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380 | VOL.1 NO.1 | 2006 | NATURE PROTOCOLS
PROTOCOL
Targeted bulk-loading of fluorescent indicators for
two-photon brain imaging in vivo
Olga Garaschuk1, Ruxandra-Iulia Milos2 & Arthur Konnerth2
1Institut für Physiologie, Ludwig-Maximilians Universität München, Pettenkoferstrasse 12, 80336 München, Germany. 2Institut für Neurowissenschaften, Technische
Universität München, Biedersteinerstrasse 29, 80802 München, Germany. Correspondence should be addressed to A.K. (arthur.konnerth@lrz.tum.de).
Published online 27 June 2006; doi:10.1038/nprot.2006.58
One of the challenges for modern neuroscience is to understand the rules of concerted neuronal function in vivo. This question can
be addressed using noninvasive high-resolution imaging techniques like two-photon microscopy. This protocol describes a versatile
approach for in vivo two-photon calcium imaging of neural networks, stained with membrane-permeant fluorescent-indicator
dyes. It is based on a targeted pressure ejection of the dye into the tissue of interest and can be used for a large spectrum of
indicator dyes, including Oregon Green 488 BAPTA-1 acetoxymethyl ester and Fura-2 acetoxymethyl ester. Through the use of dye
mixtures and multicolor imaging, this technique allows the visualization of distinct neurons and glial cells up to 500 µm below
the brain surface. It is suitable for staining the brain tissue of various different species (e.g., mouse, rat, cat and zebrafish) at
all developmental stages. When combined with brain microendoscopy, it allows the monitoring of intracellular calcium signals
in awake, behaving animals. The total time required to carry out the protocol, including dissection and cell staining, is ~2 h.
Thereafter, imaging experiments might be performed for at least 6 h.
INTRODUCTION
This protocol describes an approach for in vivo two-photon
Ca2+ imaging of large neuronal circuits at a single-cell level of
resolution. Cells are stained by a brief ‘bolus’ injection of a mem-
brane-permeant Ca2+-indicator dye into the extracellular space
(Fig. 1). The injected dye diffuses into the cells of interest, where
it is hydrolyzed by intracellular esterases1. The activity-depen-
dent Ca2+ transients in stained cells are then monitored using
two-photon laser-scanning microscopy. This approach was ini-
tially developed for in v ivo imaging of the mouse cortex, and is
termed multicell bolus loading (MCBL)2. Over the past years, it
has been successfully applied to the cerebral and cerebellar cor-
tices of other species, such as rats and cats3–6. Interestingly, the
same staining protocol is applicable to lower vertebrates and was
used, for example, for in v ivo imaging of the spinal cord7, olfac-
tory bulb8 and tectal9 neurons in zebrafish larvae.
MCBL differs from other staining methods utilizing mem-
brane-permeant acetoxymethyl (AM) ester-based indicator
dyes10,11 in that the indicators are delivered for a short period
directly to the target cells (see also the method of Regehr and
Tank12). The targeted delivery minimizes the loss of the dye
due to diffusion, nonspecific and/or glial uptake, and so on.
MCBL can be applied at various developmental stages (Fig.
2). Remarkably, there is also efficient staining of neurons in
the adult and aged brain. This is in contrast to the more con-
ventional techniques of AM ester dye loading, which work well
only in the immature tissue10. Additional advantages of MCBL
include the need for only minor surgery, the possibility of re-
staining neurons and, thus, the ability to conduct long-lasting,
perhaps even chronic, recordings13.
While MCBL allows many cell bodies to be imaged simulta-
neously, the method is not sensitive enough to be used for the
analysis of subcellular structures. There are two obvious reasons
for this reduced sensitivity. First, the image contrast is reduced
due to the relatively high background staining of the surround-
ing neuropil. Second, the dye concentration in MCBL-loaded
cells is low, on average 20 µM of the indicator dye2. These limi-
tations restrict the use of MCBL to in vivo imaging of somatic
Ca2+ transients. Note, however, that Ca2+-indicator dyes also
act as Ca2+ buffers, the presence of which within the cells per-
turbs the amplitude and kinetics of the Ca2+ signals under
study14. From this point of view, low intracellular levels of indi-
cator dyes (such as those achieved using MCBL) become an
advantage.
