High Resolution Helium Ion Scanning Microscopy of the
William L. Rice1, Alfred N. Van Hoek1, Teodor G. Pa ˘unescu1, Chuong Huynh2, Bernhard Goetze2,
Bipin Singh2, Larry Scipioni2, Lewis A. Stern2, Dennis Brown1*
1Center for Systems Biology, Program in Membrane Biology and Division of Nephrology, Department of Medicine, Massachusetts General Hospital and Harvard Medical
School, Boston, Massachusetts, United States of America, 2Carl Zeiss Microscopy, Peabody, Massachusetts, United States of America
Helium ion scanning microscopy is a novel imaging technology with the potential to provide sub-nanometer resolution
images of uncoated biological tissues. So far, however, it has been used mainly in materials science applications. Here, we
took advantage of helium ion microscopy to explore the epithelium of the rat kidney with unsurpassed image quality and
detail. In addition, we evaluated different tissue preparation methods for their ability to preserve tissue architecture. We
found that high contrast, high resolution imaging of the renal tubule surface is possible with a relatively simple processing
procedure that consists of transcardial perfusion with aldehyde fixatives, vibratome tissue sectioning, tissue dehydration
with graded methanol solutions and careful critical point drying. Coupled with the helium ion system, fine details such as
membrane texture and membranous nanoprojections on the glomerular podocytes were visualized, and pores within the
filtration slit diaphragm could be seen in much greater detail than in previous scanning EM studies. In the collecting duct,
the extensive and striking apical microplicae of the intercalated cells were imaged without the shrunken or distorted
appearance that is typical with conventional sample processing and scanning electron microscopy. Membrane depressions
visible on principal cells suggest possible endo- or exocytotic events, and central cilia on these cells were imaged with
remarkable preservation and clarity. We also demonstrate the use of colloidal gold probes for highlighting specific cell-
surface proteins and find that 15 nm gold labels are practical and easily distinguishable, indicating that external labels of
various sizes can be used to detect multiple targets in the same tissue. We conclude that this technology represents a
technical breakthrough in imaging the topographical ultrastructure of animal tissues. Its use in future studies should allow
the study of fine cellular details and provide significant advances in our understanding of cell surface structures and
Citation: Rice WL, Van Hoek AN, Pa ˘unescu TG, Huynh C, Goetze B, et al. (2013) High Resolution Helium Ion Scanning Microscopy of the Rat Kidney. PLoS ONE 8(3):
Editor: Jeff M. Sands, Emory University, United States of America
Received August 7, 2012; Accepted January 17, 2013; Published March 7, 2013
Copyright: ? 2013 Rice et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Funding was in part from an NIH grant to D. Brown to examine the role of renal intercalated cell cells in kidney function (DK42956). Additional funding
was provided by a sponsored research agreement to Dr. Brown from the Zeiss Corporation. The funders had no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript.
Competing Interests: The authors have read the journal’s policy and have the following conflicts. The work was performed partially with a sponsored research
agreement between the Massachusetts General Hospital and the Zeiss Corporation. Four of the authors are employed by the Zeiss Corporation in the Helium Ion
Microscopy Facility in Peabody, MA. The corresponding author D. Brown is the PI of the sponsored research agreement from the Zeiss Corporation. This does not
alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.
* E-mail: firstname.lastname@example.org
Helium ion microscopy (HIM) is an imaging technology that
uses a scanning beam of He+ions to produce high quality images
with the potential for sub-nanometer resolution. Such high
resolution is made possible by the high brightness of the beam
using a very small probe size, and the relatively short de Broglie
wavelength of He+, enabling the beam to be focused to dimensions
between 0.75 and ,0.25 nm [1,2]. As the He+beam scans across
the sample surface, liberated secondary electrons are collected,
forming images of the sample surface topography. The classic
choices for imaging biological samples have been: low voltage field
emission scanning electron microscopy (LVFESEM), that can
produce topographic images of samples with nanometer scale
resolution, transmission electron microscopy (TEM) providing
potential sub-nanometer resolution of thin tissue cross-sections,
and atomic force microscopy (AFM) with sub-nanometer topo-
graphic resolution in all three dimensions, but with a limited depth
of field. HIM offers a series of advantages compared to these
imaging modalities: nanometer and sub-nanometer image resolu-
tions, detailed surface topography and a high depth of field, all in
uncoated samples so that surface details are not masked or
obscured (for an in depth review of HIM image formation see ).
