Scanning probe microscopy - Cantilever Array Sensor Group

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Scanning probe microscopy - Cantilever Array Sensor Group
PRIMER
                                    Scanning probe microscopy
                                    Ke Bian 1, Christoph Gerber2, Andreas J. Heinrich                      3,4
                                                                                                              , Daniel J. Müller         5
                                                                                                                                          ,
                                    Simon Scheuring 6,7 and Ying Jiang 1,8,9,10 ✉
                                    Abstract | Scanning probe microscopy (SPM), a key invention in nanoscience, has by now been
                                    extended to a wide spectrum of basic and applied fields. Its application to basic science led to a
                                    paradigm shift in the understanding and perception of matter at its nanoscopic and even atomic
                                    levels. SPM uses a sharp tip to physically raster-scan samples and locally collect information
                                    from the surface. Various signals can be directly detected by SPM in real space with atomic or
                                    nanoscale resolution, which provides insights into the structural, electronic, vibrational, optical,
                                    magnetic, (bio)chemical and mechanical properties. This Primer introduces the key aspects
                                    and general features of SPM and SPM set-up and variations, with particular focus on scanning
                                    tunnelling microscopy and atomic force microscopy. We outline how to conduct SPM experiments,
                                    as well as data analysis of SPM imaging, spectroscopy and manipulation. Recent applications of
                                    SPM to physics, chemistry, materials science and biology are then highlighted, with representative
                                    examples. We outline issues with reproducibility, and standards on open data are discussed.
                                    This Primer also raises awareness of the ongoing challenges and possible ways to overcome
                                    these difficulties, followed by an outlook of future possible directions.

Tunnelling current
                                   Visualizing atoms on a solid surface has been a long-         changed researchers’ perception and understanding
The current created from           standing dream for researchers, and was finally fulfilled     of matter at atomic or molecular levels. It doubtlessly
electrons tunnelling through a     by the invention of scanning tunnelling microscopy            opened up new possibilities and avenues in physics,
finite barrier that is forbidden   (STM) in 1981 by Rohrer, Binnig and Gerber at IBM             chemistry, materials science, biology and medicine,
in the classic regime.
                                   Zürich1. STM uses an atomically sharp biased metal tip        and stimulates increasing numbers of students and
Raster-scanning                    to collect tiny currents from the metal surface, based        researchers around the world.
A rectangular pattern of image     on the quantum mechanical effect termed tunnelling                SPM would not be possible without the piezoelectric
capture and reconstruction.        (Fig. 1a). Owing to the highly localized nature of the        effect, that is, the deformation of materials as the result
                                   tunnelling current, atomically resolved images could be       of applying an electric field. The effect enables scanning
Tip–sample junction
The tunnelling junction
                                   obtained by raster-scanning the tip over the surface while    with picometre precision by simply applying voltages
between the tip and the            using a feedback loop to keep the tunnelling current con-     to piezo elements. The core of the SPM is the scanner,
sample where electrons             stant. Soon after the invention of STM, Binnig et al. were    which allows stably approaching the tip to the surface
tunnel through a finite barrier    able to map the tip–sample interaction by atomic forces       from a macroscopic distance to the nanometre scale. An
in between.
                                   instead of the tunnelling current, which led to the birth     atomically sharp tip is another key component of SPM
Piezoelectric effect               of atomic force microscopy (AFM)2 (Fig. 1b). AFM is able      ultimately determining the lateral resolution. In addi-
The effect showing a finite        to image almost any type of surface, unlike STM that          tion, vibrational isolation and high-gain, low-noise sig-
induced voltage on both sides      requires conducting or semiconducting samples. AFM            nal amplifiers are also critical for achieving a sufficiently
of a material when a specific
                                   and STM take advantage of different feedback signals to       high signal to noise ratio to ensure atomically resolved
pressure is applied on it.
                                   maintain the tip–sample interaction, but the basic prin-      images by SPM.
                                   ciple of operation is similar in both techniques and rem-         This Primer starts by introducing the technical aspects
                                   iniscent of a record player, where a tip senses the surface   of SPM (Experimentation) and the general features of
                                   topography of the sample via physical raster-scanning.        SPM data (Results). The applications of SPM to physics,
                                       A large family of scanning probe microscopy (SPM)         chemistry, materials science and biology are then high-
                                   methods have emerged as variations of STM and AFM,            lighted with some representative examples (Applications).
                                   by integrating nanosensors on the tip or coupling vari-       Afterwards, we discuss issues with reproducibility and
                                   ous electromagnetic waves with the tip–sample junction.       field standards on open data (Reproducibility and data
                                   The measurable physical quantities range from the elec-       deposition). We also point out the limitations of SPM and
✉e-mail: yjiang@pku.edu.cn         tric current, force and capacitance to photons, magnetic/     possible ways to overcome those difficulties (Limitations
https://doi.org/10.1038/           electric field, strain and temperature. The emergence         and optimizations). Finally, some possible future
s43586-021-00033-2                 of SPM in the then-fledgling field of nanotechnology          directions of SPM are envisaged (Outlook).

