© 2012 Nature America, Inc. All rights reserved.
nAture methods | ADVANCE ONLINE PUBLICATION | ?
understanding and treatment of spinal cord pathology
is limited in part by a lack of time-lapse in vivo imaging
strategies at the cellular level. We developed a chronically
implanted spinal chamber and surgical procedure suitable
for time-lapse in vivo multiphoton microscopy of mouse
spinal cord without the need for repeat surgical procedures.
We routinely imaged mice repeatedly for more than 5 weeks
postoperatively with up to ten separate imaging sessions and
observed neither motor-function deficit nor neuropathology in
the spinal cord as a result of chamber implantation. using this
chamber we quantified microglia and afferent axon dynamics
after a laser-induced spinal cord lesion and observed massive
microglia infiltration within ? d along with a heterogeneous
dieback of axon stumps. By enabling chronic imaging studies
over timescales ranging from minutes to months, our method
offers an ideal platform for understanding cellular dynamics in
response to injury and therapeutic interventions.
In vivo optical imaging in the live mouse cortex has been achieved
at depths of more than 1 mm with sub-micrometer resolution using
nonlinear microscopy coupled with cranial window preparations1.
This imaging approach has particular value for the study of neuro-
pathology. For example, longitudinal studies (time-lapse imaging
of the same region in the same animal over multiple days) in mouse
models have relied on two-photon excited fluorescence (2PEF)
microscopy to study the appearance and evolution of amyloid-β
plaques in Alzheimer’s disease2–4, the rate and extent of amyloid-β
clearance in response to antibody therapy5, the diapedesis of cir-
culating cancer cells and formation of metastatic tumors6 as well
as the long-term effects of occlusion and reperfusion of cerebral
blood vessels7. In all cases, a surgical protocol enabling repeated
optical access to the relevant tissue is a prerequisite to longitudinal
studies. Existing protocols include an open-skull protocol8 for a
cranial window in which a small portion of the mouse skull is
replaced with glass, thinned-skull preparations9 and a recently
described glass-reinforced, thinned-skull preparation10.
Chronic optical imaging could offer comparable experimental
advantages to the study of the spinal cord, including studies of
spinal cord injury (SCI), spinal tumors, syringeomyelia, myelitis
and spinal cord ischemia. For example, time-lapse in vivo studies
of axon trajectories after SCI would enable unambiguous iden-
tification of spared, injured and regenerating axons and provide
an ideal platform for evaluating therapies aimed at spurring
axon growth. This approach has been demonstrated in vivo in
zebrafish11, where injured axons as well as axons that regenerated
in response to therapy have been imaged over several days after
SCI. Others have performed time-lapse fluorescence imaging in
the spinal cord of mice expressing enhanced GFP (EGFP) in a
subset of dorsal root ganglia (DRG) neurons for up to 72 h after
SCI12. However, this imaging requires artificial ventilation and
the suppression of breathing during image acquisition, limiting
the timescale of cellular dynamics accessible. Similarly, 2PEF
imaging in the spinal cord of mice expressing GFP in microglia
has been demonstrated13 with up to two imaging sessions in the
same mouse separated by several days. Heavy sedation, whole-
body suspension and local clamping are used to reduce remaining
motion artifacts resulting from breathing and heartbeat. Similar
techniques have been used to study microglia dynamics after a
laser-induced microinjury14, calcium signaling of dorsal horn
neurons15, the effects of peripheral nerve lesioning on sprouting
of severed DRG axons16 and experimental autoimmune encephalo-
myelitis17. Finally, imaging at as long as 4 months after SCI with
as many as six imaging sessions in one subject has been achieved
without interfering with animal breathing during imaging18.
In all of these studies, obtaining images on days after the initial
surgery is possible only by repeated surgical opening of the
animal for each imaging session. Repeat surgeries increase the
risk of infection, add a potentially confounding source of inflam-
mation, cause tissue damage, cause additional pain and distress to
the animal and severely limit the number of imaging time points
possible. However, unlike the cranium, the relevant portions of the
spine routinely flex and are close to the heart and lungs, requiring
any chronic preparation to maintain the mechanical stability of
the spine and minimize motion artifacts during imaging.
To provide a surgical preparation that enables repeated optical
imaging of the mouse spinal cord without requiring repeated
1Department of Physics, Cornell University, Ithaca, New York, USA. 2Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA. 3Department of
Biomedical Sciences, Cornell University, Ithaca, New York, USA. 4Department of Psychology, Cornell University, Ithaca, New York, USA. 5Department of Neurobiology
and Behavior, Cornell University, Ithaca, New York, USA. Correspondence should be addressed to C.B.S. (email@example.com).
Received 10 MaRch 2011; accepted 8 deceMbeR 2011; published online 22 januaRy 2012; doi:10.1038/nMeth.1856
chronic in vivo imaging in the mouse spinal cord
using an implanted chamber
Matthew J Farrar1,2, Ida M Bernstein2, Donald H Schlafer3, Thomas A Cleland4, Joseph R Fetcho5 &
Chris B Schaffer2
© 2012 Nature America, Inc. All rights reserved.