In addition, while sample charging severely affects image quality in
SEM imaging of uncoated biological samples, He+ions are not
deflected to the same degree as an electron beam, and the active
charge neutralization of the Carl Zeiss Orion plus HIM mitigates
these effects and preserves image quality.
Recently, studies have applied HIM to the evaluation of
uncoated biological samples such as articular cartilage , colon
cancer cells , platelet aggregation , and single cell surface
topography , indicating that HIM has the potential to produce
images of animal tissue that surpass what is currently achievable
with electron microscopy. In this study we use HIM to explore the
tubule epithelium of the rat kidney, with special attention to the
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impact of sample processing on sample integrity and image
quality. In an attempt to minimize sample perturbation and
maximize the preservation of the tissue architecture, we applied
transcardial perfusion of aldehyde fixatives, and graded methanol
dehydration prior to careful critical point drying (CPD), and we
compare the preservation of overall and fine structural details of
the tissues. We also explored the use of lectin gold and secondary
antibody-gold conjugates as specific labels for highlighting specific
components of the tubule surface membrane.
Materials and Methods
Animal experiments were approved by the Massachusetts
General Hospital Subcommittee on Research Animal Care, in
accordance with the National Institutes of Health, Department of
Agriculture, and AAALAC requirements. 12 to 48 week old male
Sprague Dawley rats were anesthetized with pentobarbital sodium
(50 mg/kg body wt i.p, Nembutal, Abbott Laboratories, Abbott
Park, IL) and perfused through the heart with phosphate-buffered
saline (PBS, 0.9% NaCl in 10 mM phosphate buffer, pH 7.4)
followed by paraformaldehyde (4%) lysine (75 mM) periodate
(10 mM) fixative in 0.15 M sucrose, 37.5 mM sodium phosphate
(modified PLP) as previously described , with a measured
osmolarity of 935 mOsm/kg, or by 2 or 4% glutaraldehyde (GA)
in 0.1 M sodium cacodylate (pH 7.4). The flow rate of perfusion
was 20 ml/min and was performed for about 5–7 min with PBS
and subsequently for about 5 min with the fixative. Tissues were
post fixed overnight in modified PLP or GA at 4uC, washed in
PBS, and stored at 4uC in PBS containing 0.02% NaN3.
After fixation and removal from the animal, 500 mm thick tissue
sections were cut under PBS using a TPI PELCO 101 series 1000
vibratome (Technical Products International, Inc., St. Louis, MO).
The 500 mm thickness was chosen for ease of handling and to
maintain the slice integrity during further processing steps. Slices
were then returned to PBS containing 0.02% sodium azide at 4uC.
To label the surface glycocalyx of the kidney tissue, Triticum
vulgare (WGA, EY Laboratories, San Mateo, CA) lectin (or
agglutinin) conjugated to either 40 or 15 nm colloidal gold
particles was diluted 1:50 in PBS and incubated with the tissue
overnight at 4uC, then washed three times in PBS. To label
megalin on the PT cell membrane, the kidney tissue was incubated
overnight at 4uC with a mouse monoclonal anti-megalin (1H2)
primary antibody [8,9] diluted 1:100 in PBS, washed three times
in PBS and then incubated with a 40 nm colloidal gold conjugated
goat anti mouse IgG secondary antibody (EY Laboratories). After
labeling, samples were washed thoroughly in PBS and post fixed
for 2 h in 2% GA in 0.1 M sodium cacodylate (pH 7.4), and then
washed again in PBS prior to methanol replacement and critical
Kidney slices were placed into metal baskets and incubated with
a mixture of 25% MeOH and 75% aqueous 0.1M (NH4)2CO3for
2 hours at 2uC, while the temperature was lowered to 0uC using
the Leica AFS freeze-substitution apparatus (Leica Microsystems
Inc., Buffalo Grove, IL). The methanol-aqueous buffer was
replaced twice with a fresh batch of 25/75 mixture, while the
temperature was lowered to 210uC over a period of 4 h. A 40/60
methanol/aqueous buffer was employed two times over a period
of 4 hrs, while the temperature was lowered to 220uC. It was
followed by four 60/40 MeOH/aqueous mixture incubations over
a period of 8 h while lowering the temperature to 240uC. We
then used 80% MeOH in pure water for incubation (8 h) to drop
the temperature to 260uC, followed by 100% MeOH (8 h,
280uC) and 100% MeOH (8 hrs, 290uC), replacing the MeOH
at each step. Alternatively, a rapid series of graded methanol
solutions in PBS was applied over a 4 h period at 4uC with the
following schedule and MeOH dilutions: 25% for 60 min, 40% for
45 min, 60% for 45 min, 80% for 45 min, 100% for 45 min. For
each gradation, the MeOH solution was refreshed halfway
through the incubation.