NATURE REvIEWS | METHoDS PRimERS | Article citation ID:             (2021) 1:36                                                                             1

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 Author addresses                                                                                tunnelling current. Vibrational noise, such as shaking of
                                                                                                 the laboratory floor and/or the vacuum chambers, must
 1
  International Center for Quantum Materials, School of Physics, Peking University,              be reduced. The STM system must be built with a rigid
 Beijing, P. R. China.                                                                           scanner head that minimizes changes to the tip–sample
 2
  Swiss Nanoscience Institute (SNI), Institute of Physics, University of Basel, Basel,           distance, as some external shaking of the scanner head
 Switzerland.
                                                                                                 is unavoidable. Therefore, the equipment should be kept
 3
  Center for Quantum Nanoscience, Institute for Basic Science (IBS), Seoul,
 Republic of Korea.                                                                              on a very quiet laboratory floor, usually the basement
 4
  Department of Physics, Ewha Womans University, Seoul, Republic of Korea.                       of the building. The lowest vibration levels are achieved
 5
  Department of Biosystems Science and Engineering, Eidgenössische Technische                    in custom facilities built using heavy (100 ton) concrete
 Hochschule (ETH) Zürich, Basel, Switzerland.                                                    blocks floating on special air springs, for example, at the
 6
  Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.                       Precision Laboratory of the Max Planck Institute for
 7
  Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.            Solid State Research4. A custom building with a heavy
 8
  Collaborative Innovation Center of Quantum Matter, Beijing, P. R. China.                       concrete floor that is isolated from other buildings
 9
  Interdisciplinary Institute of Light-Element Quantum Materials and Research Center             can also provide low vibration levels. However, even a
 for Light-Element Advanced Materials, Peking University, Beijing, P. R. China.                  well-built general laboratory building can have low lev-
 10
   CAS Center for Excellence in Topological Quantum Computation, University of Chinese
                                                                                                 els of vibration below 10 Hz (the IBM Almaden labora-
 Academy of Sciences, Beijing, P. R. China.
                                                                                                 tory), despite the increased floor-level vibrations above
                                                                                                 10 Hz (Fig. 2c).
                                  Experimentation                                                    Quiet laboratory space must be complemented
                                  In this section, we introduce the basics of STM and AFM        with a rigid STM scanner design with high mechani-
                                  experimental set-ups, including the key components to          cal resonance frequencies (Fig. 2b), which makes the
                                  achieve high spatial resolution, the working principle         microscope resistant against low-frequency shaking.
                                  and a guide to conduct SPM experiments. We also intro-         In practice, the lowest frequencies of the STM scan head
                                  duce some representative SPM variations based on STM           are found at 1–5 kHz; such a scan head is good at reject-
                                  and AFM, which can map out various physical quanti-            ing low-frequency vibrational noise from the building
                                  ties besides current and force. The sensing mechanism,         but it is important to limit higher-frequency mechanical
                                  advantages and applications of those SPM variations are        noise sources, which can be effectively reduced by soft
                                  briefly discussed.                                             springs combined with eddy current damping (Fig. 2a).
                                                                                                 In practice, a properly built scanner head in a low-noise
                                  Scanning tunnelling microscopy                                 laboratory can reduce tip–sample shaking well below