? | ADVANCE ONLINE PUBLICATION | nAture methods
surgeries, we developed an implantable spinal chamber that provides
continuous optical access to the mouse spinal cord. Using this
chamber, we performed 2PEF imaging in transgenic mice express-
ing fluorescent proteins in microglia and afferent axons, and
found axon morphology to be stable over 8 weeks of imaging.
Standard tests of locomotor function did not show deficits in
mice with the implant as compared to control mice. Postmortem
histology did not show evidence of damage to the spinal cord from
the surgery but revealed increases in microglia numbers in the
dorsal portion of the spinal cord, consistent with mild inflamma-
tion. Finally, we imaged blood vessels, afferent axons and micro-
glia after laser-induced microlesioning of the spinal cord using
2PEF microscopy and quantified microglial infiltration and axon
‘dieback’ dynamics on time scales spanning four orders of magni-
tude. We found that the increase in microglial density at the lesion
site was fastest within the first 24 h after injury. Axon dieback
rates were highly heterogeneous among axons, were fastest imme-
diately after injury and slowed over 5 weeks after SCI.
the imaging chamber
The chamber consisted of two metal bars that attach to the spine
together with a top plate that attaches to the bars and holds a glass
window (Fig. 1a). The implantation procedure entailed retract-
ing muscles and scraping clean the dorsal laminae over the imag-
ing site, then fusing three vertebrae by clamping them on either
side with small metal bars (Fig. 1b) held magnetically on fixed
posts and finally performing a dorsal laminectomy with vanna
scissors. We trimmed the lateral edges of the bone as close to the
metal bars as possible and sealed the bone using a combination
of cyanoacrylate and dental acrylic. We maintained clamping
pressure as the chamber assembly was completed by bolting a
top plate onto the metal bars, applying a silicone elastomer over
the spinal cord, sealing the chamber with a glass coverslip on
top and with additional glue around the edges, and finally gluing
the skin to the base of the top plate (Supplementary Fig. 1,
Supplementary Protocol and Online Methods). During 2PEF
imaging, we reduced motion artifacts by securing the mouse to
Figure ? | An imaging chamber for longitudinal optical access to mouse
spinal cord without the need for repeated surgeries. (a) Photograph of the
imaging chamber. (b) Schema showing the implantation of the imaging
chamber in mice at the T11–T12 vertebra, just below the dorsal fat pad
(taupe). (c) Photograph showing the spinal cord imaged through the
implanted chamber 144 d after the surgery. (d) Photograph of a mouse
with an implanted chamber (same mouse as in c).
Time after surgery (d)
0 1020 304050 6070
Lateral resolution (µm)
0 1020 3040 50 6070
Time after surgery (d)
39 d53 d 67 d
Figure ? | Longitudinal 2PEF imaging of axons and blood vessels over many weeks after surgery. (a) Projections of 2PEF image stacks of afferent axons
expressing EYFP (teal) and blood vessels labeled with intravenously injected Texas Red dextran (red) taken over 9 weeks after chamber implantation.
Asterisks indicate the location of red autofluorescence from invading, likely inflammatory, cells located above the spinal cord at later time points. Arrows
denote landmark features of the axons that were visible at all time points. (b) High-resolution 2PEF imaging of EYFP-expressing axons from the same region
as in a. (c) Profile and fit (Online Methods, equation (3)) across maximum intensity projections of selected axon segments shown in the boxed region in b
and in the inset; scale bar, 30 µm). A.u., arbitrary units. (d,e) Image contrast (d) and lateral spatial resolution (e) as functions of time after surgery from
the fits for all axon segments for two mice (separate curves for each mouse, ~10 axons measured at each time point for each mouse). Error bars, s.d.
© 2012 Nature America, Inc. All rights reserved.
nAture methods | ADVANCE ONLINE PUBLICATION | ?
tapped holding posts twisted onto the set screws in the exposed
wings of the top plate, thereby stabilizing the spine and elevat-
ing the mouse off of the surgical table (Supplementary Fig. 2)
to permit free expansion of the chest cavity during inspira-
tion. Mechanical drawings for custom parts are available in
Supplementary Notes 1–6. The chamber enabled continuous
optical access to the spinal cord (Fig. 1c) without repeat surgeries.
Mice behaved normally over the weeks after surgery, with no
signs of lordosis or kyphosis (Fig. 1d). Micro-computed tomo-
graphy imaging of a mouse 6 d after implantation confirmed
alignment of the spine and revealed no signs of vertebral damage
(Supplementary Video 1).
long-term imaging of spinal cord axons and blood vessels
We implanted our chamber in transgenic mice expressing
enhanced YFP (EYFP) in afferent axons from a subset of DRG
neurons. We imaged mice at up to eight separate times as long as
67 d postoperatively, revealing that axon morphologies and num-
bers of axons were stable (Fig. 2a). We used blood vessels labeled
with Texas Red dextran and obvious features of the axons to navi-
gate to the same region of interest across different imaging sessions.
At some time points, blood vessels had increased or decreased
diameter compared to baseline but with stable morphology.
