What can we measure:An experimentalist’s

perspective

Mathematical Neuroscience conference

Theoden Netoff

Assistant Professor of Biomedical Engineering

Brain Signals that can be recorded

• Electrical• Chemical• Magnetic• Response to magnetic pulses• Changes in blood flow• Metabolic changes in cells

– Glucose consumption– Oxidative state of NADP

• Scattering properties• X-ray absorption• How Sound waves pass through the brain• Gene expression

Multiple scales neurophysiology

homepage.mac.com/dtrapp/eChem.f/labB3.html

Ion Channels

Cells

Networks Cortex

Point mutationsUpregulationModulation

Dendritic morpohology

Mossy fiber tract sproutingChanges in stim response

Pathalogical EEG

Ramon y Cajal

Lesions:

Pros:• Directly relates

brain area to behavior

Cons:• Mostly case

studies• Cannot be

repeated

What is the signal:• Functional loss following an injury

• Wallarian degeneration used to track pathways

Harlow 1868

Phineas Gage

Natural History Museum, Lausanne

3500 BC, Iron age Trepanation

neuraldump.com/2007/09/patient-hm.html

The canonical neuron

• Soma• Dendrites: Inputs• Axon: Outputs

Patch clamp recording:

Pros:• Very high fidelity

recording• Neuron can be

identified morphologically by staining

• Neuron can be stimulated

Cons:• Limited

number of cells that can be recorded

• Cell type cannot be definitively determined physiologically

What is the signal:• Glass tube filled with salt solution applied to

neuron to make low noise junction with neuron

Electrode-Cell circuit

Axon Guide

Patch clamp recording

Hamill et al., 1981

Single channel recording

Sakmann and Neher, 1984

http://butler.cc.tut.fi/~malmivuo/bem/bembook/04/04.htm

Sodium and potassium channels

http://butler.cc.tut.fi/~malmivuo/bem/bembook/04/04.htmHille, 1992

Whole cell recording

Hasselmo et al, J. Neurophysiol 2000

The “Sag” current

Intracellular and local field potentials

Netoff and Schiff, 2002

Local field recordings:

Pros:• Multiple cells

can be recorded at once

• Can be done in vivo

Cons:• Cell that is

being recorded cannot be positively identified

What is the signal:

• Electrode placed into the brain to record electric fields

www.berkelab.org/Techniques.html

Tetrode Neural recordings

Slide courtesy of Adam Johnson and David Redish

Place cells

O’Keefe, 1978

Kneirim et al., 1995 Slide courtesy of Adam Johnson and David Redish

EEG signal source:Dendritic currents

• Apical dendrite acts as a dipole

• Dendritic currents, not action potentials, summate best

• Electrical signal is strongly attenuated at the scalp.

• Inhibitory neuron populations do not produce good dipoles

http://www.biosemi.com/pin_electrode.htm

EEG Signal confounds correlation and activity

• Populations of cells that are synchronous and have dendrites lined up produce strong signals

Sensitivity of neuron depends on orientation to electric field

• Rushton, 1927:

-Excitability roughly proportional to the cosine of the ange between current and nerve.

Current perpendicular to the nerve cannot stimulate an action potential.

Degree of asymmetry of neuron determines strength of response to electric field and the field it

produces

Chan and Nicholson, 1986

Computed Tomograpy :3d X-ray reconstruction of the head

Pros:• High spatial

resolution• Non-invasive,

but does require X-rays

Cons:• Poor constrast

between tisses• Limited to

anatomical scans

www.csmc.edu/6158.html

What is the signal:• X-rays are projected through the head. The signal is

rotated around the head and a 3D reconstruction is formed with the aid of a computer.