Critical point drying
Following the final MeOH replacement, the temperature of the
samples in pure MeOH was raised to 0uC (at a rate of 3uC/min),
the baskets were closed and placed into an Erlenmeyer flask
containing ice-cold MeOH for transportation. Once MeOH and
baskets were placed and secured in the critical point drying
apparatus (Samdri-795, Tousimis Research Corp., Rockville,
MD), the samples were purged with cold liquid CO2(2uC) at
elevated pressure, and then brought to supercritical pressure and
temperature (1200 psi, 42uC) for incubation and equilibration
(.4 min). The pressure was slowly reduced (,100 psi/min), while
maintaining supercritical temperatures (.32uC), and after the
bleeding process was completed, dried samples were mounted onto
placeholders with sticky pads and stored under desiccant at room
temperature. Storage under these conditions for more than one
week did not result in obvious sample modifications.
Helium ion microscopy
Helium ion microscopy (HIM) was carried out on an Orion
helium ion microscope (Carl Zeiss Microscopy, Peabody, MA) at
35 keV beam energy, with a probe current ranging from 0.1 to
1.5 pA. No conductive coatings were applied to the samples prior
to imaging, in order to preserve the sample surface information.
Samples were transferred into the HIM via a load-lock system and
were maintained at a vacuum of 2–361027torr during the
imaging session. Charge control was maintained through the use
of a low energy electron flood gun, which was applied in a
temporally interlaced fashion with the imaging beam. Images were
formed by collecting the secondary electrons elicited by the
interaction between the helium ion beam and the sample with an
Everhart-Thornley Microchannel plate . This detector is also
widely used in SEM, and consists of a scintillator placed inside a
Faraday cage, that draws the elicited low voltage secondary
electrons towards it. The resulting photons are collected, turned
into electrons and amplified by a photomultiplier tube (PMT). The
PMT signal is then digitized using an A/D converter and
displayed as a grey value in a given pixel of the resulting image.
The scanning of the helium ion beam and the formation of the
image are synchronized so that for any given coordinate there is a
corresponding signal or grey value in the resulting image. No post-
processing procedures were applied to the digital images besides
brightness and contrast adjustment . The image signal was
acquired in a line-averaging mode, with either 32 or 64 lines being
integrated into each line in the final image. Charge neutralization
was applied after each individual line pass of the beam.
Scanning electron microscopy
Conventional scanning electron microscopy (SEM) was per-
formed for comparison purposes. Wherever indicated, sputter
coating was carried out at the Harvard University Center for
Nanoscale Systems (Cambridge, MA) using a Cressington HR208
Helium Ion Scanning Microscopy of the Kidney
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sputter coater (Cressington Scientific Instruments, Watford,
England) and a Pt at 40 mA. The SEM was performed with a
Merlin field emission scanning electron microscope (Carl Zeiss
Microscopy) using either an SE2 or an in-lens detector.
Measurement of cellular and cell membrane features
Images were imported into ImageJ software version 1.42q
(NIH, Bethesda, MD), and the scale was set based on the scale bar
in the annotated image file. To measure features in the image, the
line bar was used, and measurements were expressed in
micrometers. To measure pore size the line tool was used to
determine the diameter of the pore at its largest axis.