Image contrast visibly diminished over time, which we quantified
by fitting projections of axon segments to a simple model (Fig. 2b,c
and Online Methods). We found a decrease in image contrast and
a loss of lateral resolution over time (Fig. 2d,e), with the greatest
change occurring over the first 14 d owing to the formation of a
fibrous growth over the surface of the spinal cord. The duration
over which we could resolve individual axons expressing fluores-
cent proteins using 2PEF imaging varied between as few as 5 d
and as many as 140 d (Supplementary Fig. 3). We found that in
mice that had only minimal fibrosis 1–2 weeks after surgery, axons
could routinely be resolved up to more than 5 weeks. We could
image for more than 5 weeks in ~50% of the mice with implants.
At all time points, in mice in which fibrous tissue growth was
minimal, imaging depth was limited to 30–50 µm by the short
scattering length of myelin19. In cases in which fibrous growth
was dense, we could not resolve axons at
any depth. In some mice, we observed a
myelin-poor region between adjacent
dorsal roots that enabled imaging up to
depths of 300 µm, well into the dorsal horn
(Supplementary Fig. 4).
1 d7 d
1 d7 d
Figure ? | Histological analysis of reactive microglia and astrocytes,
and tissue morphology after chamber implantation. (a,b) Wide-field
fluorescence images of 30-µm-thick coronal tissue sections from the
laminectomy site 1 d and 1 week after implantation and in non-surgical
controls for mice expressing EGFP in microglia (a) or astrocytes (b).
(c) Hematoxylin and eosin–stained tissue section taken 7 d after
implantation. Magnifications of the left and right boxed regions show
the fibrous connective tissue that covered the dorsal aspect of the spinal
cord under the implant and the neural tissue, respectively. (d,e) Microglia
(d) and astrocyte (e) densites in spinal cord sections 1 and 7 d after
implantation for sections one vertebra rostral to the surgical site (rost.),
at the surgical site (surg.) and one vertebra caudal to the surgical site
(caud.) and in controls (*P = 0.012; **P = 0.0010; ***P = 0.0098;
#P < 0.0001; n ≥ 15 measurements per segment per time point; 3 mice per
time point). Error bars, s.e.m.
Baseline 60 min 1 d 2 d 3 d7 d Control
60 min 1 d2 d3 d7 d
Number of microglia
Size of glial aggregate (µm)
Time after injury Time after injury
Figure 4 | Imaging and quantification of
microglial scar formation at the site of a laser-
induced SCI. (a,b) Projections of 2PEF image
stacks of EYFP-labeled axons (teal) and EGFP-
labeled microglia (mauve) before (a), 1 d (b)
and 1 week (c) after producing a ~200-µm-long
laser-induced microlesion in the spinal cord.
(d,e) Boxplots of the number of microglia (d)
and the microglial scar size (e) in the 300-µm
field of view over time (four lesions in two
mice). Horizontal red lines denote the median,
blue boxes bound the 25th and 75th percentiles
of the data, and the whiskers denote non-
outlier extrema (defined as outside the box by
less than 1.5 times the interquartile range).
© 2012 Nature America, Inc. All rights reserved.
4 | ADVANCE ONLINE PUBLICATION | nAture methods
locomotor function was preserved after implantation
We used two behavioral assays to assess the impact of the implant on
motor function. We first tested mice for gait abnormalities during
normal movement20. Mice with inked paws ran the length of a
narrow enclosure, after which we analyzed the patterns of their
footprints to measure base of support (lateral distance between
hindlimb placement), stride length and running speed for mice
with spinal chamber implants as well as sham controls (shaved
and anesthetized but not receiving surgery; three mice per group).
We found no remarkable differences in gait attributable to the
implant at any time point (Supplementary Fig. 5).
In the second assay, we assessed spontaneous activity,
rearing behaviors and movement speed by video-monitored
open-field testing. We determined the cumulative time spent
immobile, grooming, rearing and speed distributions from
post hoc video analysis. Grooming time in mice with implants
was significantly higher on days 1–3 after surgery than in sham
controls, but this difference did not persist over time (P = 0.0069;
n = 3 mice per group). We observed no differences in immobility
or rearing times. We derived nominal top speeds from speed
distributions as the average speed above the 75th percentile.
Although we observed a slight reduction in top ambulatory speed
in mice with implants, as compared to sham controls, it was not
statistically significant (Supplementary Fig. 5). Finally, mice with
implants did not exhibit any difficulty in grooming hindquarters
or climbing (Supplementary Video 2).