                                  STM has at its heart a very simple idea: a metal needle        1 pm, which limits the fluctuation of the detected tunnel
                                  that is sharpened to a single atom is approached very          current within several per cent.
                                  close to a surface while a biased voltage between the tip          It is seemingly an impossible task to move the STM
                                  and the surface is applied. When the tip–sample distance       tip by atomic-scale dimensions without adding noise,
                                  reaches the atomic-scale range, some electrons will jump       but this has been made possible with the use of piezo-
                                  between the tip and the sample, known as the tunnel-           electric materials such as lead zirconate or lead titanate
                                  ling current. The tunnelling current is sensitive to the       ceramics1. A typical piezoelectric material used in STM
                                  tip–sample distance; it has exponential dependence on          will change its size by about 1 nm when a voltage of 1 V
                                  the tip–sample distance. For example, in a clean vacuum        is applied across its sides1. Hence, stable high-voltage
                                  tunnel junction, the tunnelling current decreases by a         sources can hold the tip stable to better than 1 pm while
                                  factor of ten when the tip–sample distance increases by        allowing a maximum scan range around 1 μm. However,
                                  0.1 nm (the typical tip–sample distance is in the range        as for STM systems under ultra-high vacuum (UHV)
                                  0.3–1 nm). This effect gives STM its atomic-scale lateral      conditions, it is necessary to change samples without
                                  spatial resolution as the majority of the tunnelling current   opening the vacuum chamber. The tip must be moved at
                                  stems from only the last atom of the tip apex3 (Fig. 1a).      least 1 mm away from the sample before the sample can
                                     The STM tip is usually attached to piezoelectric con-       be extracted. Although piezoelectric materials are good
                                  trol elements that allow the tip to be moved with atomic-      at atomic-scale length changes, they cannot provide
                                  scale precision (Fig. 2a,b). In almost all STM systems, the    such large displacements; instead, this task is achieved
                                  tip and the sample should be replaced with new ones            by the coarse approach mechanism with a type of piezo
                                  in a convenient manner without violently changing the          motor, which is the kernel component of the STM scan-
                                  STM configuration. Generally, STMs are very sensitive          ner head (Fig. 2b). The action of such a motor can be
                                  to noise, which includes electronic noise and vibra-           easily visualized: the tip is held on a body — often made
                                  tional noise from the laboratory environment. Here, we         from a ceramic — which is mounted on piezo­electric
Biased voltage                    focus on controlling some of these noise sources, from         materials. When the piezo materials move slowly,
The DC voltage applied to the
                                  large to atomic scale. The scanner head of the micro-          the ceramic body will follow. However, when the piezo
tunnelling junction, either on
the sample or on the tip.         scope, or the STM body, has macroscopic dimensions             materials move rapidly (>100 nm in 10 µs), the body will
                                  typically in the range of a few centimetres. By contrast,      hold still owing to its inertia. Each step gives a motion in
Eddy current                      the tip–sample distance is often smaller than 1 nm.            the range of 100 nm. This process can then be repeated
Loops of electrical current       Ideally, the tip–sample distance is kept stable at approx-     many thousands of times to arrive at a macroscopic
induced within a conductor
by changing the magnetic field
                                  imately 1 pm. As the tunnelling current is sensitive to        motion. Such a stick–slip motion5,6 is reliable in provid-
through this conductor based      the tip–sample distance (and, hence, to fluctuations in        ing coarse motion in the range of a few millimetres, but
on Faraday’s law of induction.    this distance), mechanical shaking causes noise in the         is among the most difficult parts of STM design as it is

