RESEARCH REPORT TECHNIQUES AND RESOURCES
Development 140, 1364-1368 (2013) doi:10.1242/dev.091844
© 2013. Published by The Company of Biologists Ltd
ClearT: a detergent- and solvent-free clearing method for
neuronal and non-neuronal tissue
Appreciation of neural circuitry and single-cell morphology has
benefited from new labeling methods, including fluorescent tracers
and genetically encoded fluorescent proteins (Luo et al., 2008).
Although these methods produce superb detail of labeled cells and
pathways, tissue opacity limits the depth of imaging, necessitating
imaging sectioned material in order to attain high microscopic
resolution. However, because images must be reconstructed in three
dimensions (3D) post-acquisition, imaging and reconstructing sections
is neither as efficient nor as accurate as imaging thicker tissue samples.
New reagents that clear or render tissue transparent include Scale,
benzyl-alcohol and benzyl-benzoate (BABB), and a combination of
tetrahydrofuran and BABB, all of which preserve genetically
expressed fluorescent signal, allowing deep imaging of neural
circuitry in 3D (Dodt et al., 2007; Hama et al., 2011; Ertürk et al.,
2012). However, these reagents change tissue volume and require
several days to weeks to fully clear the tissue (Hama et al., 2011;
Ertürk et al., 2012). More importantly, owing to their reliance on
detergents or organic solvents, Scale and BABB disrupt the
fluorescent signal of immunohistochemistry, of conventional
lipophilic carbocyanine dyes [such as 1,1?-dioctadecyl-3,3,3?,3?-
tetramethylindocarbocyanine perchlorate (DiI)] and of fluorescent
tracers such as cholera toxin subunit B (CTB). Here, we describe a
rapid clearing method that maintains tissue volume and preserves
fluorescent signal from tracers, immunohistochemistry and
genetically expressed fluorescent proteins.
MATERIALS AND METHODS
For ClearT, 20%, 40%, 80% and 95% formamide solutions were made by
adding formamide (99.6%, considered 100%) (Fisher) to PBS (pH 7.4)
For ClearT2, a 50% formamide/20% polyethylene glycol (PEG) solution
was made by mixing formamide (99.6%, considered 100%, as made for
ClearT) with 40% PEG/H2O (wt/vol) at a ratio of 1:1 (vol/vol). A 25%
formamide/10% PEG solution was made by mixing 50% formamide plus
20% PEG/H2O (wt/vol) at a ratio of 1:1 (vol/vol). A 40% PEG solution was
made by stirring powdered PEG 8000 MW (Sigma-Aldrich) in warm H2O
for 30 minutes, and is stable at room temperature for several months.
Preparation of specimens and clearing procedures
Procedures for the care and breeding of mice follow regulatory guidelines
of the Columbia University Institutional Animal Care and Use Committee.
Noon of the day on which a plug was found was considered to be E0.5.
C57BL/6J wild-type and actin-GFP mouse embryos were removed from
mothers anesthetized with ketamine-xylazine (100 and 10 mg/kg,
respectively, in 0.9% saline); postnatal wild-type, Thy1-GFP (M-line) (a gift
from J. A. Gogos, Columbia University, NY, USA) and adult Tcf/Lef:H2B-
GFP mice (a gift from E. Laufer, Columbia University, NY, USA) were
anesthetized with ketamine-xylazine (100 and 10 mg/kg, respectively, in
0.9% saline), fixed in 4% paraformaldehyde (PFA)/PBS (pH 7.4) overnight,
or perfused and washed with PBS at 4°C. Embryos were perfused
transcardially for optimal clearing. All clearing protocols took place at room
ClearTand ClearT2tissue-clearing method
Incubation times in each solution vary according to tissue thickness for the
desired transparency (see Table 1 for details).
ScaleA2 has been described previously (Hama et al., 2011). E14.5
embryos were cleared with ScaleA2 for 14 days; DiI-labeled embryos or
CTB-labeled sections were treated overnight or 2 hours, respectively.
BABB has been described (Dodt et al., 2007). DiI-labeled embryos or
CTB-labeled sections were treated with BABB overnight or for 2 hours,
respectively, after dehydration with 30%, 50%, 70% and 100% ethanol for
1 hour each and with hexane for 1 hour.