The mean feature size and standard deviation from the sample
mean were calculated in Excel version 12.3.4 (Microsoft Corp.,
Results and Discussion
preparation is an important determinant of image quality .
Consequently, in the present study we compared the sample
quality associated with various tissue fixation methods, previously
reported to produce good results for electron microscopy studies,
such as in situ fixation of kidney tissue by transcardial perfusion
with either glutaraldehyde (GA) or modified paraformaldehyde
lysine periodate (PLP). Formaldehyde-based PLP penetrates the
tissue quickly, initiating the stabilization of tissue (defined as the
initial protein-formaldehyde cross link), but cross-linking of
proteins (formation of a methylene bridge between two proteins)
is a slow process. In contrast, GA penetrates the tissue more slowly,
but the chemical reaction to cross-link proteins is faster than for
PLP . Transcardial perfusion with either 4% GA or modified
PLP, containing 4% paraformaldehyde, was used to preserve renal
tubules such as proximal convoluted tubules (PT) and collecting
ducts (CD) in a physiological, open conformation, which allows
better visualization of the tubule lumen and apical surfaces of the
Critical point drying (CPD).
tissue water is replaced by a suitable solvent that can be mixed
with liquid carbon dioxide. However, little is known about the
effects of methanol, acetone, or ethanol replacement on fixed
tissue. Initially we systematically employed a lengthy series of
graded methanol solutions while lowering the temperature to
values above the freezing points of the methanol series to minimize
sample–solvent interactions. Given the success of this procedure
we found that a similar level of post CPD tissue quality was also
achievable with a more rapid procedure using a graded methanol
series at 4uC over approximately 4 h, indicating that a careful
CPD protocol was important for tissue preservation. In this study,
the kidney was sectioned into 500 mm thick sections to ensure ease
of handling. The length of time needed for methanol to penetrate
and replace the tissue water will vary with the tissue thickness, and
methanol replacement is recommended for all samples. Indeed,
even in thin samples consisting of only a few cells, a simple freeze
drying procedure without methanol pre-treatment leads to poor
tissue preservation . The freeze-substitution/CPD technique
was, therefore, used for the images shown here, unless otherwise
For all high resolution imaging techniques, sample
CPD of tissues requires that
Even at relatively low magnification, the high quality and depth
of field of the HIM images is striking. Fig. 1A shows a whole
glomerulus and neighboring tubules in the renal cortex. The
branching processes of the podocytes surrounding the glomerular
capillaries can be imaged at a resolution allowing the identification
of fine features, such as the podocyte processes that envelop the
capillaries. Fig. 1B shows the interior of a Bowman’s capsule from
which the glomerular capillaries (seen in Fig. 1A) were removed
during the cutting process used to prepare the tissue. Long, single
cilia project from each of the flat parietal epithelial cells that form
At a higher magnification (Fig. 1C) the complex interdigitations
of the podocyte foot processes can be better appreciated. While
these features have been described by conventional scanning EM
in many studies [13,14], the clarity of the HIM images and the
specimen preparation method also allow clear visualization of
numerous filamentous nano-protrusions originating from the
major and minor processes and projecting into the urinary space
(Fig. 1D). The width of these protrusions averaged 49.866.6 nm
(mean 6 SD, n=26). At higher magnification, many of these
protrusions had a bulbous end that was wider than the rest of the
structure (Fig. 2A). However, in contrast to their paucity on
podocytes from ‘‘normal’’ animals, longer filamentous projections
have been described emerging from rodent podocytes that were
subjected to injurious treatments such as puromycin  or cofilin
depletion coupled with protamine sulfate exposure . The role
of these structures is unknown.
When imaged at an appropriate angle, membrane surface
features in the form of 20–30 nm depressions were detectable on
the podocyte plasma membrane. While these structures are
reminiscent (in size and shape) of intramembrane particles,
representing integral membrane proteins, that are visualized
within the lipid bilayer by freeze-fracture electron microscopy
, their nature is currently unknown. In well-oriented fields of
view, a ladder-like structure was visible at the interface between
adjacent foot processes, corresponding to the location of the
podocyte filtration barrier (Fig. 2B). Throughout the glomerulus
we measured pore widths with a mean of 22.068.0 nm (n=12). A
closer inspection of some filtration slits that possibly were damaged
during tissue processing or perfusion provides a view of what may
be the basal lamina below the podocytes (Fig. 2B). Recently
Gagliardini and coworkers  described similar ‘‘slit diaphragm’’
structures by scanning EM of metal-coated samples using an ‘‘in-
lens’’ detector to increase the sensitivity of the procedure.