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Mechanical resonance
                                    challenging to provide a rigid enough movable motor          Atomic force microscopy
frequency                           with mechanical resonance frequency larger than several      As STM can only probe conductive surfaces relying on
The frequency at which a            kilohertz. The well-known types of motor for the coarse      the tunnelling current, AFM was conceived to extend
mechanical system vibrates          approach include the louse type7, beetle type5, Pan type6    atomic resolution to non-conducting surfaces2. The
with greater amplitude than
it does at other frequencies,
                                    and various single-tube types.                               advantage of AFM is that it can be employed in a vacuum,
generally determined by the             There is no way to sharpen the tip to a single atom,     an ambient atmosphere and a liquid, and from high to
stiffness and mass of this          and so in situ protocols have been developed for this        ultra-low temperatures. AFM shares many basic features
mechanical system.                  task. Most often, we start with either a cut platinum/       and key components with STM, such as the vibrational
                                    iridium wire or with an etched tungsten wire8. A cut wire    isolation, scanning process, coarse-approaching mech-
Quantum corrals
The barriers constructed by
                                    has the advantage of fewer oxide films on its surface,       anism and tip treatments. However, as AFM detects
individually positioning the iron   whereas an etched tip has a much better macroscopic          local force instead of the tunnelling current, there are
adatom through the scanning         shape. The platinum/iridium tip can be produced by           some differences in the signal acquisition and the feed-
tunnelling microscopy tip.          mechanical cutting or electrochemical etching, whereas       back loop (Fig. 1b). In AFM, a tip is mounted at the end
Local force
                                    the tungsten tip can only be made by etching owing to        of a flexible cantilever, which deflects linearly with the
The local interaction between       tungsten’s brittleness. For most STM measurements, the       force applied. Contact mode AFM measures tiny deflec-
the atoms on the tip apex           overall shape of the tip does not matter as the tunnel-      tions of the scanning cantilever and uses a force-feedback
and the surface within a            ling only occurs from the atom or cluster of atoms at the    circuit to move the sample or tip held by a piezoelec-
volume of several cubic
                                    very end of the tip. However, for some applications —        tric element in the z direction (maintaining a constant
nanometres.
                                    most notably optical experiments — the macroscopic           tip–sample distance) to keep the deflection, and thus the
Dynamical AFM                       shape can have a pronounced effect on the plasmonic          applied force, constant. Plotting the z-direction position
A type of atomic force              enhancement of Raman scattering and fluorescence9.           (height) of the scanned surface pixel by pixel provides the
microscopy (AFM) where                  Lower temperatures are desirable for STM because         sample topo­graphy. An important development for AFM
an oscillator (for example,
cantilever, tuning fork) works
                                    of improved stability compared with room tempera-            was the optical lever system18, which reflects a laser beam
at its resonance frequency,         ture, as well as higher energy resolution owing to the       on the backside of the cantilever to efficiently magnify the
detecting interactions between      smaller thermal broadening of the electrons in both          tiny cantilever deflections resulting from the interactions
the tip and the sample              the tip and the sample. Eigler introduced a machine          of the tip and the sample (Fig. 3a), thus largely enhanc-
through the changes of
                                    with a stable design operating at about 5 K reaching         ing the signal to noise ratio during data acquisition. An
frequency, amplitude and
energy compensation of this
                                    a tip–sample distance noise below 1 pm, which was            important development towards enabling biological AFM
oscillator.                         used to build quantum corrals10 and move individual          was the invention of a liquid cell in which the cantilever
                                    atoms11,12. Eventually, lower operating temperatures —       and the sample are immersed in physiological solution19.
                                    down to 10 mK (ref. 13 ) — were achieved; such                   Dynamical AFM uses oscillating cantilevers20. Concomi­
                                    ultra-low-temperature STM is also functional under           tant amplitude modulation modes (for example, ‘inter-
                                    high magnetic fields up to 30 T (ref.14). On the other       mittent contact’, ‘tapping’ or ‘oscillating’ mode) use
                                    extreme, STM has been used to image the growth of            feedback controls to oscillate the cantilever at resonant
                                    materials in situ at temperatures up to several hundred      frequency and constant amplitude21 (Fig. 3b). Other oscil-
                                    degrees Celsius15. STM has also been used to study cata-     lating modes apply frequency (frequency modulation) or
                                    lytic processes under near-ambient pressures16. Whereas      phase (phase modulation) for feedback control (Fig. 3b).
                                    operation of STM in air is often complicated owing to        Such dynamic modes control the tip–sample interaction
                                    the presence of water films on the surfaces of samples,      more gently compared with static AFM modes so that
                                    STM can work in a more stable manner at a solid–liquid       interaction forces are minimized.
                                    interface, where both the potential stability and the            Frequency modulation AFM (FM-AFM) is used
                                    chemical composition inside the aqueous environments         for UHV and low-temperature physics22, as well as for
                                    are well controlled17.                                       biological applications23. FM-AFM is usually more

