Systems Neuroscience (online course)


Marty Sereno (homepage) — email: OR
Example lecture times: Mon/Wed/Fri, 9:00-9:50 AM
Example advanced/grad section: Fri, 8:00-8:50 AM
See also Foundations of Neuroimaging (online course)

Course Description:
This is a comprehensive online course on systems neuroscience: neuroanatomy and neurophysiology with a signals and systems perspective. We cover the following topics:
  • cellular neurophysiology (Nernst, voltage/ligand gating, dendritic currents, H-H)
  • relation to simple neural-like models (Hebb, attractor, backprop)
  • neuronal development (early, cylindrical coordinates, cortical plate, maps)
  • visual system (receptors, streams, cortex, maps, motion, attention, objects)
  • somatosensory system (receptors, spinal cord, pathways, cortex, plasticity)
  • auditory system (receptors, time/amplitude, binaural, cortex, owls, bats)
  • eye movements (VOR/OKN/pursuit, saccades, multisensory align)
  • motor system (anatomy, evolution of pattern generators, motor cortex)
  • cerebellum (anatomy, physiology, maps, learning)
  • striatum (anatomy, cellular physiology, hierarchical loops)
  • limbic systems (connections, place/head-direction/grid, models)
  • neuroimaging (Bloch equation, Fourier transform image formation)
  • origin of language (primate evolution, birdsong, scene assembly)
Special thanks to SDSU Physics Professor Matt Anderson and SDSU Instructional Technologies Services for the use of Matt's Learning Glass lecture recording system, and David Poddig and Stan Greene for inspiration and production. This course was developed and taught at UCSD, Birkbeck/UCL (London), and SDSU.

• Sereno lecture recordings: direct video links or youtube playlist (equivalent)
     (52 one-hour lectures: about one semester or two quarters)
• Sereno lecture notes PDF (169-page PDF [28MB], rough draft)
• References: background reading PDFs
• Neuroscience reference texts:
     Squire, Berg et al., eds. (2008/2013) Fundamental Neuroscience, 3rd/4th ed.
     Kandel, Jessell, Schwartz, eds. (2008/2012) Principles of Neural Science, 5th/6th ed.
     Nieuwenhuys, Voogd, van Huijzen (2008) The Human Central Nervous System, 4th ed.
• Neuroscience ugrad textbooks:
     Nicholls et al. (2012) From Neuron to Brain, 5th ed.
     Bear, Connors, & Paradiso (2006/2015) Neuroscience: Exploring the Brain, 3rd/4th ed.

multiple question short-answer, each question with a few subsections
2 midterms, final exam, short paper (midterms: 24% each, final exam: 32%, paper: 20%)
example tests: midterm1, midterm2, and final

Lecture Topics (e.g., Spring semester course) (1-page PDF syllabus)

Week 1Introduction

introduction to course, folk theory of brain function
resting/Nernst/reversal potential
[no grad lecture]

Week 2 (Mon/Wed/Fri)Cellular Physiology

action potential, voltage-gated channels
voltage-sensitive dendritic currents, bursting
neurotrans.-gated post-synaptic potentials, NMDA, LTP/STDP
grad lecture: Hodgkin-Huxley, integrate-and-fire models

Week 3 (Mon/Wed/Fri)Relation to Neural Models

current flow in dendrites, equivalent circuits
simple Hebbian network model of orientation selectivity
simple attractor network model, energy analysis
grad lecture: covariance/eigenvector analysis of Hebbian learning

Week 4 (Mon/Wed/Fri)Neural Development

blastula, gastrula, neural plate, neural tube, optic cup
cylindrical coord system, temporal lobe formation, 'rule of Sereno'
grad lecture: later development, gyrification, cortical subplate

Week 5 (Mon/Wed/Fri)Visual System I

retinal circuitry, origin of processing streams
retina to dLGN as a conformal map, layers
visual cortical maps: V1, V2, MT and the rest
grad lecture: achiasmatic sheepdog map mechanics, backpropagation

Week 6 (Mon/Wed/Fri)Visual System II

cortical layer scheme, streams: edges/brightness/motion in V1
V2 compartments, simple/complex/hypercomplex, 1st midterm review
Gabor filter model, aperture problems for color, pattern translation
1st Midterm Exam Due

Week 7 (Mon/Wed/Fri)Visual System III

aperture problem for complex motion, position invariance, contour analog
explicit V1-to-MT model, Horn and Schunck gradient model
grad lecture1: smoothness constraint, line processes, stereo
cortical-wide mechanisms of visual attention
grad lecture2: true color, stereo and motion, object recognition

Week 8 (Mon/Wed/Fri)Somatosensory System

somatosensory receptor types, spinal cord
arm muscle diagram, ascending pathways: dorsal column, spinothalamic
somatosensory cortical areas, discontinuities, plasticity

Week 9 (Mon/Wed)Auditory System I

hair cell receptors, lateral line, electric fish
cochlear structure/transduction, 1D vs. 2D maps, mammalian brainstem
[no class Fri]

Week 10 (Mon/Wed/Fri)Auditory System II

cochlear nuclei responses, auditory streams
nucleus laminaris coincidence detection
construction of the owl space map
grad lecture: auditory thalamus, cortex, freq vs. pitch


[no class Mon]
[no class Wed]
[no class Fri]

Week 12 (Mon/Wed/Fri)Motor System I

bat echolocation and speech sound processing
gaze stabilization (VOR, OKN, pursuit)
superior colliculus retinal and motor maps, double-step remapping
grad lecture: bat FM, phonetics, auditory attention

Week 13 (Mon/Wed/Fri)Motor System II

multisensory map alignment: superior colliculus, VIP, LIP
motor system overview, spinal/brainstem pattern generators
motor cortex, 2nd midterm review
grad lecture: spatial->temp and temp->spatial, WTA, human VIP

Week 14 (Mon/Wed/Fri)Motor System III

2nd Midterm Exam Due
cerebellum: connections, microanatomy, learning
striatum: connectional/functional overview, hierarchical sequencing
grad lecture: origin of language I: vocal learning

Week 15 (Mon/Wed/Fri)Limbic System

connectional overview limbic system
hippocampus: H.M./intermediate term memory vs. inertial guidance
head direction and grid cells, attractor models
grad lecture: origin of language II: language and scenes

Week 16 (Mon/Wed)Neuroimaging MRI/EEG/MEG

source of EEG/MEG, MRI hardware, spin vs. precession, Bloch equation
Fourier transform, relation to MRI image formation
Course review

Week 17Finals Week

Final Exam
Short final paper due

last modified: Jul 2023
Scanned/video'd class notes (pdf, links above) © 2023 Martin I. Sereno
Supported by NSF 0224321, NIH MH081990, Royal Society Wolfson
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