Retinal axon labeling with DiI and CTB
Anterograde DiI labeling has been described previously (Plump et al.,
2002). The eye was placed back into the optic cup and heads were incubated
in PBS containing 0.1% sodium azide as follows: E14-E16, 5-7 days at
room temperature; E17-P0, 5-7 days at 37°C. The retinogeniculate
projection was labeled with CTB as described previously (Jaubert-Miazza
et al., 2005; Rebsam et al., 2009), and single neuron labeling in the CTB-
labeled dLGN was performed as described previously (Krahe et al., 2011).
Vibratome and cryosections were blocked in 5% BSA/1% Tween (Sigma-
Aldrich) in PBS (pH 7.4) for 1 hour at room temperature. Mouse
monoclonal anti-RC2 (IgM) antibody (Developmental Hybridoma Bank)
1Department of Pathology and Cell Biology, Columbia University, College of
Physicians and Surgeons, 630 West 168th Street, 14-509 P&S, New York, NY 10032,
USA. 2Department of Neuroscience, Columbia University, College of Physicians and
Surgeons, 1051 Riverside Drive, New York, NY 10032, USA. 3Department of
Anatomy and Neurobiology,Virginia Commonwealth University, Richmond, VA
‡Present address: Department of Anatomical Sciences and Neurobiology, School of
Medicine, Health Science Center, University of Louisville, Louisville, KY 40202, USA
*Author for correspondence (firstname.lastname@example.org)
Accepted 9 January 2013
We describe a clearing method for enhanced visualization of cell morphology and connections in neuronal and non-neuronal tissue.
Using ClearTor ClearT2, which are composed of formamide or formamide/polyethylene glycol, respectively, embryos, whole mounts
and thick brain sections can be rapidly cleared with minimal volume changes. Unlike other available clearing techniques, these
methods do not use detergents or solvents, and thus preserve lipophilic dyes, fluorescent tracers and immunohistochemical labeling,
as well as fluorescent-protein labeling.
KEY WORDS: Clearing reagent, Whole mount, Retinal axon pathway, Immunohistochemistry, Fluorescent protein, DiI
Takaaki Kuwajima1, Austen A. Sitko2, Punita Bhansali1, Chris Jurgens3, William Guido3,‡and Carol Mason1,2,*
Clearing methods for DiI and immunohistochemistry
(1:4) and mouse monoclonal anti-neurofilament (IgG) antibody (2H3) (a
gift from T. Jessell and S. Morton, Columbia University, NY, USA) (1:5)
were incubated in 1% BSA/1% Tween in PBS overnight at 4°C. After
washes with 1% Tween in PBS, Cy3-conjugated anti-mouse IgM and Cy5-
conjugated anti-mouse IgG (1:500) secondary antibodies (Jackson) were
applied, incubated in 1% BSA/1% Tween in PBS overnight at 4°C. Hoechst
33258 (Molecular Probes) was used for nuclear staining. Whole-mount
immunolabeling of embryos with anti-neurofilament antibody has been
described previously (Huber et al., 2005).
Whole brains or sections with DiI, CTB or immunolabeling, or sections of
GFP-labeled mice were imaged on a Zeiss AxioImager M2 microscope with
Apotome, AxioCam MRm camera, Neurolucida software (V10.40,
MicroBrightField Systems); with a 5× objective lens (FLUAR, NA=0.25,
working distance=12.5 mm), a 20× objective lens (PLAN-APOCHROMAT,
NA=0.8, working distance=550 μm) or a 40× objective lens (PLAN-
NEOFLUAR, NA=0.75, working distance=710 μm) (Fig. 2B,C; Fig 2D,
bottom; Fig. 3C,D,F; supplementary material Fig. S3B, Fig. S4). Using the
principle of structured illumination, the Apotome provides confocal-like
resolution with epifluorescence imaging. The Apotome improves the signal
to noise ratio by acquiring three images of an optical section and subtracting
background fluorescence signal. Imaging of whole heads and brains was
performed using a Zeiss dissecting microscope StemiSV11, Axiovision
software, AxioCam camera (Fig. 1; Fig. 2A; Fig. 3A,B; supplementary
material Fig. S1; Fig. S2A). Imaging of whole embryos with
immunolabeling was performed using Nikon SMZ 1500 zoom
stereomicroscope and DS-Qi1Mc camera (Fig. 3E). A Zeiss Axioplan 2
microscope, AxioCam camera and Axiovision software was used to image
thin brain sections using a 10× objective lens (PLAN-NEOFLUAR,
NA=0.3) or a 20× objective lens (PLAN-NEOFLUAR, NA=0.5)
(supplementary material Fig. S2B, Fig. S3A, Fig. S5). Thick samples were
imaged using a home-made slide to keep tissue submerged in formamide
solutions and covered with a regular glass coverslip: a square rim of plastic
or silicone elastomer was super-glued to a regular glass slide.