However, the HIM images offer the possibility of visualizing these
structures at higher magnification than was previously achievable.
Indeed the podocyte filtration slit is visible with remarkable clarity
compared to that seen by Gagliardini et al. in their studies
performed using LVFESEM . The range in pore size
dimensions measured in the current study are in good agreement
with those described by Gagliardini et al., but the mean pore size
we find in this study is 22 nm whereas they reported an average of
12 nm. This discrepancy may be due to the supraphysiologic
perfusion fixation flow rate of 20 ml/min used in our study,
leading to high arterial pressures compared to the flow rate used
by Gagliardini et al., which was matched to the measured arterial
pressure prior to fixation. However, we repeated the HIM study
using kidneys that were fixed by immersion only and the results
were essentially similar to our perfusion fixed tissues (data not
shown). Another possible source for this discrepancy could be the
difference in the dehydration method used in the two studies,
given that Gagliardini et al. employs either dehydration in alcohols
followed by CPD or dehydration in hexamethyldisilazane
(HDMS) for their samples . The different pore diameters
measured in these studies could also possibly indicate that the
filtration slit pores are dynamic, but more studies will be needed to
examine this possibility.
Helium Ion Scanning Microscopy of the Kidney
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Figure 1. HIM imaging of kidney cortex. (A) Image of renal cortex (GA-fixed, dehydrated using the extended methanol freeze-substitution
protocol) showing the glomerulus, formed of capillary loops covered with specialized epithelial cells called podocytes. Several cut open tubules
surrounding the glomerulus are visible. Bar=20 mm. (B) Kidney cortex (same fixation and dehydration procedures) showing the interior of Bowman’s
capsule from which the glomerular capillaries were removed during the tissue preparation process. Each parietal epithelial cell displays a single, long
central cilium (arrows) that is very well preserved and visualized without heavy metal coating. Bar=10 mm. (C) Intermediate magnification of the
surface of a glomerular capillary loop (modified PLP-fixation, extended methanol freeze-substitution dehydration protocol) showing complex
interdigitations of podocytes and their foot processes. Bar=2 mm. The podocyte processes are decorated by fine, thread-like protrusions that are
shown at higher magnification in panel D (arrows). Bar=0.5 mm.
Figure 2. High magnification imaging of glomerular structures. (A) Detail of a glomerular podocyte showing a secondary projection and
interdigitating foot processes (GA-fixation, extended methanol freeze-substitution dehydration protocol). Many tubular projections with more
bulbous ends (white arrows) emerge from the podocyte membrane. Small (20–30 nm) irregularities of unknown nature can be seen on the external
surface of the podocyte membrane (black arrows). Bar=120 nm. (B) Detail of four ‘‘filtration’’ regions (slit diaphragms) between five adjacent
podocyte foot processes. Numerous cross-bridging filaments extend at regular intervals across the space between adjacent foot processes (smaller
arrows). In some regions, these delicate structures appear damaged, revealing another structure below, which may represent the glomerular
basement membrane (larger arrows). Bar=100 nm.
Helium Ion Scanning Microscopy of the Kidney
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In order to establish that the quality of these high magnification
images is due to the HIM technology and not to the tissue
processing method we employed, we also imaged these tissues by
conventional scanning electron microscopy (SEM) (Fig. 3). Fine
structural details of the slit diaphragm are less well defined when
imaged by SEM, both without (Fig. 3A) and with sputter coating,
whether using the standard SE2 detector (Fig. 3B) or an in-lens
detector (Fig. 3C).