                                    a                                                           b

                                                     Sharp metal tip                                                                Cantilever
                                                                                       I

                                                                                       V

                                             e–                                                        Force

                                                                          Sample

                                    Fig. 1 | Basic set-up for scanning probe microscopy. Scanning tunnelling microscopy (STM) and atomic force microscopy
                                    (AFM) both use a tip to scan the sample. Both techniques use different feedback signals to maintain constant tip–sample
                                    interaction, but their basic principle of operation and image acquisition mechanisms are similar. a | STM collects the
                                    tunnelling current between the tip apex and the sample when a bias voltage is applied. b | AFM detects local forces and
                                    corresponding mechanical parameters through a spring-like cantilever.

NATURE REvIEWS | METHoDS PRimERS | Article citation ID:                (2021) 1:36                                                                         3

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                                   a                                                                                                                                  Phase     f2 – f1       f2 + f1
                                                                                                                                                             V0(f2,t) shifter ~
                                                                                                                                                                       φ      V
                                                                    Vibration            Constant current
                                                                    isolation     z                                                                        V0(f2,t,φ)                     f
                                                                                                                                                             V(f1,t)
                                                                                         Constant height                                         STS                                                DC output

                                                          Coarse                                                                                                  Multiplier       Low-pass filter
                                                          motor                                 Time

                                                  3D                                                                                              High voltage                                PID
                                                  scanner                             Preamplifier                                                 output
                                                                                         Bias
                                                                                                                                                       x    y    z

                                                                                                                                    Tunnelling
                                                   Raster-scan              Summator

                                                                                                                                    current
                                                Magnet
                                                                                                                                                                                         Controller
                                             Damping                                                                                                                           Data
                                                                                                                                                           Analogue input
                                                                                  Modulator

                                   b                                                                  c                         10–5

                                                                                                                                10–6

                                                                                                  1/3 octave spectral density
                                                                                                      RMS velocity (m s–1)
                                                         Tip         Coarse
                                                                     motor                                                      10–7

                                            Sample
                                                                                                                                10–8

                                                                                                                                10–9

                                                                                                                                10–10
                                                                                                                                        1                                10                          100
                                                                                                                                                                     Frequency (Hz)
                                                                                                                                                                        IBM Almaden                 QNS floor
                                                                                                                                                                        IBM ETH Zurich              QNS block
                                                                                                                                                                        MPI Stuttgart

                                   Fig. 2 | Scanning tunnelling microscopy set-up. a | Scanning tunnelling microscopy (STM) set-up consisting of a coarse
                                   motor, three-dimensional (3D) scanner, vibration isolation device, damping device, preamplifier and controller unit. The
                                   frame shields the external electric noise. The proportional integral differential unit (PID) is used for controlling the tip–sample
                                   distance in constant current operational mode. Inset: schematic showing lock-in for scanning tunnelling spectroscopy
                                   (STS) measurements. The basic electric circuit demonstrates both the process of modulations and its corresponding
                                   demodulations, where V is the modulated signal and V0 is the reference. b | Photograph of STM scan head with tip, sample
                                   on sample holder and slip–stick walker, all mounted on a metal base plate. c | Vibration levels in various STM laboratories
                                   from around the world between 1 and 200 Hz. y axis represents the velocity scaled in a fashion typical for architectural
                                   comparisons. The lowest vibration levels are dependent on floating concrete blocks (IBM ETH Zurich, MPI Stuttgart,
                                   QNS block), high-quality basement levels of laboratory buildings (QNS floor) and regular basement-level laboratory
                                   floors (IBM Almaden). RMS, root mean square. Part c reprinted with permission from ref.4, Royal Society of Chemistry.