All experiments were performed three or more times with similar results.
Data were analyzed and graphs constructed using Metamorph or Microsoft
Excel. Error bars represent s.e.m. and statistical analysis was performed
using Student’s t-test; P>0.05 indicates non-significance.
RESULTS AND DISCUSSION
ClearTis a rapid tissue clearing method
After observing that 20 μm cryosections of embryonic mouse brain
became transparent in the hybridization buffer used for in situ
hybridization, we found that a component of the buffer, formamide,
could clear thick tissue samples. Here, we demonstrate the
versatility of our method, named ClearTfor neuronal and non-
neuronal tissue, and compare its clarity, rapidity and tissue
expansion/shrinkage to existing clearing methods.
Intact embryos, embryonic and postnatal dissected heads, brains,
and thick (up to 1000 μm) brain sections, were fixed and
sequentially immersed in graded concentrations of formamide
(Table 1A, Fig. 1A). The ClearTprocedure rendered embryonic
brains as transparent as with ScaleA2, but did so significantly faster
(1 day versus 14 days) (Fig. 1B). Completely cleared postnatal day
0 (P0) brain sections were similar to their original size (before
clearing=1.0±0 versus ClearT=1.04±0.02, not significant, n=6
sections) (Fig. 1C). Even after prolonged treatment with ClearT,
sample volume only increased slightly, significantly less than in
ScaleA2 [1 day, ClearT=1.33±0.09 versus ScaleA2=1.81±0.05,
P<0.01; 2 days, ClearT=1.27±0.09 versus ScaleA2=1.83±0.06,
P<0.01, n=5 (ClearT), 4 (ScaleA2) sections] (supplementary
material Fig. S1). Although formamide is not harmful to tissue in the
short term, it is unsuitable for long-term tissue storage. Therefore,
Table 1. Clearing procedures
Whole embryos or headsWhole dissected brains (E16-P11)Half embryonic brainsSections (20-1000 mm)
15 minutes5-16 hours; E11-E15, respectively
Embryonic heads or brainsSections (20-1000 mm)
25% formamide/10% PEG
50% formamide/20% PEG
50% formamide/20% PEG
15-60 minutes5-16 hours; E11-E15, respectively
Incubation times vary with tissue thickness. Time in final buffer can be determined by visual inspection for desired transparency. O/N, overnight.
Fig. 1. Rapid tissue clearing with ClearT. (A) Fixed whole embryos
(E14.5) and dissected postnatal brains (P0) were cleared overnight. The
grid is visible through tissue cleared by ClearT. (B) E14.5 embryos cleared
with ClearTor ScaleA2 reach full transparency in 1 day or 14 days,
respectively. (C) ClearTdoes not lead to volume changes. P0 sections (800
μm), surface area measured: pre-cleared, red line; ClearT, blue line.
(D) Clearing is reversible with PBS (30 minutes). Scale bars: 1 mm.
we transferred samples treated with ClearTinto PBS, where they
became opaque within 30 minutes and could be safely stored for at
least 1 month (Fig. 1D).