Magnetic Resonance Imaging :Interaction with tissue and magnetic field

Pros:• High spatial

resolution• Non-invasive• Good white/Gray

matter contrast

Cons:• Water signals do

not provide good temporal signals, but other signals can be measured

• Expensive to run

http://en.wikipedia.org/wiki/Image:MRI_head_saggital.jpg

What is the signal:• Hydrogen atoms are pumped to high energy state with

Electromagnetic wave. • Turn off EMF wave and measure time of relaxation to low

energy state• Strength of signal varies with water density. Gray matter

has higher water density than white matter• Frequency is different as field strength falls off allowing

for depth imaging

Functional MRI:MRI of signals that change over time

Pros:• Medium spatial

resolution with depth• Non-invasive• Flexibility in signals

that can be measured• Can be laid directly

over an anatomical scan

Cons:• Slow temporal scale• Assumes relation of

activity to blood flow, but what causes increase in metabolism is not a unique set

• Expensive to runen.wikipedia.org/wiki/Positron_emission_tomography

What is the signal:• Changes in MR signal with time.• Depending on the RF pulse frequency, different

molecules can be imaged besides hydrogen.• BOLD- hemoglobin changes from paramagnetic to

diamagnetic when oxygenated

MRI Imaging signals:HemoglobinCholine

http://www.cem.msu.edu/~reusch/VirtTxtJml/Spectrpy/nmr/nmr1.htm

CreatineLactateN-acetlyaspartate

Positron Emission Tomography:Sequestration of radioactive isotopes in tissue

Pros:• Medium spatial

resolution with depth

• Non-invasive• Flexibility in signals

that can be measured

Cons:• Only slow

metabolic activity can be imaged

• Exposure to radiation

• Very Expensive to run

en.wikipedia.org/wiki/Positron_emission_tomography

What is the signal:• Radioactive isotope of a molecule is developed using an

accelerator• A neurotransmitter or glucose are made with the isotope

and injected into the subject• The brain sequesters the radioactive molecules into

active spots where it makes hot spots of gamma • Using a scintillator material gamma radiation is converted

to light and imaged.

PET molecules:Fluorodeoxyglucose2-Deoxy glucoseWaterAmmoniaDopamineSeretonin

Magnetoencephalography:Magnetic signals from the brain

Pros:• Non-invasive• Source localization

is done to estimate depth from signal

• Provides signals that cannot be measured in any other way

Cons:• Low spatial

resolution with respect to EEG

• Low signal to noise with respect to EEG

www.acoustics.org/press/153rd/hertrich.html

What is the signal:• Magnetic fields generated by electrical activity of the brain• SQUIDs detect magnetic signal

en.wikipedia.org/wiki/Magnetoencephalography

Intrinsic Optical Imaging:Reflectance of the brain

Pros:• Does not require

dye• High spatial

resolution

Cons:• Signal not well

understood• Requires

exposing the brain

• Signal is slow and on the order of a metabolic signal

• Cannot be used to resolve single cells

Cerne and Haglund

Neuroscience Letters(2002)

What is the signal:• Infrared light is used to illuminate the tissue• CCD camera detects changes in brightness of tissue over

time• Caused by changes extracellular space volume

(scattered light) or by changes in blood flow to the area (absorbed light)

Intrinsic Optical Imaging:Flavoprotein imaging

Pros:• Does not

require dye• High spatial

resolution

Cons:• Signals are of

metabolic processes, not limited to neuronal activity

• Slow, on order of metabolic demand

What is the signal:• Excitation light is used to illuminate brain tissue• Autofluorescent flavoproteins (such as NADH) change fluorescence with

oxidative state. This is a direct measurement of the metabolic process

Reinert et al, J Neurosci Research, 2007

Non-invasive optical imaging:Optical reflectance and scattering

Pros:• Non-invasive

recording• Useful on children• Useful in MRI

where electrode leads can be difficult to deal with

Cons:• Very low resolution

spatially and low signal to noise ratio

• Signal, not very well understood

What is the stimulus:• Bright long wavelength light is shined onto the surface of the scalp

penetrating to the brain• Photo sensors detect reflected and scattered light• Signal changes caused by bloodflow or swelling of cells increasing

reflectance

http://rabi.nmr.mgh.harvard.edu/DOT/research/probe-gallery.htm

Voltage dye imaging:Directly imaging membrane voltage

Pros:• Signal is very fast• Direct measure of

neuronal activity

Cons:• Voltage dyes stain

all membranes, neurons are only a small fraction

• To keep SNR high light must be very bright

• Cannot be used to image large numbers with single cell resolution

• Dyes can be toxic

What is the signal:• Membranes are stained with a fluorescent protein that indicates voltage

change

Zochowski, et al.