20 min1 h
21 d30 d36 d
Distance from lesion (µm)
< 3 h
3–24 h 48–72 h 7–22 d 29–43 d
Dieback speed (µm h–1)
Figure 5 | 2PEF imaging and quantification of axon dieback after a laser-induced SCI. (a) Projection of a 2PEF image stack from mice expressing EYFP (teal)
in a subset of DRG neurons with the vasculature labeled with Texas Red dextran (red). (b) Projections of 2PEF image stacks of EYFP-expressing axons
shown in the boxed region in a before and at indicated times after a lesion produced by translating high-energy, tightly focused femtosecond laser
pulses through the cord. Mauve circles indicate easily recognizable patterns in spared axons that were identified at all time points and provide a point
of origin. Yellow arrows, axon that exhibited rapid degeneration; blue arrows, axon that died back more slowly; red arrows, axon that persisted near the
lesion site and made an ultimately aborted growth response (the morphology of this axon’s tip is shown in the insets; scale bar in inset, 10 µm); and *,
location of early sprouting responses that did not persist over time. (c) Position of axon endings over time after the lesion, with positive and negative
values corresponding to positions rostral and caudal to the lesion site, respectively (see schematic in inset) (107 individual axon trajectories over nine
lesions in five mice). Axon trajectories in color correspond to the locations marked by respectively colored arrows in b. (d) Speed of axon-tip dieback for
axons remaining in the field of view over time after the lesion. Black circles denote measurements of dieback speed from individual axon tips, horizontal
red lines represent the median, the blue boxes bound the 25th to 75th percentage of the data, and the whiskers extend 1.5 times the interquartile range
beyond the boxes. Points outside the whiskers were considered outliers and have a red cross through them. Because axons died back beyond the imaging
field over time, the dieback speed at early times includes data from ~100 axons, and the last time point includes data for only 16 axons.
© 2012 Nature America, Inc. All rights reserved.
nAture methods | ADVANCE ONLINE PUBLICATION | 5
inflammation but no focal trauma to the spinal cord
We performed histological analysis using mice expressing EGFP
in microglia (CX3CR1-GFP) or in astrocytes (GFAP-GFP) or via
standard hematoxylin and eosin staining (Fig. 3a–c).
We implanted the spinal chamber in the transgenic mice and
perfused them for histology analysis 1 d and 1 week after surgery.
We used mice that did not undergo surgery as controls (three mice
per group). In mice that received implants, we analyzed sections
from the site of laminectomy as well as the immediately rostral
and caudal vertebrae. Both 1 d and 1 week after surgery, micro-
glia in sections under the surgical site showed a more condensed
structure with fewer processes compared to controls, but we
observed no ameboid structures indicative of phagocytic micro-
glia21 (Fig. 3a). Microglia densities (Fig. 3d) in the dorsal aspect
of the rostral segment of the spinal cord 1 d after surgery and in
the dorsal aspect of all segments 1 week after surgery were elevated
compared to controls. Astrocytes showed no obvious changes in
morphology or cell density (Fig. 3b,e) across all groups.
For standard histopathology studies, we killed and perfused
mice 1 d, 1 week and 1 month postoperatively (two mice per
group). In all cases, control regions showed normal tissue in
nerves, bone, muscle and spinal cord. Mild dermatitis was present
at the skin-implant junction in all mice. Focal meningitis at the
caudal edge of the window occurred in one mouse in the ‘1-week’
group. We observed no signs of meningitis or disruption of neural
tissue in the other mice (Fig. 3c) or in other regions of the mouse
exhibiting focal meningitis. Neutrophils were absent in spinal cord
tissue of all mice at all time points. The fibrous tissue (Fig. 3c)
over the dorsal surface of the cord progressively thickened over
time and was the limiting factor to the duration of imaging. We
observed indications of muscle injury including myositis, myo-
degeneration and myoregeneration along with epidural neutro-
philic fascitis at the site of implantation at the 1-d and 1-week
time points. Reactive bone growth and fibroplasia occurred at the
lateral edges of the window at the 1-month time point. The silicone
elastomer showed no signs of cellular infiltration.
numbers of microglia increased over 7 d after sci
We used double-transgenic mice expressing EYFP in a subset of
DRG axons and EGFP in microglia to evaluate the dynamics of
microglial scar formation after a ~200-µm-long, 35-µm-deep
laser-induced transection injury to the dorsal column produced
using tightly focused femtosecond laser pulses (Fig. 4a–c; four
lesions in two mice). We intentionally spared blood vessels in the
creation of the lesion. Microglial cell counts increased dramati-
cally during the first day and continued to increase more slowly
over the following 6 d (Fig. 4d). The spatial extent of the densely
packed microglial scar increased steadily over 7 d (Fig. 4e).
?PeF imaging of axon dieback after sci
We evaluated axonal response to injury in nine laser lesions in
five mice expressing EYFP in DRG afferent axons (Fig. 5a). We
imaged two mice for 5 weeks after injury (four lesions). We col-
lected several image stacks at the lesion site at different times after
SCI (Supplementary Video 3). We used characteristic features of
spared axons to define a common point of origin across different
imaging sessions (Fig. 5b). We used manual tracking both from
three-dimensional (3D) stacks and 2D projections to determine
the distance of individual axon tips from the lesion along the
rostral-caudal direction (Fig. 5b,c). Owing to axon density and
insufficient spatial extent of the image stacks, we could not dis-
tinguish ascending axons from descending branches of the DRG
neurons. Owing to a loss of image contrast immediately after
injury, tracing was possible for most but not all axons (95 of 107
axons traced) on acute timescales (0–2 h). The average response
of axons was to die back from the lesion site, but the extent and
rate of axon dieback was highly heterogeneous (Fig. 5b,c). Some
axons exhibited the rapid acute axonal degeneration that has been
previously described12. Other axons persisted near the lesion site
for several days or even weeks, with some mounting an abortive
growth response (Fig. 5b,c). Axon tip morphology (Fig. 5b) also
varied from day to day. The average dieback speed of the axons
(defined as the change in an axon tip’s axial position between suc-
cessive imaging sessions divided by the elapsed time, with growth
phases excluded) declined by nearly three orders of magnitude
over the 5 weeks after injury (Fig. 5d).