Beneath the podocytes and the basal lamina lie the endothelial
cells of the glomerular capillary. Random cuts frequently expose
the glomerular endothelium and this allows visualization of the cell
surface (Fig. 4). The dominant feature of these endothelial cells are
the numerous fenestrae with a diameter of 74.0614.8 nm (mean
6 SD, n=35). Fig. 4B shows a radial patterning visible in the
center of some fenestrae, which is similar to what has been
described for the endothelial diaphragm (arrows) using a rapid-
freeze, deep etching procedure for other fenestrated endothelial
cells , although such structures were reported to be absent
from the glomerular endothelium. Raised ridges corresponding to
the location of the junction between adjacent endothelial cells can
also be seen (Fig. 4A).
Reabsorption of the ultrafiltrate begins with the proximal tubule
(PT), which is characterized by a well-developed brush border that
increases considerably the apical surface area of the tubule. This
brush border often appears bright at low magnification in HIM
(Fig. 5A), making the PT easily identifiable. The prominent brush
border of the PT was evident with all fixation methods. Complex
interdigitations of the lateral cellular membranes of proximal
tubule cells were readily visualized (Fig. 5B). Figs. 5C, D show the
long, slender structure of the brush border microvilli. These
Figure 3. Glomerular podocyte slit diaphragms from the same
kidney as shown by HIM in Fig. 2, imaged by conventional
scanning electron microscopy (SEM). (A) Sample imaged without
sputter coating, using an in-lens detector. (B, C) Coated samples imaged
using either the standard SE2 detector (B) or an in-lens detector (C).
Structural details of the slit diaphragm are less well defined than in the
HIM image shown in Fig. 2B. Bar=100 nm.
Figure 4. HIM imaging of glomerular endothelial cells. (A) Two
adjacent endothelial cells from a glomerular capillary (GA-fixed,
dehydrated using the extended methanol freeze-substitution protocol),
imaged from the luminal side. The most striking features of these cells
are the numerous, round fenestrations that are present over the entire
cell surface. The raised ridges (arrows) represent the location of the
tight junction between the two cells. Bar=175 nm. (B) Higher
magnification showing details of the fenestrations. In some of them,
a substructure consisting of faint spokes like a bicycle wheel can be
seen (arrows). Bar=80 nm.
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microvilli appear to be quite uniform in size, with a length of
2.7360.13 mm (n=10) and a diameter of 48.566.4 nm (n=28).
The microvilli can be imaged at very high magnification, where
their surface appears pitted rather than uniformly smooth
(Fig. 5D). As determined for the slit diaphragm (Fig. 3), the clarity
and detail of the brush border images is superior by HIM imaging
than by conventional SEM (Fig. 5E, F).
The collecting duct (CD) is the main site for vasopressin-
regulated water reabsorption in the kidney, and distal acid/base
regulation, processes mediated by the principal and intercalated
cells respectively . HIM imaging reveals the surface architec-
ture of the CD cells in great detail (Fig. 6A). Previous scanning EM
studies have shown that the principal cells (PC) are clearly
distinguishable from the intercalated cells (IC) based on structural
features [13,21]. The surface area of the PC is smoother than that
of the IC and is populated by short, stubby microvilli (Figs. 6A, B),
and all PC have a prominent solitary cilium measuring
2.9060.32 mm (n=13) in length, with a diameter of approxi-
mately 100 nm. In Fig. 6B and the inset, a closer inspection of PC
cilia reveals ring-like structures at their base, possibly representing
the ciliary necklace that has been described by freeze-fracture
electron microscopy . Details of the CD cell membrane
Figure 5. Imaging of renal proximal convoluted tubule. (A) Lower magnification showing GA-fixed proximal tubule (dehydrated using the
extended methanol freeze-substitution protocol) and its extensive brush border (BB). Bar=5 mm. (B) shows a lateral section of modified PLP-fixed
proximal tubule dehydrated as in (A), demonstrating the apical brush border (BB) and the extensive basolateral plasma membrane infoldings and
invaginations (arrows) that are characteristic of the S1 segment of the proximal tubule. Bar=1 mm. (C) shows the tightly packed, slender brush border
microvilli in greater detail (GA fixation, extended methanol freeze-substitution dehydration protocol). Bar=0.5 mm. (D) Brush border microvilli at high
magnification showing that their surface membrane has numerous micropits of unknown significance (arrows). Bar=100 nm. Similar regions from
the same kidney were also imaged by conventional SEM after coating using the in-lens detector and are shown at lower (E, bar=0.5 mm) and higher
magnification (F, bar=100 nm). The conventional images have considerable less clarity and surface detail than the HIM-imaged brush border region.