To study neuronal Ca2+ dynamics in awake, behaving ani-
mals, the MCBL technique was recently combined with in vivo
brain endoscopy15. A thin (diameter, 200 µm) optical fiber was
implanted into the brain area with cells stained using MCBL.
The optical fiber was used both for transmitting the excitation
light and for collecting the emitted light. The authors detected
fluorescence signals with a single photomultiplier and, thus,
monitored the compound activity of a large neuronal popu-
lation. Such an optical fiber can be implanted at any desired
depth, allowing the detection of calcium responses in deep
and/or hidden brain regions. This approach can be developed
further by substituting a single optical fiber with fiber bundles
and/or gradient refractive index (GRIN) fibers16. Such new
approaches might soon allow the monitoring of behavior-relat-
ed Ca2+ signals in individual neurons of any brain region.
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NATURE PROTOCOLS | VOL.1 NO.1 | 2006 | 381
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MATERIALS
REAGENTS
• Experimental animals (see REAGENT SETUP)
• Anesthetic agent (e.g., isoflurane, ketamine/xylazine or urethane)
• Local anesthetic agent (e.g., lidocaine)
• Membrane-permeable calcium-indicator dye (e.g., Oregon Green 488
BAPTA-1 AM (OG-1 AM), Calcium Green-1 AM, Fura-2 AM, Fura-PE3
AM, Fluo-4 AM or Indo-1 AM from Molecular Probes or TefLabs)
• Sulforhodamine 101 (SR101; Sigma)
• 20% Pluronic F-127 in DMSO (e.g., 2 g Pluronic F-127 in 10 ml DMSO;
Sigma) ! CAUTION Strong detergent; skin, eye and respirator y system
irritant. Wear suitable protective clothing
• Standard pipette solution: 150 mM NaCl, 2.5 mM KCl and 10 mM HEPES
• Standard external saline: 125 mM NaCl, 4.5 mM KCl, 26 mM NaHCO3,
1.25 mM NaH2PO4, 2 mM CaCl2, 1 mM MgCl2, 20 mM glucose, pH 7.4,
when bubbled with 95% O2 and 5% CO2
• Low melting point agarose (Invitrogen GmbH)
EQUIPMENT
• Recording chamber with central access opening: custom-made from a
standard tissue-culture dish (diameter, 35 mm2)
• Glass capillaries (e.g., from Hilgenberg GmbH)
• Pipette puller (e.g., PP830 from Narishige)
• Brain atlas (e.g., from Academic Press)
• Surgical equipment, including a stereotaxic instrument, drill and
warming blanket to ensure a constant body temperature; available from
many providers (e.g., TSE-Systems)
• LN-Mini manipulator (Luigs & Neumann GmbH)
• Picospritzer II (General Valve) or pneumatic drug-ejection system (NPI)
• Patch-clamp amplifier (e.g., from HEKA)
• Two-photon laser-scanning microscope commercially available from
several providers (e.g., Zeiss)
• Felt polisher (e.g., from Dr. Ihde Dental)
• Cyanoacr yl glue (available from many providers; e.g., UHU GmbH)
• Millipore filter (Millipore)
REAGENT SETUP
Experimental animals So far, the protocol has been tested in mice, rats,
cats and zebrafish. ! CAUTION All experiments must be performed in
accordance with the relevant authorities’ guidelines and regulations.
EQUIPMENT SETUP
Anesthesia unit Including a chamber for pre-anesthetic medication, a flow
meter and a vaporizer (the latter items are for volatile anesthetic agents
only). Consult the literature (e.g., ref. 17) for the best choice of anesthesia
for each species.
Anesthesia-monitoring system Used to measure the blood pressure,
arterial oxygen concentration, body temperature, and respiratory and
pulse rate of the animal. The monitoring equipment is available from
many providers, but it is not always suitable for small laboratory animals
(e.g., mice and neonatal rats). We use equipment from ADI Instruments
to monitor the respiratory and pulse rate, body temperature and blood
pressure in mice.
Manipulator and pressure-application device To inject the staining
solution into the brain we use the LN-Mini manipulator and either
Picospritzer II or the pneumatic drug-ejection system.