Our study of microglial invasion after laser-induced SCI revealed
that although the number and spatial extent of microglia contin-
ued to increase over time, the largest fractional change occurred
within the first 24 h after injury, consistent with previous stud-
ies14. Microglia are known to phagocytose growth-inhibitory
axon debris22 in white-matter tracts23, suggesting that the chronic,
gradual recruitment of microglia may be related to the progres-
sive degeneration of the axons involved. Thus, imaging of micro-
glia infiltration and the clearance of axon debris will be critical
for developing optimal therapeutic strategies to manipulate the
One of the key challenges in studies of regenerative strategies
for SCI is the establishment of an optimal therapeutic time win-
dow24–27. Although the delay of treatment has been discussed at
length with respect to the glial scar25, our observation of hetero-
geneity in axon dieback, instances of early but transient sprouting
and decrease in dieback rate at longer timescales may suggest
an optimal therapeutic window based on axon dynamics. Our
axon-by-axon characterization of axon dieback rates agreed with
previous studies of acute12 and longer-term28,29 measurements
but revealed details of this transition and allowed classification of
subpopulations of axons by response: ~15% were stable (remained
within 400 µm of the lesion for at least 4 weeks), ~15% rapidly
disintegrated (died back beyond the field of view within the first
day) and ~70% progressively degenerated over the first month.
Such dynamic data are inaccessible to postmortem histology or
analysis of gross lesion size. In future studies we will attempt
to correlate these classes of heterogeneity in axon dieback with
heterogeneity in regenerative responses to therapy.
Previous studies12,13,16,18 have demonstrated time-lapse imag-
ing of the spinal cord via repeated surgical opening of the skin
above the spinal cord. Because of the inherent stresses and risks
of repeated surgeries or restrictions placed by the Institutional
Animal Care and Use Committee, the number of times these proce-
dures may be performed places severe limitations on longitudinal
studies. For example, in one long-term longitudinal study, only
six imaging sessions were possible in 4 months18. To effectively
study disease dynamics and especially response to therapeutic
agents, imaging must span a sufficiently long period of time to
establish therapeutic limits with an imaging frequency that enables
© 2012 Nature America, Inc. All rights reserved.
? | ADVANCE ONLINE PUBLICATION | nAture methods
capture of transient responses. The chamber we developed requires
only a single surgery and grants continuous optical access, with
the frequency of imaging being limited only by the ability of the
mouse to endure multiple rounds of anesthesia. We imaged imme-
diately after SCI up to 2 h after injury, then every 12 h for 1 d,
then daily for 3 d and finally weekly for 5 weeks, for a total of 13
imaging time points after SCI.
We observed microglia at the surgical site to have higher densi-
ties and fewer processes 1 week after surgery compared to control
mice, suggesting an activated but not phagocytic phenotype21.
This result is consistent with an analogous study that considered
inflammatory responses under cranial windows30, and care will
need to be taken when using our spinal cord window in studies
sensitive to even mild inflammatory responses. However, we
observed that even a minimal laser injury to the spinal cord
results in an order of magnitude increase in microglia den-
sity near the injury, including microglia showing phagocytic
ameboid morphologies. This increase far exceeds the less than
twofold increase in microglia density owing to the surgery,
suggesting that our chamber does not substantially confound
studies in which microglial responses are more drastic.
When combined with 2PEF imaging of transgenic mice
expressing fluorescent proteins in axons, microglia, astrocytes,
oligodendrocytes, endothelial cells and immune cells and with
nonlinear microscopy techniques to visualize myelin (for example,
third harmonic generation19), the spinal chamber described here
is an ideal tool for longitudinal studies of healthy and diseased-
state spinal cord, including pathologies such as multiple sclerosis,
implanted spinal cord tumors or the establishment of meningitis
after bacterial challenge. As our chamber does not lead to motor
deficits, functional loss or recovery may be straightforwardly
correlated with cellular images.
Methods and any associated references are available in the online
version of the paper at http://www.nature.com/naturemethods/.
Note: Supplementary information is available on the Nature Methods website.
We thank the US National Institutes of Health (DP OD006411 to J.R.F. and R01
EB002019 to C.B.S.) and the National Science and Research Council of Canada
(to M.J.F.) for financial support, IMRA America, Inc. for the loan of their FCPA
µJewel D-400 laser, J. Siebert for critically reading this manuscript, N. Ellis for
his assistance in the machine shop and M. Riccio for his assistance with the
M.J.F., T.A.C., J.R.F. and C.B.S. conceived and designed the experiments. M.J.F.
performed surgeries and imaging experiments, I.M.B. performed behavioral
assays, and D.H.S. performed histopathology. M.J.F., I.M.B., J.R.F. and C.B.S.
analyzed data. J.R.F., T.A.C. and C.B.S. contributed reagents and materials.