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structural features are more clearly defined by HIM than when
SEM is used (Fig. 6C). Indentations in the apical plasma
membrane of the PC may represent various configurations of
endo- or exocytotic events (see also arrows in Fig. 7C) that are
common in this membrane domain. Clathrin mediated endocy-
totic events frequently occur at the base of the microvilli
[23,24,25], consistent with the membrane depressions highlighted
in Fig. 7C.
In contrast to PC, the collecting duct IC can be identified based
on their extensive apical microplicae and by the absence of cilia.
IC can be activated by various agents via metabolic pathways,
involving enzymes such as protein kinases A and C [7,26]. When
activated, IC not only significantly increase their rates of proton
secretion into the CD lumen, but also undergo morphological
modifications, corresponding to a noticeable elongation and
increase in number of their apical microvilli or microplicae
[7,26,27,28,29]. In Fig. 6A, an IC appears activated based on the
number and length of its apical microplicae, which are shown in
progressively greater detail in Figs. 7A, B, and in comparison with
some other IC (data not shown) that typically exhibit fewer and
shorter microplicae. The extensive infoldings and microplicae of
the IC apical surface form very characteristic, channel-like
passages adjacent to the membrane folds that could represent a
microdomain of specific ionic composition and pH, and which
plays a role in the specialized proton-secreting function of these
cells. This unusual membrane configuration is quite different from
the usual type of membrane amplification seen in other cells,
including proximal tubule brush borders and principal cell
External gold labeling
Besides imaging uncoated samples at high resolution, we were
able to use colloidal gold probes to label tissue samples without a
separate detector and with no additional enhancement. Immuno-
gold labeling has previously been applied using conventional
scanning microscopy but optimal visualization requires the use of
secondary electron imaging (SEI) and EDS (energy dispersive X-
ray microanalyzer) . Combining the SEI mode with backscat-
tered electron imaging (BEI) can also provide a correlation
between gold labeling and surface topography [31,32], but with
considerably less surface detail that is possible with HIM. The SEI
mode alone can also be used if gold particles are revealed by silver
enhancement, but this requires subsequent post-acquisition image
analysis to provide images of acceptable quality . Because we
can easily visualize and determine the size of the gold labels
morphologically using HIM, it will now be possible to detect the
association of multiple antigens with cellular structures in the same
sample. As an example of gold labeling, we chose the previously-
described proximal tubule marker gp330/megalin  and
Triticum vulgare (wheat germ) agglutinin (WGA), which labels
PT cell membranes in addition to other cell types in the kidney
[35,36]. The membrane of PT cells, including the apical
microvilli, can be labeled with WGA conjugated to 26 nm
colloidal gold (commercially available as 40 nm gold-conjugated
lectin, but having an actual measured size of 26 nm, as determined
through HIM) (Figs. 8A, B) or with a megalin primary antibody
and a 15 nm gold conjugated secondary antibody (Fig. 8B, inset).
The gold particles are easily distinguishable as bright spheres at
higher magnification, indicating the suitability of HIM for
uncovering the spatial distribution of antigens on the membrane
surface. Indeed, while the WGA-gold probe labels the entire
length of the microvillar surface, the megalin-gold label is more
concentrated towards the base of the microvilli, as previously
described using conventional, thin section immunostaining
[9,34,37]. The lack of megalin-associated gold labeling in the
Figure 6. Imaging of renal collecting duct. (A) Luminal surface of an outer medullary collecting duct (GA-fixation, dehydration using the rapid
graded methanol procedure) showing principal and intercalated cells. Each principal cell (PC) has one long, solitary cilium (arrows) and numerous
short, stubby microvilli. The intercalated cell (IC) has numerous elaborate apical microplicae and no cilium. Bar=2 mm. (B) High magnification view of
a principal cell cilium (Bar=200 nm). At its base, a concentric pattern of surface protrusions (arrows) can be seen in the position of the ciliary
necklace. A similar structure is shown on another principal cell cilium in the inset (arrows, Bar=100 nm). A principal cell cilium from the same kidney
was also imaged by conventional SEM without sputter coating, using an in-lens detector (C). Structural details of the cilium, ciliary necklace, microvilli,
and membrane indentations are more clearly distinguishable in the HIM than in the SEM images. Bar=300 nm.
