neural population coding of sound level adapts to stimulus statistics.
  (optional) Kanitscheider et al., 2015: Measuring Fisher Information Accurately in Correlated Neural Populations
  

• Class14 Projects presentations.