Patch-clamp amplifier Used to monitor the resistance of the pipette
during dye injection. Monitoring of the pipette resistance is not
mandator y, but is advisable because it allows pipette clogging to be
recognized and the point when the pipette reaches the surface of the cortex
to be estimated.
Two-photon laser-scanning microscope We use a custom-built
microscope based on a mode-locked laser system operating at 710–920
nm wavelength (MaiTai, Spectra Physics) and a laser-scanning system
(Fluoview, Olympus) coupled to an upright microscope (BX51WI,
Olympus). Such a custom-built system can be assembled following the
instructions in refs. 18,19.
Brain atlas Used to obtain stereotaxic coordinates of the respective brain
region (for example, see refs. 20,21).
PROCEDURE
Preparation
1| Anesthetize the animal and place it onto a warming blanket (38 °C) in front of the oxygen supply22. Affix the sensors
of the anesthesia-monitoring system. Ensure that the surgical level of anesthesia has been reached (e.g., by testing the
pinch withdrawal and the eyelid reflex). We anesthetize mice by inhalation of isoflurane (1–1.5% (vol/vol) in pure O2).
Alternatively, adult mice can be anesthetized with either ketamine/xylazine or urethane (0.1/0.01 and 1.9 mg per g body
weight, respectively, i.p.).
ab
Dye-ejection
pipette
Figure 1 | Experimental arrangement for in vivo
staining of neuronal populations with Ca2+-
indicator dyes. (a) A custom-made recording
chamber is glued to the skull to allow head
fixation and the use of a water-immersion
objective. The chamber is perfused with warm
(37 °C) standard external saline. Two small
craniotomies are performed: one for the insertion
of the staining-patch micropipette (obligatory)
and one above the field of view for improvement
of the imaging depth (optional). Cells, stained
using MCBL, are shown in green. The stained area
has a diameter of 200–400 µm. Modified from
ref. 2. (b) Photograph of the recording chamber
(upper panel) and schematic drawing of its cross-
section (lower panel). Note that a circular region
around the perforation is thinned to fit the
curvature of the animal’s skull.
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382 | VOL.1 NO.1 | 2006 | NATURE PROTOCOLS
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2| Use a stereotaxic device to identify the location of
the brain area of interest. Inject ~ 50 µl local anesthetic
agent (e.g., 2% lidocaine; 20 mg lidocaine in 1 ml standard
external saline) subcutaneously at the location where the
skin is to be removed (optional).
3| Remove the skin above the desired brain area. Decide
whether to image through the skull; the stability of the
preparation is higher when imaging through the skull (lower
impact of heart beat and breathing artifacts), but the
efficiency of photon detection is higher when the skull is
removed (images are crisper and imaging depth is greater).
4| Thin the skull and polish it with a felt polisher. Imaging
through the thinned skull provides optimal results when the
skull is thinned down to 10–20 µm2. We suggest stopping
thinning as soon as the bone bends when gently touched
with the tweezers. If the skull is to be removed, less thinning
is necessary.
▲ CRITICAL STEP The skull thinning must be performed as
gently as possible; never press onto the skull. Inaccurate
thinning often causes brain damage.
5| Use cyanoacryl glue to adhere the custom-made recording chamber to the skull.
6| Transfer the animal into the recording set-up (we use a set-up similar to that described in ref. 23, equipped with a
two-photon laser-scanning microscope; see above) and place it onto a warming blanket (38 °C). Affix the sensors of the
anesthesia-monitoring system. If necessary, adjust supply of anesthetic to keep physiological levels of monitored parameters.
▲ CRITICAL STEP The quality of recordings critically depends
on the good condition of the experimental animal. Therefore,
starting now, continuously monitor the following vital
parameters: respiratory and pulse rate, body temperature,
arterial oxygen concentration and blood pressure.
7| Perfuse the recording chamber with a warm (37 °C)
standard external saline.
8| Perform a craniotomy above an area devoid of large
blood vessels. This should be small (≤0.5 mm) for imaging
through the skull and larger (or two small craniotomies
should be performed near each other; Fig. 1) for ‘open-
access’ imaging.
▲ CRITICAL STEP Do not remove the dura mater; removal
is not required for cell staining and strongly enhances
movement artifacts. The stability of recordings also
critically depends on the diameter of the craniotomy.
