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a b c
Figure 1 | circuit-mapping strategies. examples of the three main following the injection of radioactive proline into one eye40. c | serial electron
approaches that have been used to study the connectivity of neurons. microscopy can be used to reconstruct neurons and their processes with the
a | single-cell staining by dye impregnation. The best-known of these tech- Nature Reviews
best attainable resolution. shown here is a reconstruction from | Neuroscience
the adult rat
niques is the golgi staining method, which was used by ramn y Cajal to barrel cortex that was segmented from a three-dimensional image stack
describe the principles of neuronal circuit organization39. b | The introduction obtained by serial block-face imaging16. Part a reproduced, with permission,
of diffusible or transportable labelling agents to discrete areas. In some cases from reF. 39 (1914) Herederos de santiago ramn y Cajal. Part b repro-
the label crosses a synapse to reach a second-order target. A classical exam- duced, with permission, from reF. 40 (1977) royal society of London.
ple is the identification of ocular dominance columns in the visual cortex Part c reproduced, with permission, from reF. 16 (2006) elsevier sciences.
Despite the encouraging progress that brain tissue by looking at backscattered elec- each section. However, the need for sparse
there has been along these lines, difficulties trons with a scanning electron microscope15. labelling when using monochromatic labels
remain. First, tracing from a set of somata After taking the image, the top section of the remained an intractable limitation until
to a terminal field, or vice versa, will in most block is removed with a diamond knife and recently. The obvious solution is to use
cases leave local interneurons unlabelled or the block face is reimaged. This procedure multiple, distinct labels so that nearby pro-
impossible to resolve. Second, because these can now be iterated thousands of times cesses can be distinguished from each other.
methods typically label groups of neurons to give perfectly aligned stacks of digital This approach is exemplified by the use of
rather than individual cells, tract-tracing electron micrographs from which neuronal rainbow cables in electronic devices: the
methods can seldom be used to trace the processes can be traced (FIG. 1c). Other various colours of the wires help people keep
highly complex branching patterns of the approaches use new microtome designs track of them. Several methods designed
thousands of interdigitated axons and involving a rotary lathe and a tape transport along this principle have been applied to
dendrites in each cubic m of brain. system to automate the cutting and collec- the task of neuronal circuit visualization.
tion of serial thin sections. Along with new One, called Diolistics, involves shooting
Electron microscopy. Serial section electron methods in computational segmentation tissues with biolistic metal beads that have
microscopy has been the method of choice that improve tracing and three-dimensional been coated with various combinations
for overcoming the limited resolution reconstruction (see below), these innovations of different coloured lipophilic dyes, such
of light microscopy and the insufficiencies of are likely to restore electron microscopy to as DiI, DiO, and DiD, with the result that
tract-tracing. In pioneering work, levinthal, a position of prominence in circuit analysis. impregnated cells are labelled with different
lopresti and Macagno used this method to Nonetheless, large-scale reconstruction, colours18. However, Diolistic labelling is best
map connections in the optic lobe of the small especially over long distances, remains a dis- done ex vivo on slices, so it is poorly suited
crustacean Daphnia13, and white et al. used tant hope. For example, reconstructing paths for long-range reconstruction.
it to provide a nearly complete map of con- from the retina to the thalamus or from Another approach is based on the green
nectivity in the roundworm, Caenorhabditis the thalamus to the cortex would require fluorescent protein (GFP) revolution19,
elegans14. Serial electron microscopy is so hundreds of thousands or even millions of which has led to a technical renaissance in
laborious, however, that its application has sections to be acquired and analysed, and imaging. Over the past several years, dozens
been infrequent. Fortunately, this situation is even then there would be no obvious way to of spectral and photophysical fluorescent
now changing thanks to recent developments verify the accuracy of the tracing. protein variants (XFPs) have been discov-
in the automation of electron microscopy1517. ered or engineered20, and many of these have
One promising approach is to image the thin The multicolour solution been introduced as intrinsic neuronal labels
surface layer (tens of nanometers) of a block Introducing a marker into the reconstructed in transgenic mice. In some of the mice
of plastic-embedded and heavy-metal-stained neuron allows its identity to be verified in that produce these XFPs, the expression is
a b c
Figure 3 | Multicolour neuronal labelling in Brainbow transgenic mice. co-integration of several tandem copies of the transgene into the mouse
a | A motor nerve innervating ear muscle. b | An axon tract in the brainstem. genome and the independent recombinationNature of each by Cre recombinase
Reviews | Neuroscience
c | The hippocampal dentate gyrus. In the Brainbow mice from which these (see FIG. 2c). The images were obtained by the superposition of separate red,
images were taken, up to ~160 colours were observed as a result of the green and blue channels. The image in part a is courtesy of ryan Draft.