                                   precise than amplitude modulation AFM, as the time                                         It is more challenging to obtain high-resolution images
                                   and frequency can be measured with higher accuracy                                      in AFM systems, as forces have multiple long-range and
                                   than amplitude changes. However, force detection by                                     short-range components and the force–distance rela-
                                   amplitude modulation AFM is simpler and faster, and                                     tion between tip and sample can be more complicated
Temporal resolution
                                   the amplitude changes with the tip–sample distance in                                   than the current–distance relation in STM26,27. Presently,
The duration of time for
acquisition or capture of a        a nearly monotonic manner. Time-lapse AFM imaging                                       subatomic details such as orbitals or chemical bonds can
single event in measurements.      can monitor cellular machines at work at the nanoscale                                  be observed by probing short-range forces with chem-
                                   level24. When using a small cantilever with a high res-                                 ically functionalized tips in high vacuum. Meanwhile,
Functionalized tips                onant frequency, time-lapse AFM can work at much                                        researchers developed a plethora of new AFM-based
Modified tips with a single
molecule or specific clusters in
                                   faster speeds, which allows observation of machinery                                    approaches to probe chemical, magnetic and friction
order to make the tip adapted      at a temporal resolution of ~100 ms (ref.25); this set-up is                            forces, and to introduce different spectroscopies such as
for specific applications.         known as high-speed AFM.                                                                force spectroscopy with sub-piconewton sensitivity28,29

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Quality factor
                                or single-molecule and single-cell force spectroscopy in          corresponding image will be measured at constant cur-
The dimensionless factor        biology30–32. Now, we approach the time at which AFM              rent in STM or constant force in AFM. On the other
describing the dissipation      imaging simultaneously quantifies and structurally maps           hand, when the feedback is not used, the tip height is
and damping of the mechanical   the various physical, chemical and biological properties          kept constant, resulting in the constant-height imag-
oscillator during a single
oscillating cycle.
                                of non-living and living objects24,33,34 (Fig. 3c).               ing mode. Under the constant-current/force mode,
                                    Progress in instrumentation has been key to recent            the tip–sample distance is determined by the preset
Thermal drift                   AFM developments. After the quartz tuning fork was                current/force and typically higher resolution is obtained
The steady and monotonic        first used as the force sensors for non-contact AFM35,            at smaller tip–sample distance, simultaneously with
changes of the specific
                                one example of prominent progress is the development              higher risk of tip damage. By contrast, constant-height
location or parameter with
time resulting from the
                                of the qPlus sensor, with one prong fixed to enhance              imaging only works for flat surfaces, and the results are
changed temperature.            the quality factor up to ~100,000 at small amplitude              more straightforward to interpret owing to the absence
                                (
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Young’s modulus
                                     (d2I/dV2), such as inelastic electron tunnelling spectros­        The SPM tip is not only a perfect probe for surface
A mechanical property that           copy (IETS) (Fig. 4A). To obtain dI/dV and d2I/dV2 spec-      characterization but also acts as a nanoscale hand
quantifies the relationship          tra, a small voltage modulation is added to the bias, and     for manipulating single atoms or molecules11,41,42. Precise
between tensile stress and           the first-order and second-order components of I–V            manipulation is usually achieved through voltage pulses
axial strain, which reflects
the tensile stiffness of a
                                     curves are extracted by lock-in amplifiers (Fig. 2a). In      or forces when the tip is positioned directly above the
solid material.                      AFM-based force spectroscopy, the tip is approached           target sites. During such a process, the injected electrons
                                     and withdrawn from a sample surface while record-             can excite the vibrational modes of atoms or molecules
                                     ing a force–distance curve (Fig. 4B). The force–distance      and lead to diffusion, desorption and selective bond
                                     curves allow analysis of repulsive and adhesive interac-      breaking or formation42–44. For vertical manipulation,
                                     tions between the tip and the sample, as well as sample       an adsorbed molecule is picked up by an STM tip by
                                     deformation and elasticity40 (Box 1). AFM can combine         injecting electrons into the surface, transferred above a
                                     imaging with force spectroscopy to simultaneously             target site and then released from the tip by applying
                                     map mechanical, chemical and biological properties.           a reversed bias voltage, leading to the formation of a new
                                     Therefore, the AFM record for each pixel of the result-       complex42 (Fig. 4C). For the lateral manipulation, the tip
                                     ing AFM topography represents a force–distance curve,         is brought close to the atom or molecule on the sur-
                                     from which multiple parameters such as Young’s modulus        face, such that the tip–sample interaction force is large
                                     and energy dissipation, pressures and tension can be          enough to pull or push the atom or molecule moving
                                     extracted (Fig. 3c).                                          over the diffusion barrier41,45 (Fig. 4D).