M.J.F., J.R.F. and C.B.S. wrote the paper.
comPeting FinAnciAl interests
The authors declare no competing financial interests.
Published online at http://www.nature.com/naturemethods/.
reprints and permissions information is available online at http://www.nature.
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Surgical procedure. We anesthetized mice under 5% isoflu-
rane on a custom-built surgery table (Supplementary Fig. 2)
and then maintained on ~1.5% isoflurane in 100% oxygen. We
injected 0.05 mg of glycopyrrolate (an anticholinergic) per 100-g
mouse intramuscularly. We also injected 1 ml per 100-g mouse of
5% (w/v) glucose in normal saline subcutaneously hourly. We used
a rectal thermometer and feedback-controlled heating blanket
to maintain body temperature at 37.5 °C. We shaved the dorsal
surface above the thoracic spine and applied three alternating
washes each of 70% (v/v) ethanol and iodine to the skin to reduce
the likelihood of infection. We gave a subcutaneous injection of
0.1 ml of 0.125% (v/v) bupivicaine at the site of skin incision.
We made a small incision in the skin at the T11–T13 level of the
mouse’s spine and held back the skin with retractors. We made an
incision three vertebrae long on either side of T12 and scraped the
bone clean on the top and the sides. We severed tendons attached
to the three vertebrae using surgical scissors. We trimmed all
incongruous tissue to reduce necrosis. We used sterile cotton
applicators to control bleeding. We clamped the three vertebrae by
magnetic stainless steel bars with a notched groove and held under
pressure on 30-mm stainless steel posts with a three-pronged plug,
consisting of two pins to prevent rotation and a central magnet to
hold the bar. We removed the dorsal lamina of T12 using vanna
scissors, and used sterile gel foam (Pharmacia & Upjohn Co.)
or cotton applicators along with sterile saline to control bleed-
ing and keep blood off the surface of the cord. We trimmed the
lateral edges of the bone back as close as possible to the edges of
the bars and the surface of the bone sealed with dental acrylic and
cyanoacrylate. Where possible, we left the dura intact.
Keeping the cord irrigated with normal saline, we positioned
a top plate and screws inserted into the metal bars. We injected
Kwik-Sil silicone elastomer (World Precision Instruments) into the
space between the cord and the top plate and sealed the chamber
with a 5-mm diameter coverslip. We used cyanoacrylate glue
and dental acrylic to seal the chamber at the rostral and caudal
vertebrae. With pressure maintained by the screws, we removed
the three-pronged steel posts. We pulled the skin to the edge of the
implant and secured it with cyanoacrylate glue and dental acrylic.
We inserted set screws into the wings of the top plate. An illustra-
tion of the procedure with accompanying photographs is avail-
able in Supplementary Figure 1. We again injected bupivicaine
(0.1 ml, 0.125%) around the edge of the implant. During recovery,
we placed the mouse on a heated surface and administered keto-
profen (5 mg kg−1 d−1) and dexamethasone (0.2 mg kg−1 d−1) every
24 h for 72 h. A step-by-step description of how to perform the
procedure, with suggested solutions to common problems, is avail-
able in the Supplementary Protocol. We performed all surgery
under a stereomicroscope (Leica MZ12.5).
All animal procedures performed were approved by the Cornell
Institutional Animal Care and Use Committee and were per-
formed under the guidance of the Cornell Center for Animal
Resources and Education.
Mice. For imaging, we used mice of the YFP-H line (Jackson
Labs), which express EYFP in a subset of pyramidal neurons
and dorsal root ganglia. In addition we used CX3CR1-GFP mice
(Jackson Labs), which express EGFP in microglia. We also used
crosses between the YFP-H and CX3CR1-GFP lines.
For histopathological analysis, we used mice of the YFP-H
line and mice of the Emx-1-cre (Jackson Labs) lines. We used
CX3CR1-GFP mice and GFAP-GFP (Jackson labs), which express
GFP in astrocytes, to study reactive gliosis in microglia and astro-
In all cases, mice were of both sexes and 3–12 months in age
when the device was implanted, and they were heterozygous
for each transgene. Mice were group-housed before chamber
implantation and were singly housed in rat-size cages after
implantation to minimize the risk of the mouse bumping the
implanted chamber against the cage lid.
Histology. We deeply anesthetized mice and perfused them tran-
scardially with phosphate buffered saline (PBS; pH 7.4) (Sigma-
Aldrich) to clear the blood, followed by fixation with 4% (w/v)
paraformaldehyde (PFA) (ThermoFisher Scientific) in PBS.
For gliosis studies in GFAP-GFP and CX3CR1-GFP mice, we
immersed whole spines in PFA for 1 d after perfusion followed by
removal of the spinal cord from the vertebral canal by microsurgical
dissection. We immersed dissected spinal cords in 30% (w/v)
sucrose in PBS until saturated. We froze spinal cords in optimal
cutting temperature (OCT) compound (Tissue-Tek) and cut
sections at a nominal thickness of 30 µm on a Microm HM550
cryotome (ThermoFisher Scientific). We took sections at the ros-
tral and caudal edges of the implant, under the glass and control
regions located one vertebrae in the rostral and caudal direction
from the edges of the implant. We examined tissues under an
Olympus BX41 wide-field fluorescence microscope.