Calcium dye imaging :Directly imaging membrane voltage

Pros:• Intracellular

measurement of activity

• Bath or intracellular application

• Very bright changes

Cons:• Slow• Indirect measure

of activity

What is the signal:• Cells stained with fluorescent dyes that indicate changes in intracellular

calcium concentration.

http://probes.invtrogen.com

Ikegaya et al, Neuroscience Research, 2005

Calcium dyes:Bath applied AM dyes

Badea, et al. J. Neurobiol, 5;48(3):215-27 (2001)

Multiple cell recordings using Calcium dyes

• Imaging population over time and parsing image up results in time series from multiple neurons

Cossart et al, Cell Calcium (2005)

4-AP induced Seizure activity in CA1

DIC

100 μm

Str. Pyr Str. Ori

Str. Rad

Resting Fluorescence

Calcium imaging of seizures in the hippocampus

Ion sensitive electrodes

Pros:• Measure many

different signals:– Gasses:O2

– pH– Salts: K+, Na+,

Ca++

Cons:• Slow• Low spatial

resolution• Interference

across ion species

What is the signal:Ion selective exchange across membrane creates voltage. Membranes can be made of glass, crystal, resin or polymer. Enzyme electrodes

Potassium concentrations after stimulationGorji et al, Epilepsia, 2006

Stimulating the brain

• Patch electrode:– can be used for

recording and stimulating

• Extracellular electrodes:– Playing back

measured signal is like playing a tape recording of planes taking off at the airport to make planes take off.

Walter Freeman

Deep brain stimultion

http://www.sctimst.ac.in/hospital/neurology/movementdisorder.htm

mcrais.googlepages.com/implants.htm

en.wikipedia.org/wiki/Image:Parkinson_surgery.jpg

Electroconvulsive therapy:Electric fields and the brain

Pros:• Non-invasive

stimulation• Used for

treating depression

Cons:• Not localized• Mechanism?

Inducing Seizures!

What is the stimulus:• Current is applied to the head to induce seizures

http://www.humanillnesses.com/Behavioral-Health-Br-Fe/Electroconvulsive-Therapy.html

Transcranial magnetic stimulation:Magnetic fields and the brain

Pros:• Non-invasive

stimulation• Short duration• Some localization of

field• Used in place of

electroconvulsive therapy

Cons:• Localization is

poor (compared with an implanted electrode)

• Effects not well understood

What is the stimulus:• Short pulse of magnetic field induces small current flows in the brain.

www.princeton.edu/~napl/methods_h.htm

Stimulating neurons: Caged compounds

Rothman et al, Epilepsy Research 74(2):201-209 (2007)Jin et al, J. Neuroscience 26(18):4891-4900 (2006)

Caged glutamate stimulation Caged GABA

Closing the loop

• Dynamic clamp• Brain Machine/Computer Interface• Neurotransmitter uncaging• Photosensitive ion channels

Dynamic clamp:Real time computer interfaced with a neuron

Pros:• Flexible system for

complex protocols• Simulation of ion

channels• Simulation of

synapses• Simulation of

neurons to make “hybrid” networks

Cons:• Limited number

of channels

What is the stimulus:• Voltage measurement can be used to calculate current to inject

Vm

Iapp

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Optical stimulation:Real time computer interfaced with a neuron

Pros:• Single cell

resolution of 100s of cells

• Millisecond time scale

Cons:• Requires

genetic alteration of cells

What is the stimulus:Channel rhodposin-2 a light sensitive cation channel activated by yellow light

Boyden et al, Nature Neuroscience (2005)

Inhibiting neurons

• Light driven chloride pump

• Genetically spliced to cell type specific promoter

• Shining light hyperpolarizes the cell with msec time constants

• Single action potentials can be inhibited.

Han and Boyden, PLoS ONE, 2007

Summary

Churchland and Sejnowski, 1988