Thus, openings larger than 1 mm in diameter are often
accompanied by large movement artifacts occurring at the
heartbeat frequency.
Staining neurons with a calcium-indicator dye
9| Dissolve AM ester of the preferred indicator dye (e.g.,
OG-1 AM) in the solution containing 20% Pluronic F-127
in DMSO (e.g., 2 g Pluronic F-127 in 10 ml DMSO) to yield
a dye concentration of 10 mM. Dilute this solution 1/10
to 1/100 with the standard pipette solution to prepare the
Newborn (P8)
Juvenile (P23)
Adult (2 month old)
Aged (1-y-old)
Figure 2 | MCBL allows staining of cortical tissue at various developmental
stages. The microphotographs illustrate layer 2/3 cells in the visual cortex
of mice at different ages. Cells were stained using OG-1 AM and images were
taken using a 60× Nikon water-immersion objective (1.0 NA).
a b
Figure 3 | Assessment of the staining quality. (a,b) High-magnification
images of cells in layer 1 (upper panels) and in layer 2/3 (lower panels)
taken at two different locations in the visual cortex of a 64-d-old mouse.
Both areas were stained using the same protocol, but in (b) a large brain
vessel was damaged prior to staining.
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NATURE PROTOCOLS | VOL.1 NO.1 | 2006 | 383
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staining solution. The same recipe is used to dissolve other
Ca2+-indicator dyes (e.g., Fura-2 AM, Fluo-4 AM, Calcium
Green-1 AM, Indo-1 AM, Fura-PE3 AM, Fura Red AM and
Magnesium Green AM)2,7.
▲ CRITICAL STEP Note that the standard pipette solution
(a simplified Ca2+-free Ringer’s solution) is designed to
minimize precipitation of the dye. Filter the staining
solution if necessary (we use a Millipore filter with a pore
diameter of 0.45 µm).
? TROUBLESHOOTING
10| Pull a staining micropipette from a glass capillary
using a pipette puller (we use standard-patch pipettes with
a resistance of 6–9 MΩ when filled with standard pipette
solution). Fill with staining solution. Insert the pipette
into the cortex (under an angle of, for example, 30°) while
monitoring the pipette resistance with a patch-clamp
amplifier. The pipette resistance can increase slightly (up
to 15 MΩ) when penetrating the dura mater, but must
decrease to the initial level either immediately thereafter
or, at the latest, upon the application of ejection pressure
(see below). Advance the pipette along its axis until it
reaches the desired depth (Fig. 1). With the dye-application pipette located 150–200 µm below the cortical surface, all
cortical cells between the surface and a 400-µm depth are stained2. For staining the cells in deeper cortical layers, the
pipette is positioned 650–750 µm below the pia3. Apply a pressure pulse (1 min, 70 kPa) to eject ~400 femtoliters staining
solution near the cells of interest (see ref. 3 for the slightly modified protocol for labeling deep cortical layers). Remove
the pipette.
■ PAUSE POINT Wait ~1 h to obtain a stable maximal fluorescence level in stained cells2. This protocol yields a stained
area with a diameter of 200–400 µm.
Figure 4 | Spontaneous Ca2+ transients in the visual cortex of an adult mouse.
Spontaneously occurring Ca2+ transients (lower panel) in seven individual layer
2/3 neurons, marked with corresponding numbers in the upper panel. Data are
derived from a series of time-lapse images recorded at 10 Hz.
Figure 5 | Ca2+ transients in the individual cortical neurons evoked by sensory stimulation. Line-scan recordings of Ca2+ transients (sampled at 200 Hz; right
panel) in two layer 2/3 neurons of the mouse visual cortex marked with the respective numbers in the left panel. The vertical broken line in the right panel
marks the beginning of a brief (100 ms) light flash. Note that whereas cell 2 responded reliably to this stimulus, no responses were seen in the neighboring
cell 1, which instead exhibited frequent spontaneous Ca2+ transients.
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Two-photon imaging of stained cells
11| Choose the wavelength of the
excitation light (depends on the
indicator dye used). Consult ref. 24
for two-photon excitation spectra
of common Ca2+-sensitive dyes.