Helium Ion Scanning Microscopy of the Kidney
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Figure 7. Detail from Fig. 6A showing the principal cell (PC) and an intercalated cell (IC) at higher magnification. The apical membrane
of the intercalated cell has a highly complex organization that is formed of many microplicae and membrane furrows between these structures.
Bar=1 mm. (B) Higher magnification image of the elaborate intercalated cell apical membrane microplicae showing the deep infoldings of this
membrane domain. Bar=200 nm. (C) Apical membrane of a principal cell showing surface features that may represent exocytotic or endocytotic
events. These depressions were frequently seen at the base of the short microvilli - a location in which clathrin mediated endocytosis often occurs.
Figure 8. HIM imaging of external gold labeling in the kidney. (A) Lower magnification of a modified PLP-fixed proximal tubule with its brush
border after labeling of surface glycoproteins (and/or glycolipids) with gold-conjugated WGA. The tissue was dehydrated using the rapid graded
methanol procedure. The gold particles appear as discrete, white globular entities associated with the external surface of brush border microvilli and
other parts of the cell surface adjacent to the microvilli. Bar=1 mm. The gold label can be seen more easily at higher magnification (B - arrows), where
it extends along the entire length of the microvilli. Bar=200 nm. The inset in panel B shows a modified PLP-fixed proximal tubule brush border that
has been immunolabeled with a monoclonal anti-megalin antibody followed by a secondary, gold-conjugated anti-mouse antibody. In this case, the
pale gold particles (arrows) are concentrated towards the base of the microvilli and do not extend along their entire length (inset; Bar=200 nm). (C)
The apical surface of a collecting duct principal cell from the same kidney immunolabeled with the anti-megalin antibody and the respective gold-
conjugated secondary antibody. The image shows no gold particles, attesting to the specificity of the proximal tubule megalin binding. Bar=500 nm.
Helium Ion Scanning Microscopy of the Kidney
PLOS ONE | www.plosone.org8 March 2013 | Volume 8 | Issue 3 | e57051
collecting duct cells further attests to the specificity of the Download full-text
immunostaining (Fig. 8C).
The relatively pale appearance of the gold particles (distinct
from their dark, electron dense appearance in transmission EM)
does make it somewhat difficult to examine tissues rapidly at low
magnification. A probe yielding a greater degree of contrast with
respect to the surrounding tissue would, therefore, be preferable.
He ion–sample interactions can produce sample fluorescence
through the cathodoluminescence effect [2,6]. Since quantum dots
are approximately 11 nm in size, this would make them an
interesting possibility for dual fluorescence/size HIM contrast
labels. These and other alternative probes for immunolabeling
specimens will be tested in future studies.
Typically, high resolution, topographical imaging of biological
specimens with SEM often requires low voltage high-resolution
field-emission SEM  to achieve sub 5 nm resolution in coated
samples. Imaging of uncoated samples, while ideal for preserving
the fidelity of the tissue architecture, presents challenges for SEM
due to sample charging artifacts that are easily mitigated in HIM.
Here, we have presented images from uncoated biological
specimens with resolutions in the 2–5 nm range without compli-
cated tissue preparation. The highest resolution images were taken
at a digital resolution of 0.48 nm per pixel, resulting in a
theoretical resolution of 1.4 nm.
We are grateful to Ann Tisdale of the Schepens Eye Research Institute,
Boston, for providing access to their critical point drying apparatus.
Conceived and designed the experiments: WLR AVH TGP BG DB.
Performed the experiments: WLR AVH TGP CH LS BG DB. Analyzed
the data: WLR AVH TGP DG CH LS BG DB. Contributed reagents/
materials/analysis tools: WLR AVH TGP CH BG BS LS LAS DB. Wrote
the paper: WLR AVH TGP DB.
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