Visualization of DiI- or CTB-labeled axons in tissue
cleared with ClearT
The projections, connections, and growth cone (GC) morphology of
developing axons can be visualized by anterograde labeling with
lipophilic dyes (Little et al., 2009; Bielle et al., 2011). Here, we use
the mouse visual system, a classic model for studying neural
circuitry development, to demonstrate the advantages of clearing
the mouse brain with ClearTin preserving lipophilic fluorescent dye
labeling. We anterogradely labeled retinal ganglion cell (RGC)
axons in embryonic day (E) 14.5 embryos with DiI and treated
embryos with ClearT, ScaleA2 or BABB for 1 day. DiI labeling of
retinal axons in the optic nerve and chiasm was preserved after
treatment with ClearT, but treatment with either ScaleA2 or BABB
degraded the fluorescent signal (supplementary material Fig. S2A).
We then examined DiI-labeled RGC axons in cleared tissue at
the optic chiasm at E15.5 (Fig. 2A). The DiI-labeled retinal
projection was not visible prior to clearing, but could be seen
through both dorsal and ventral aspects of the cleared head, with
jaw and tongue removed but skin and skull intact (Fig. 2A). We
examined the resolution of fine morphological detail of DiI-labeled
axons and GCs in the proximal ipsilateral optic tract at E14.5 before
and after clearing (Fig. 2B). The number and resolution of DiI-
labeled axons and GC processes (e.g. filopodia and lamellopodia)
were markedly increased after clearing with ClearT(Fig. 2B).
Development 140 (6)
Furthermore, E18.5 DiI-labeled RGC axons in the thalamus and
superior colliculus were not visible before clearing when imaged
from the midline of parasagittal hemisections, but the full tract was
distinctly visible after clearing with ClearT, even through a depth of
~1 mm (Fig. 2C).
CTB is widely used for the analysis of postnatal RGC axon
targeting in the dLGN (Jaubert-Miazza et al., 2005; Rebsam et al.,
2009). To test the compatibility of CTB with ClearT, we
anterogradely labeled each eye of P5 pups with CTB conjugated to
either Alexa Fluor 488 or 594. CTB labeling was preserved after
ClearTand BABB treatments, but BABB reduced tissue size by half
(before clearing=1±0 versus cleared=0.50±0.02, P<0.05, n=4
sections), while labeling was diffuse following ScaleA2 treatment
(supplementary material Fig. S2B). CTB labeling was visible
through the entire depth of a 700 μm section of P5 brain treated with
ClearT, whereas fluorescence could not be seen beyond 250 μm
before clearing (Fig. 2D). Moreover, it is possible to successively
clear, unclear (in PBS) and re-clear DiI- or CTB-labeled samples
without compromising tissue or label integrity (supplementary
material Fig. S3A,B).
ClearT2clears tissue with fluorescent protein and
with immunohistochemical label
Our original ClearTprotocol diminished green fluorescent protein
(GFP) intensity in E14.5 actin-GFP embryos (Ikawa et al., 1995).
Because polyethylene glycol (PEG) stabilizes protein conformation
(Rawat et al., 2010), we investigated whether PEG would stabilize
GFP expression in formamide. Whereas 50% formamide failed to
Fig. 2. Retinal axon projections in brain
tissue cleared with ClearT. (A) E15.5 eye
was labeled with DiI, the jaw and tongue
were cut away and the head was cleared
with ClearT. DiI-labeled contralateral (C)
and ipsilateral (I) retinal axons and optic
chiasm are detected in both dorsal and
ventral views after clearing with ClearT.
(B) Merged stack (41 images, 5 μm steps)
of E14.5 DiI-labeled growth cones (GCs)
(arrows) and axons (arrowheads) of the
ipsilateral optic tract; imaged from the
ventral surface of 200 μm brain section,
before and after clearing. (C) DiI-labeled
contralateral RGC projection to the
thalamus and superior colliculus at E18.5.
Brains were cut sagittally at the midline
and cleared with ClearT. Merged stack (51
images, 20 μm steps), viewed from the
midline. DiI-labeled RGC axons in the
dLGN in the thalamus (TH) and superior
colliculus (SC) were undetectable in pre-
cleared tissue, but easily visible after
clearing. (D) CTB conjugated to Alexa
Fluor 488 or 594 was injected into each
eye and a 700 μm frontal section of P5
brain was cleared with ClearT. Optical
slices at 250 μm, 450 μm and 600 μm
below the tissue section surface are
shown (from 71 images, 10 μm steps).