Excitation light of 800 nm can be used
for the initial visualization of neurons
stained with the following indicator dyes: Fura-PE3 AM, Fura Red AM, Indo-1 AM, Calcium Green-1 AM, OG-1 AM, Fluo-4 AM
and Magnesium Green AM.
12| Check the average power of the excitation light under the objective (must be at least 50–70 mW). Reduce the
excitation power to the minimum and focus the objective (for example Nikon, 60×, numerical aperture (NA) 1.0, water
immersion) of the two-photon microscope onto the brain surface. Raise the excitation power carefully (to avoid dye
bleaching) and inspect the upper cortical layers using high-resolution settings (frame rate, 1 Hz). The following structures
become clearly visible: large epithelial cells on the top of the cortex; layer 1 cells up to the depth of 100–200 µm,
depending on the age of the animal (Fig. 3a, upper panel); and layer 2/3 cells (Figs. 2–7). When imaging through the
a
b
Double staining
Depth profile
Figure 6 | Double staining and depth profile.
(a) Microphotographs of layer 2/3 cells in the
mouse visual cortex (30-d-old mouse) stained
simultaneously using a dye mixture containing
OG-1 AM and the glial marker SR101. The
fluorescence of OG-1 AM was directed to the
green channel (left) and the fluorescence
of SR101 was directed to the red channel
(middle). The merged image on the right shows
neurons in green and glial cells in yellow.
(b) Microphotographs of the visual cortex of a
juvenile (32-d-old) mouse taken at different
depths. The excitation light’s pulse width under
the objective was optimized by compensating
group-velocity dispersion with a pair of
prisms28.
a
b
cd
Figure 7 | MCBL using a low concentration of the indicator dye. (a,b) High-
magnification images of layer 2/3 cells taken from neighboring locations in
the visual cortex of two different animals. Cells stained with 100 µM OG-1
AM are shown in the panels on the left, whereas cells stained with 1 mM
OG-1 AM are shown in the panels on the right. (c) Normalized histograms
showing the distribution of decay-time constants of spontaneous Ca2+
transients in cells stained with 1 mM OG-1 AM (black) and 100 µM OG-1
AM (red), respectively. (d) Bar graph illustrating the mean values of the
respective decay-time constants.
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thinned skull, individual cells can be well resolved up to 250 µm below the cortical surface. Removing the skull above the
imaging field further improves depth resolution. The maximal depth at which individual cells can be resolved depends on
the shape and density of cells, the density of blood vessels in the imaged region and the age of the animal. In juvenile
and young adult animals, the depth limit for single-cell imaging in the cortex is ~500 µm (Fig. 6b; consult ref. 25 for
optimization of the imaging depth). In general, all cells in the preparation are stained; the only dark areas correspond to
blood vessels, which are easily identified when focusing through the tissue. Furthermore, characteristic astrocytes often
surround the blood vessels (see below).
? TROUBLESHOOTING
13| Monitor Ca2+ transients of interest, for example, with a frame rate of 10 Hz. Use online brightness-versus-time analyses
to monitor photobleaching. Adjust excitation power to levels just below the bleaching ‘threshold’. Use a commercially
available software package for collection of time-lapse images and online data analyses.
? TROUBLESHOOTING
● TIMING
Dissection (Steps 1–8), 1h
Staining (Steps 9–10), 1h
Imaging (Steps 11–13), at least 6 h
? TROUBLESHOOTING
See Table 1.
ANTICIPATED RESULTS
Figures 2–5 illustrate MCBL-stained layer 2/3 cells in the visual cortex of mice of different ages. At each age, stained
cortical neurons show spontaneous (Fig. 4) as well as light-evoked (Figure 5) Ca2+ transients. Data shown in Figure 4 are
derived from a series of time-lapse images recorded at 10 Hz. Light-evoked responses in Fig. 5 were recorded as a series
of line scans at 200 Hz. Note that in each case, the signal-to-noise ratio is sufficient to allow individual non-averaged
somatic Ca2+ transients to be distinguished clearly from the background. As was shown by Kerr et al.3 in rat somatosensory
cortex, spontaneous Ca2+ transients reflect action-potential firing. Also, in the mouse visual cortex, both spontaneous
(Fig. 4) and light-evoked (Fig. 5) Ca2+ transients required firing of action potentials (O.G. and A.K., unpublished
observations).