It will also be valuable to use Brainbow Finally, Brainbow can be used to highlight antibodies to detect the XFPs themselves
transgenes to learn how connectional connections of another sort: the lineage rela- is unfortunately not yet feasible, because
patterns change over the lifespan of an tions among cell populations. If recombina- several of the XFPs (for example, GFP, cyan
animal. For example, the neurobiological tion is induced in neural progenitors with a fluorescent protein and yellow fluorescent
underpinnings of healthy aging remain a ligand-activated Cre recombinase (for exam- protein) differ by only a few amino acids
mystery. Solving this mystery is not only ple, Tamoxifen-dependent CreeR) (Box 1), all and are, in effect, antigenically identical. If
important in its own right, but might also offspring of a particular blast cell should be immunohistochemical detection is used, one
be required if we are to understand the labelled with the same colour. This approach can also localize sites of synaptic contacts on
pathological alterations to which the aging might allow the analysis of the interactions of or between marked cells, using antibodies to
nervous system is especially vulnerable. many clonal sets of cells (each with their own pre- or postsynaptic components. Methods
likewise, circuit modifications that under- colour) in the same piece of tissue. such as array tomography, in which thin
lie the critical period in early postnatal sections of brain material are assayed with
life are incompletely understood, as are Technological challenges an assemblage of antibody probes, provide an
the compensatory changes that make the For more complex circuits, the diffraction- elegant protocol for detecting many antigens
young nervous system so resilient limited resolution of the light microscope (or epitope tags) in single thin sections31.
following injury. is a serious limitation. Fortunately, several A more radical solution to the resolution
In studying these issues, the microscopic solutions to this problem are already emerg- problem might be provided by the new and
analysis that we have used so far will be use- ing. One is to cut extremely thin sections of rapidly growing field of nanoscopy, which
ful. Greater insights might eventually come labelled tissue31,32. By cutting sections that overcomes the resolution limitations of
from time-lapse imaging of circuit altera- are several-fold thinner than the optical light diffraction3438. These new imaging
tions as they occur. XFPs make ideal labels section thickness, the superimposition of modalities provide resolutions of tens of nm
for this purpose, and time-lapse methods multiple neurites in the same focal thickness which, alone or with the addition of spectral
have now been applied to many parts of the is avoided. In addition, the thin samples information, might be sufficient to trace the
peripheral and central nervous systems of scatter light much less, and this improves the finest neuropil.
one- and two-colour XFP mice2730. Further contrast and clarity of the labelled material. In parallel, it will be important to design
improvements in spectral separation, acqui- To make such thin sections, the neural new Brainbow transgenes to increase the
sition rate and detector sensitivity should tissue must be embedded in a hard resin. range of neuronal types and developmental
make it possible to expand the method to This, in turn, requires the XFPs to retain stages to which the method can be applied.
Brainbow mice. their fluorescence following the dehydra- There are several major limitations of
So far, we have only discussed con- tion and embedding steps. To some extent the first-generation Brainbow lines. The
nections among the minority cellular this might be possible; however, Brainbow regulatory elements that are used (from
population of the brain: neurons. Brainbow transgenes could alternatively be redesigned the Thy1 gene) direct high levels of expres-
methods can also be used to map connec- to include epitope tags that would be rec- sion in many projection neurons, but most
tions among the majority population, glia, ognized by antibodies33. This would allow interneurons are poorly marked21. Also,
or between neurons and glia. Indeed, some traditional staining methods to be used after in most lines, transgene expression is low in
Brainbow lines already label some glial sub- the tissue has been cut and would therefore embryos and during the first postnatal week,
sets, including astrocytes, Schwann cells and allow the labelling by the endogenous fluor- so these lines are unsuitable for develop-
Bergman glia; it should be straightforward to escent protein to be augmented or replaced. mental studies. Furthermore, some colours
generate others. The seemingly simple solution of using are dim (especially red shades), primarily
because the proteins are insufficiently photo- Jeff W. Lichtman and Joshua R. Sanes are at the 19. Tsien, R. Y. The green fluorescent protein. Annu. Rev.
Biochem. 67, 509544 (1998).
stable. Additionally, several bright XFPs Department of Molecular and Cellular Biology and
20. Shaner, N. C., Steinbach, P. A. & Tsien, R. Y. A guide to
Center for Brain Science, Harvard University,
are difficult to distinguish from each other choosing fluorescent proteins. Nature Methods 2,
Cambridge, Massachusetts 02138, USA. 905909 (2005).
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Jean Livet is at INSERM, UMR S592, Institut de la
versus red) because their spectra are insuf- mice expressing multiple spectral variants of GFP.
Vision, F-75012, Paris, France and at UPMC University Neuron 28, 4151 (2000).
ficiently distinct. Moreover, although the of Paris 06, UMR S592, F-75005, Paris, France. 22. Walsh, M. K. & Lichtman, J. W. In vivo time-lapse
number of colours is presently large (~100), imaging of synaptic takeover associated with naturally
Correspondence to J.W.L. occurring synapse elimination. Neuron 37, 6773
it is nonetheless insufficient for some pur- e-mail: jeff@mcb.harvard.edu (2003).
poses. There are few conceptual difficulties doi:10.1038/nrn2391
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identity in synaptic competition. Nature 424,
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