This document discusses various techniques for studying the brain, including: - Diffusion Spectrum Imaging (DSI) allows mapping of axonal trajectories but not individual neurons due to MRI resolution limitations. - Two-photon microscopy can image live mouse brains up to 1mm depth. Confocal laser scanning microscopy provides high-resolution images of brain structures in vitro. - Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) provide the highest magnifications up to 1 million times but require thin samples and only work in vitro.

1. BRAIN ART
How and Why We Study
the Brain
This slide-show was completed
with the help of Roberto Gradini
MD, PHD, Associate Professor of
General Pathology, Sapienza
University School of Medicine,
Rome, Italy

2. Why Study the Brain?
In 1801, French psychiatrist Phillipe Pinel
asked the question: “Does insanity
depend upon organic lesion of the
brain?” Pinel proceeded to perform
numerous autopsies and eventually
concluded: “no facts, yet clearly
established, relative to the influence of
the size and configuration of the cranium
upon the faculties of the mind”.

3. Psychiatric Illnesses Are
Diseases of The Brain
In the past two decades advanced
functional brain mapping technologies
have become widely available, thus the
so called “organic lesions” that Pinel
failed to locate in the brains of mentally ill
have been finally delineated so that we
can now state with some certainty that
psychiatric illness is caused by neural
damage that we can characterize by the
neuropathology involved.

4. How Do We Study The Brain?
In vivo: by non-invasive neuroimaging
studies such as Diffusion Spectrum
Imaging (DSI), MRS, PET, SPECT
In vivo: by microscopy of live mice brain
In vitro: by microscopy of the dead brain
In vitro: by cultured neurons

5. Limitations of Neuroimaging
 In vivo neuroimaging does not allow us to study
individual neurons or their axons, because the resolution
of MRI is 1 mm of the brain surface which contains
about 1000 neurons.
 We are much better at visualizing white matter (axons)
than gray matter (neurons) because axons lump
together in tracts that are larger than 1 mm. The largest
tract, corpus callosum, can be seen by naked eye.
 Connectomics is visualization of white matter tracts and
for this reason is also called white matter tractography.
 Beautiful images of white matter tractography can be
seen at:
 http://www.youtube.com/watch?v=CySDbTH46P4

6. Diffusion Spectrum Imaging
 Diffusion spectrum imaging (DSI) is a
variant of diffusion-weighted imaging
(DWI) that is sensitive to the diffusion
directions of water molecules caused by
crossing fiber tracts and thus allows more
accurate mapping of axonal trajectories
than other diffusion imaging approaches.
 DSI is being used in deriving the
Connectome data because it visualizes
bundles of axons traveling together.

7. Diffusion Spectrum Imaging (DSI)
(Human Connectome Project)
 DSIvisualizes white matter tracts (bundles
of axons) but not individual axons.

8. In Vivo Microscopy of Mouse Brain
 Two-Photon Microscopy is a fluorescence imaging technique
that allows imaging of living brain up to a depth of about one
millimeter. Two-Photon microscopy is a special type of
confocal laser scanning microscopy (CLSM).
 Two-photon Images can be seen at:
http://www.youtube.com/watch?v=W9bn_XYDbUo

9. In Vitro Microscopy
 Confocal laser scanning microscope (CLSM) is a
valuable tool for obtaining high resolution images and
3-D reconstructions from in vitro individual brain neurons,
axons and dendrites.

10. DENDRITIC SPINES
- Ultra High resolution byConfocal Laser
Scanning Microscopy

11. Confocal Laser Scanning
Microscopy – dendritic spines
 More images at:
denhttp://www.youtube.com/watch?v=zsp
vdjjmWsY

12. Dendritic Spines by Confocal
Laser Scanning Microscopy

13. Spiny Neurons -Dendritic
mitochondria

14. Confocal Laser Scanning Microscope
(CLSM): Dendrites with Spines

15. Transmission Electrone
Microscopy (TEM)
A transmission electron microscope (TEM)
can magnify a sample up to one million
times. The sample must be cut extremely
thin. An electron beam is directed onto
the sample to be magnified and some of
the electrons pass through and form a
magnified image of the specimen.


16. Transmission Electron
Microscope (TEM)

17. TEM: A Canopy of Dendrites

18. Transmission Electron Microscope (TEM):
Dendrites “conversing”

19. Transmission Electron Microscopy (TEM):
Mouse Neuron

20. TEM: Visualizing Actin in Dendritic Spines

21. TE: image of neuronal tissue.
Segmented structures are: dendrite (yellow),
chemically labeled buton (red) and a spine
head (green). Blue arrows point to synapses.

22. TEM - DENDRITIC SPINES

23. Scanning Electron Microscopy
(SEM)
 Scanning electron microscope (SEM) can magnify a
sample up to 100,000 times. A sharply focused electron
beam moves over the sample to create a magnified
image of the surface. Some electrons in the beam
scatter off the sample and are collected and counted
by an electronic device. Each scanned point on the
sample corresponds to a pixel on a television monitor;
the more electrons the counting device detects, the
brighter the pixel on the monitor is. As the electron
beam scans over the entire sample, a complete image
is displayed on the monitor. SEMs are particularly useful
because they can produce three-dimensional images
of the surface of objects

24. Scanning Electron Microscope (SEM)

25. Scanning Electrone Microscop
(SEM): Striatum A Spiny Neuron

26. SEM: Dendritic Spine Density
by Cortical Layer

27. Automated tape-collecting
ultramicrotome (ATUM)
 (ATUM) is a new technique of obtaining
ultrathin slices of brain tissue.
 - ATUM uses an electron opaque tape to
continuously collect serial sections into
ribbons of literally infinite length.
 -ATUM is invaluable for the study of the
connectome.

28. Automated tape-collecting
ultramicrotome (ATUM)

29. Conclusions
 Neuroimaging technology has improved during
the past two decades, but not enough as to allow
us to visualize individual neurons, axons or
dendrites.
 Human Connectome Project is done by various
MRI techniques and is able to visualize bundles of
axons traveling together (regional connectomics).
 Microscopy has a much higher resolution than
MRI, but it does not allow us to visualize live human
brain.
 In order to be able to visualize individual neuron
connectomics in vivo, the future MRI machines will
need to have 1000 times higher resolution than
they have today.