A                                                     B                                                                          Ca                  [110]
                                                          F
                                                                                                                                                             [001]
                                                                                                                                               Tip
                               Elastic tunnelling                                                                                         e–
                                                                                                                                      O
                                   hω                                                                                                                   Fe
                  eV                                                                                                                C
                               Inelastic tunnelling                                                                                Ag

                                                                                                                         z       Cb

      Tip                        Sample

                     I
                                         Elastic
                                          Inelastic                   Pauli repulsion                    Attractive              Cc
     –E0                            E0       V                        Short-range chemical force         Repulsive
                                                                      Long-range electrostatic/          Total interaction
                                                                      van der Waals interaction

              dI/dV
                                                                                                                                                      e–
                                                      D
     –E0                            E0   V
                                                          Tip path
                                                                                                                                 Cd

            d2I/dV2                                                               Force
                                                          Substrate
     –E0
                                    E0     V

Fig. 4 | Schematics of scanning probe spectroscopy and manipulations.              the attractive force and repulsive force versus tip distance, respectively.
A | Schematic revealing inelastic tunnelling (red) and elastic tunnelling          C | Schematic showing formation of a single bond through scanning
(blue). Vibrational excitation indicated by wavy lines, which leads to an          tunnelling microscopy. A single molecule can be detached (part a),
increase in conductance. Graphs show an I–V curve and corresponding                translated (part b) and attached onto another adatom through precise
dI/dV and d2I/dV2 spectra where extra tunnelling conductance caused                manipulation of the scanning tunnelling microscopy (STM) tip (parts c,d).
by inelastic tunnelling appears at ±E0. Dashed lines reflect the elastic and       D | Schematic showing the process of laterally pulling an adatom
inelastic tunnelling channels, whereas solid lines show the actual data.           through the STM tip. Jump height (green arrow), lateral distance between
B | Schematic showing typical force–distance curves. Both short-range              the tip apex and the manipulated adatom (red arrow), and tip height
(green region, Pauli repulsion; blue region, short-range chemical force)           (blue arrow) during manipulation are indicated. Part C adapted with
and long-range (orange region, long-range electrostatic or van der Waals           permission from ref. 42, AAAS. Part D adapted with permission from
interaction) components are indicated. Black and grey curves represent             ref.41, APS.