For hematoxylin and eosin staining–based histopathology
studies, we examined whole fixed mice for gross pathology, and
gently freed and removed the skin surrounding the chambers.
We separated the chambers from their attachment to the subja-
cent vertebral bodies starting at one end by gentle dorsal traction.
Once freed from the vertebral bodies, we carefully separated the
chambers from subjacent soft tissues (epaxial muscle and con-
nective tissues). We removed any material (mostly injected sili-
cone) that had adhered to the ventral surface of the glass windows
using a scalpel and reserved it for staining. After removing ribs
and organs from the vertebral column, we collected 3-mm cross-
sections of the vertebral column, including surrounding muscle,
from ~1 cm rostral, 1 cm caudal and directly below the center of
the window by making cuts perpendicular to the vertebral column
using a broad tissue blade. We inserted tissues into cassettes and
immersed them again in PFA. We decalcified tissues by rinsing
tissue cassettes under running water for 15 min, followed by
placement in a vacuum jar containing equal volumes of 20% (w/v)
sodium citrate dihydrate and 50% (v/v) formic acid. Tissues were
held under vacuum at room temperature (20–25 °C) with constant
stirring using a magnet for ~24 h. After this procedure, we rinsed
tissues under running water for 10 min and put in a solution of
70% (v/v) ethyl alcohol. We then embedded tissues in paraffin wax
using an automated tissue processor (Tissue-Tek VIP), sectioned
(4-µm thick sections) them and stained them with hematoxylin
and eosin using an automated stainer (Shandon Varistain 24-4;
Thermo Scientific). We sealed slides with a coverslip and examined
them using an Olympus BX40 microscope.
2PEF microscopy. To image (or reimage) the spinal cord, we
anesthetized mice with isoflurane and placed them on the custom
© 2012 Nature America, Inc. All rights reserved.
surgery table described previously for the laminectomy procedure.
Mice also received glycopyrrolate and glucose as described above.
We used tapped 30-mm posts secured in an optical post holder to
screw finger-tight onto the set screws of the wings of the top plate
of the implant to locally immobilize the spine (Supplementary
Fig. 1g). We elevated mice slightly by the implant to allow room
for chest expansion and contraction during breathing. After imag-
ing, we twisted off the posts and the mouse was allowed to recover
on a heated surface.
We performed imaging using a custom-designed multiphoton
microscope with a 20× water-immersion objective lens (numerical
aperture (NA) = 1.0; Carl Zeiss MicroImaging), a 40× water-
immersion objective (NA = 0.8; Olympus) or a 4× objective (NA =
0.28; Olympus). We performed 2PEF imaging using 1,043-nm
wavelength, 1-MHz, 300-fs pulses from a fiber laser (FCPA µJewel
D-400; IMRA) and/or 920-nm, 87-MHz, 100-fs pulses from
a Ti:sapphire laser oscillator (MIRA HP; Coherent). We used
emission filters at 645/65 nm (center wavelength/bandwidth),
550/50 nm and 517/65 nm (Chroma Technology) to isolate
fluorescence from Texas Red dextran, YFP and GFP, respectively
(see Supplementary Note 7 for individual image details).
Spinal cord lesioning. We made lesions measuring 100–300 µm
long, 5–10 µm wide and 30–40 µm deep in the dorsal spinal
cord by femtosecond laser ablation using ~100-nJ pulses from
a regenerative amplifier (800-nm wavelength, 50-fs pulse dura-
tion, 1-kHz repetition rate; Legend, Coherent). We used custom
software in Matlab (MathWorks) to define a 2D trajectory by
tracing a pattern on a z-dimension projection of a 3D image
stack. To minimize the loss of image contrast caused by excessive
bleeding, we intentionally avoided cutting blood vessels where
possible. To execute the pattern, the mouse was translated at
500 µm s−1 along the traced trajectory in the x-y plane while a
shutter controlling the femtosecond pulses was opened, produc-
ing a cut ~2–3 µm deep. The mouse was then translated by 1 µm
in the z direction, and the cut pattern was repeated. This proce-
dure was iterated until a cut depth of 30–40 µm was achieved.
The shutter was closed during translation in the z dimension.
When deemed necessary, we repeated the cut to ensure complete
transection of axons. Because the damage was mediated by an
electron-ion plasma formed by nonlinear optical absorption and
there was very little thermal energy deposited, the damage was
largely confined to the focal volume.
Image processing. We computed image projections by taking
the s.d. along the z axis of three-dimensional image stacks. For
contrast and resolution measurements, we used maximum pixel
intensity projections of isolated axon segments. As we over-
sampled image stacks, we manually removed frames with large
motion artifacts resulting from breathing without loss of informa-
tion. Owing to the high density of microglia observed after SCI,
there was ambiguity in distinguishing cell bodies from densely
packed processes. We manually identified microglia cell bodies
as fluorescent ameboid structures with visible boundaries, traced
them and counted them in 2D projections using custom Matlab
software. We defined microglia scar size as the mean square
radius in manual traces of the boundary of the largest contiguous
aggregate of microglia. For axon tracing, we Fourier filtered
high-resolution (0.59 µm pixel−1) 3D image stacks, took the
s.d. projection and stitched the images together using PanaVue
stitching software. We used spared axons that were stable over the
duration of the experiments to define a common point of origin
among imaging sessions. We marked axon endings and tracked
them using custom software in Matlab. We resolved ambiguities
by examining trajectories in the 3D stacks.