Both CTB labels were observable, though
deeper, in cleared dLGN compared with
the same tissue before clearing. Scale bars:
1 mm in C (top); 100 μm in A and bottom
of C,D (bottom); 10 μm in B.
clear brains, a 20% PEG/50% formamide mixture successfully
cleared brain tissue and preserved fluorescence. This modified
method, named ClearT2, also requires immersion in a graded series of
formamide/PEG solutions (25% formamide/10% PEG then 50%
formamide/20% PEG) (Table 1B, Fig. 3A). Although tissue
transparency with ClearT2was less complete than with ClearT,
application of ClearT2induced robust transparency of thick P0 brain
sections without volume changes (before clearing=1.0 versus
ClearT2=0.98±0.02, n=6, not significant) (Fig. 3B). Sections treated
with ClearT2for 1 or 2 days were slightly larger than pre-cleared
sections, but these changes were significantly less than with ScaleA2
[1 day, ClearT2=1.30±0.02 versus ScaleA2=1.81±0.05, P<0.01; 2
days, ClearT2=1.30±0.01 versus ScaleA2=1.83±0.06, P<0.01, n=6
(ClearT2), n=4 sections (ScaleA2)] (supplementary material Fig. S1).
ClearT2also maintained DiI and CTB labeling in axons as
successfully as ClearT(supplementary material Fig. S2A,B).
We next examined whether neurons genetically labeled with
fluorescent proteins, such as in Thy1-GFP (M-line) mice (Feng et
Clearing methods for DiI and immunohistochemistry
al., 2000), could be visualized with ClearT2(Fig. 3C). After clearing
thick hippocampal sections with ClearT2, Thy1-GFP+neurons were
visible deeper within the granule cell layer (Fig. 3C, top) and details
of GFP+pyramidal neuron dendrites in the CA1 region were more
distinct than without clearing (Fig. 3C, bottom). To determine
whether ClearT2could be applied to adult or non-neuronal tissue, we
used Tcf/Lef:H2B-GFP mice, in which reporter expression is
detected in neuronal and non-neuronal tissues from early embryonic
to adult stages (Ferrer-Vaquer et al., 2010). H2B-GFP nuclear
labeling in neurons of the cerebral cortex, cells within the granule
cell and molecular layers of the hippocampus, progenitor cells of
the small intestine and satellite cells of skeletal muscle were more
apparent after clearing with ClearT2(supplementary material Fig.
Immunohistochemistry is used to visualize protein expression,
but labeling is usually visible only superficially in thick tissue
sections. To examine whether immunohistochemistry labeling is
compatible with tissue clearing, we immunostained E14.5
Fig. 3. ClearT2clears tissue with
fluorescent proteins or
immunohistochemistry. (A) ClearT
cleared E14.5 actin-GFP embryos, but
reduced GFP fluorescence. Formamide
(50%) maintained fluorescence, but failed
to clear embryos. ClearT2cleared embryos
and maintained fluorescence. (B) P0
sections (800 μm) were transparent after
ClearT2, with no volume change. (C) P11
Thy1-GFP (M-line) hippocampus section
(800 μm), before and after clearing with
ClearT2; 38 images, 20 μm steps (top and
middle). GFP+pyramidal neurons (arrows)
and dendrites (arrowheads) in CA1 region
are markedly more visible after clearing;
52 images, 2.5 μm steps (bottom). GCL,
granule cell layer; ML, molecular layer.
(D) Sections of E14.5 optic chiasm (200
μm), immunolabeled with the radial glial
marker RC2, cleared with ClearT2; 51
images, 3 μm steps; three optical slices
shown. RC2+staining was observed
deeper in cleared compared with pre-
cleared tissue. Blue indicates Hoechst
staining. (E) E11.5 whole embryos,
immunolabeled with neurofilament
antibody (NF) and treated with ClearT2.