As mentioned above, the MCBL technique is not cell-type specific. It provides a relatively homogeneous staining of
different cell types (although glial cells are generally brighter than neurons). An identification of the various cell types
can be achieved using additional markers (e.g., cell-type specific expression of green fluorescent protein) and multicolor
two-photon imaging. A versatile approach for distinguishing between neuronal cells and astrocytes was developed by
Nimmerjahn et al.5 and is based on the use of the astrocyte-specific marker SR101, which emits fluorescence light at
TABLE 1 | Troubleshooting table.
PROBLEM SOLUTION
Step 9: the staining patch micropipette
gets clogged
Clean glass capillaries used to manufacture the pipettes; dissolve Ca2+-indicator dyes
immediately before use; filter the staining solution before use (e.g., with a Millipore filter;
pore diameter, 0.45 µm)
Step 12: cells are not, or are only
poorly, stained
There are two likely scenarios, either (i) the tissue is intact but the dye delivery failed, or (ii)
the tissue is damaged (Fig. 3); for (i) monitor the pipette resistance during dye injection
(a value above 20 MΩ indicates that the pipette is clogged); for (ii) check the anesthesia
monitoring parameters, try to thin the skull as gently as possible, avoiding damage to large
blood vessels, and increase the speed of dissection and staining (the latter should be
accomplished in less than 2 h)
Step 13: recording conditions are
unstable; occurrence of high-frequency
vibrations of cells and/or slow drift of
the plane of focus
These problems are more profound when the skull is removed; cover the skull opening with
2% low melting point agarose (e.g., 20 mg in 1 ml standard external saline) and keep the
temperature of the external saline stable (with a precision of 0.1 °C); the high-frequency
vibrations are usually the result of heart-beat pulsation (compare with measurements of the
anesthesia-monitoring system) and are more profound in regions with a high density of
blood vessels
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wavelengths (550–750 nm) that are significantly longer than those of common Ca2+ indicators. For targeted SR101
staining, we modify the protocol of Nimmerjahn et al.5. We dilute 1 mg SR101 in 4 ml standard pipette solution and use it
to dilute the concentrated solution containing 10 mM Ca2+ indicator (Step 9). The combined staining cocktail, containing
SR101 and the Ca2+-sensitive dye, is then injected into the brain (Step 10). This results in a good loading of neurons and
glia cells with the Ca2+ indicator, and specific staining of glia cells with SR101 in the same brain region (Fig. 6a).
The MCBL technique was originally designed to apply 400 femtoliters of the concentrated Ca2+-indicator dye-containing
solution (yielding a final pipette concentration of the dye of 1 mM). Because membrane-permeant Ca2+-indicator dyes are
dissolved in DMSO, the staining solution also contained 10% DMSO (vol/vol). Although similar and/or higher detergent
concentrations are routinely used to stain intact tissues with indicator dyes11,26,27, we recently found that such a high
dye/detergent concentration is not needed. As shown in Figure 7a,b, the MCBL protocol can provide high-quality staining
of the mouse cortex with 100 µM OG-1 AM and 1% DMSO (vol/vol)-containing pipette solution. However, the use of the
lower dye concentration imposes higher demands on the quality of preparation. The time constants of spontaneous Ca2+
transients were, on average, 0.81 ± 0.04 s (n = 123) in cells stained with 100 µM OG-1 AM and 1.10 ± 0.08 s (n = 88)
in cells stained with 1 mM OG-1 AM (Fig. 7c,d). This similarity suggests that the intracellular indicator levels obtained
with 100 µM OG-1 AM-containing staining solutions are nearly as high as those reached with 1 mM OG-1 AM-containing
solutions (in the range of 20 µM2).
ACKNOWLEDGMENTS We thank M.A. Busche for help with experiments
shown in Figure 6b. This work was supported by grants from the Deutsche
Forschungsgemeinschaft (SFB 391 and SFB 596) and the Bundesministerium für
Bildung und Forschung (NGFN-2).
COMPETING INTERESTS STATEMENT The authors declare that they have no
competing financial interests.
Published online at http://www.natureprotocols.com
Rights and permissions information is available online at http://npg.nature.
com/reprintsandpermissions
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