In double-transgenic mice expressing YFP in axons and GFP in
microglia, we used emission filters with 517/65 nm and 550/50 nm
(center wavelength/bandwidth) with 920-nm excitation for
2PEF imaging. We linearly unmixed images in custom software
written in Matlab. Briefly, we manually selected image features
corresponding to axons (YFP) or microglia (GFP) in both imag-
ing channels and generated a mixing matrix. We then solved for
the inverse matrix and calculated the resultant unmixed images
containing separate fluorescent species.
Contrast and resolution fitting. To characterize the contrast
and resolution, we first used ImageJ to isolate axon segments of
~40–50 µm in length from image stacks the same region across
multiple days. We performed subsequent analysis in Matlab. We
computed the maximum projection along the z axis and median-
filtered the resulting image with a 1-pixel filter radius. To orient
the segment so that the axis ran parallel to the y axis, we used a
radon transform to find the angle of orientation and rotated the
As we considered the maximum intensity projection across
the axon volume, the intensity profile is equal to the value of
the intensity profile taken immediately through the center of the
axon, where, to good approximation, the excited fluorescence
in the axon is approximately constant in the x direction. For an
axon of radius R, and displaced from the origin by an amount δ,
the fluorophore concentration profile, C, in a single scan at the
where C0 is the axonal fluorophore concentration and θ(x) is the
Heaviside step function. For a Gaussian excitation beam with
where I0 is the peak laser intensity and a is a measure of the beam
waist. The image intensity, F(x), is given by the convolution of
equations (1) and (2) with the addition of a background noise
We fit equations (3) to each line of the axon profile (Fig. 2c)
and averaged the results. Failure to converge by nonlinear
© 2012 Nature America, Inc. All rights reserved. Download full-text
least-squares fitting or an R2 value less than 0.85 was used to
exclude data points. We defined contrast as
which ranges between 0 (no contrast) and 1 (noiseless contrast),
where F(–δ) is the intensity peak in the axon. We took resolution
as the parameter a.
Behavioral assays. We subjected mice to open-field and runway
assays. We first made measurements 1 d before implantation of
an imaging window, followed by measurements each day for the
first 7 d and a final time point at 14 d after implantation. We made
all measurements at the same time of day to avoid circadian vari-
ability. We tested mice that were shaved and anesthetized, but not
operated on, simultaneously as sham controls.
We constructed analysis of footprints from the runway assay in
which mice with inked paws traversed the length of a Plexiglass
enclosure (76 cm long × 8 cm wide × 20 cm high) to enter a dark
goal box at the end of the runway. We placed mice on an inked
pad in a 15-cm-long staging area separated from the main run-
way by a sliding insert. We placed paper tape on the floor of the
runway to collect ink pawprints. Removal of the insert marked the
beginning of the trial. All trials were video-recorded from above.
We performed three trials at each time point, and took footprint
measurements from 5 consecutive steps in each trial. We then
returned mice to their home cage between trials to minimize the
effects of fatigue. Mice received 10–14 d of behavioral training
before surgery. During training, we encouraged mice to traverse
the length of the runway without pausing, receiving prompting
from the experimenter where necessary. We deemed training
complete when mice traversed the length of the runway without
pausing or prompting. We assessed hindlimb base of support as
the lateral distance between hindlimbs and stride length as the
distance between the central pads of two consecutive hindlimb
prints on the left or right. We determined average speed by divid-
ing the runway length by the total time of the trial, as determined
by the video clock.
We assessed rearing, grooming, mobility and top ambulatory
speeds in open-field measurements. We placed mice in the center
of a Plexiglass enclosure (46 cm long × 46 cm wide × 47 cm high)
with black sides and a white base. We recorded mice from above
for 5 min under red-light illumination. Video tracking analysis
was performed based on the videos using ANY-maze software
(Stoelting Company) and Matlab. We defined rearing as any period
during which the mouse lifted both of its forelimbs off the ground
simultaneously. We defined grooming as any period during which
the animal licked its fur or moved its forelimbs over the head.
Top speeds were determined as the mean of the speeds greater
than the 75th percentile.
Statistical analysis. We compared grooming time, time spent
immobile, rearing time, base of support, stride length and aver-
age speed using the analysis of variance (ANOVA) test. Where
the null hypothesis was rejected, we performed post hoc analyses
using Tukey’s honestly significant difference for pairwise com-
parisons. We compared top speeds of mice receiving surgery and
sham treatments each day using a Mann-Whitney U test.
We compared microglia and astrocyte densities using ANOVA.
Where the null hypothesis was rejected, we performed post hoc
analyses using Tukey’s honestly significant difference on mean
to compare groups.
We performed statistical tests in Kaelidograph (Synergy)
and Matlab. We set the criterion for significance in all cases to
be α = 0.05.