NF+axons were much more visible in
cleared embryos (top); magnification of
trigeminal axons reaching epithelial
targets (bottom). (F) Section (300 μm) of
postnatal mouse brain, dLGN
anterogradely labeled with CTB
conjugated to Alexa Fluor 594. A single
neuron was filled with biocytin and
immunostained with streptavidin-Alexa
Fluor 647. Clearing with ClearT2enhanced
resolution and visibility of the dendritic
arbor of the neuron. Merged stack, 55
images, 2 μm steps. CTB label is in red;
biocytin-filled neuron is pseudo-colored
green. Scale bars: 1 mm in A,B,E; 40 μm in
C; 20 μm in D,F.
1368 RESEARCH REPORT
Development 140 (6)
cryosections through the optic chiasm with an antibody to the radial
glia marker RC2 and treated sections with ClearT, ClearT2, ScaleA2
or BABB (supplementary material Fig. S5A,B). ClearTand
ScaleA2 disrupted RC2 immunolabeling, and BABB maintained
fluorescent signal but produced labeling artifacts in bone and cell
nuclei that should not express RC2. As ClearT2successfully
preserved immunolabeling (supplementary material Fig. S5A-E),
we applied it to 200 μm RC2-immunolabeled vibratome sections of
the optic chiasm at E14.5 (Fig. 3D). RC2+glial processes were
visible as deep as ~120 μm in cleared tissue, twice as deep as in pre-
cleared tissue (Fig. 3D). Finally, ClearT2treatment of whole mouse
embryos immunostained with an antibody to neurofilament (NF)
provided a complete view of axon tracts and arbors in the CNS and
PNS in distal appendages (Fig. 3E).
Finally, we examined whether ClearT2is compatible with
multiple fluorescent labels. After applying ClearT2to a thick brain
section with CTB-labeled dLGN, a biocytin-filled relay neuron was
visualized more deeply and at higher resolution than before clearing,
with both labels successfully maintained (Fig. 3F).
ClearTand ClearT2are solvent- and detergent-free
rapid tissue clearing methods
We have developed two clearing methods, ClearTand ClearT2,
which aid analysis of fluorescent labeling in embryonic and mature
neuronal and non-neuronal tissue. ClearT2clears specimens while
effectively maintaining the fluorescent signal of genetically encoded
proteins, immunohistochemistry labeling, and dye tracers such as
DiI and CTB. Whereas ClearT
immunohistochemistry and genetically encoded fluorescence
proteins (supplementary material Table S1), transparency of whole
brains treated with ClearTis better than with ClearT2(Fig. 3A).
Therefore, tissue samples labeled with DiI or CTB alone are best
cleared by ClearT.
ClearTand ClearT2provide several advantages over other
available clearing methods. Clearing time for thick sections, whole
brains or embryos is significantly faster than with ScaleA2 or
BABB. In addition, ClearTand ClearT2produce minimal tissue
volume changes, significantly less than ScaleA2 or BABB. Most
importantly, our methods maintain DiI- and CTB-labeling in axons,
unlike ScaleA2 and BABB (supplementary material Table S1).
ClearTand ClearT2successfully clear postnatal and adult brain and
other tissues. ClearT2provides a final important advantage over
ScaleA2 and BABB, in that it can clear immunolabeled tissue. Thus,
ClearTand ClearT2provide improved clearing of embryonic and
adult neuronal and non-neuronal tissue for viewing fluorescent
labeling of cells and fiber tracts by high-resolution optical imaging.
is incompatible with
We thank members of the Mason lab and Columbia University colleagues,
Wes Grueber for advice and reading the manuscript, Joseph Gogos for Thy1-
GFP (M-line) mice, Ed Laufer for Tcf/Lef:H2B-GFP mice, and Tom Jessell and
Susan Morton for the anti-neurofilament antibody. Thomas E. Krahe in William
Guido’s laboratory produced additional slice preparations of biocytin-filled cells
in the dLGN (not shown).
This work was supported by the National Institues of Health [R01 EY012736
and EY015290 to C.M., T32 EY013933 to A.A.S. and R01 EY012716 to W.G.]
and the Uehara Foundation (T.K.). Deposited in PMC for release after 12
Competing interests statement
The authors declare no competing financial interests.
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