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                                 Tip preparation and functionalization                          Box 1 | Single-molecule force spectroscopy
                                 Atomically sharp tips are the key to achieving high res-
                                 olution in SPM. They are usually produced by mechan-           The uniqueness of directly probing physical interactions
                                 ical cutting or milling, electrochemical etching or more       between the atomic force microscopy (AFM) tip and
                                 complicated nanofabrication such as focused ion beam           the biological sample has been exploited to develop single-
                                                                                                molecule force spectroscopy. This technique measures
                                 systems46. However, the tip apex obtained by those meth-
                                                                                                the bonds of single receptor–ligand pairs. In the early
                                 ods is not sharp enough for atomically resolved imaging.       days of single-molecule force spectroscopy, the AFM
                                 To obtain an ideal tip terminated with a single atom or a      tip (or a bead glued to the tip) was functionalized with
                                 small cluster of atoms, the tip needs to be treated (which     ligands and the surface of the support, such as a bead
                                 includes both sharpening and functionalization) during         on top of the substrate, with receptors30,288. If the tip
                                 scanning by poking the tip into the surface and grasping       and sample are brought into sufficient proximity, the
                                 a small cluster of atoms. In STM experiments, the appli-       ligand and receptor can bind. The AFM tip is then
                                 cation of high voltages up to 10 V can be used for tip         withdrawn, and the force required to separate the
                                 treatment, at a tip–sample distance of ~1 nm to induce         specific bond is measured. This unbinding force describes
                                 field emission47. The atoms at the very end of the tip         the mechanical strength of the receptor–ligand bond.
                                                                                                Typically, such experiments are repeated several
                                 determine the spatial resolution of SPM, not the overall
                                                                                                thousand times to characterize a sufficient number
                                 radius of curvature at the apex. In order to obtain high       of successful binding and unbinding events. The use of
                                 chemical resolution besides topography, one can also           short cantilevers in high-speed AFM set-ups extends
                                 evaporate noble metal films such as gold and silver onto       the accessible dynamic range in force spectroscopy
                                 the conventional silicon AFM tip; this type of tip has         experiments to measure molecular dynamics
                                 been extensively used for nanoscale chemical analysis          simulations319, whereas low-noise AFMs reach force
                                 under ambient conditions48,49.                                 sensitivity comparable with that of optical tweezers320.
                                     For SPM experiments performed in UHV and low-
                                 temperature conditions, the most controllable and pre-        chemical and biological interactions40. One approach to
                                 cise way to get a well-defined sharp tip is functionalizing   study these interactions is to functionalize the AFM tip.
                                 the tip apex by picking up a single atom or molecule
                                 on the surface50,51. Under such conditions, SPM with          Variations of SPM
                                 a CO-functionalized tip can image molecular orbitals52,       By integrating microsensors on the tip or coupling the
                                 owing to the p-wave orbitals of the CO molecule. The          electromagnetic waves with different wavelengths into
                                 CO tip also allows access to the short-range Pauli            the tip–sample junctions, a large family of SPM methods
                                 repulsions, reflecting the variations of electron density     have been developed since the invention of STM and
                                 in individual chemical bonds53. As the CO tip has a           AFM. In this section, we introduce some representative
                                 quadrupole-like charge distribution, it is also sensitive     variations of SPM, which can map out various physical
                                 to the high-order electrostatic force54. One drawback         quantities besides current and force, such as magnetic/
                                 of the CO tip is the lateral relaxation of the CO mole-       electric field, photons, strain, temperature, and dielectric
                                 cule at the tip apex, which leads to distortion or even       and physiological responses. The sensing mechanism,
                                 artefacts in the SPM images. Functionalizing the tip at       advantages and applications of those SPM variations are
                                 the atomic level, for example replacing the C–O group         briefly discussed in the following sections.
                                 with oxygen55 and chlorine56, yields a more rigid tip with
                                 smaller relaxation of the tip apex. However, the reso­        Time-resolved STM. Despite achieving high spatial reso-
                                 lution of those tips is usually poorer than for the CO tip,   lution in real space, one of the most interesting questions
                                 as strong relaxation of the CO molecule is also crucial       about SPM is the speed at which such a device could
                                 to obtain sharply resolved structural resolution when         capture a signal in real time. High-speed image acqui-
                                 the tip–sample distance is within the region of Pauli         sition could be achieved by video-rate STM15,61, which
                                 repulsion57.                                                  typically scans a frame within a millisecond timescale.
                                     For biological AFM imaging applications, tips             Recently, with the pulsed voltages, fast spin dynamics
                                 are typically made of silicon or silicon nitride, which       such as spin relaxation was investigated by electrical
                                 upon exposure to air and immersion into physiologi-           pump-probe STM at the level of a single atom62. As the
                                 cal buffer will feature an oxide layer at their surface58.    bandwidth of the preamplifier and other electronics of
                                 To achieve sharper tips with higher aspect ratio, elec-       SPM is limited to megahertz, ultra-fast dynamics within
                                 tron beam deposition can be used, resulting in the            picoseconds and femtoseconds should be captured by
                                 growth of an amorphous carbon-based apex, which is            incorporating pump-probe techniques into STM, lead-
                                 subsequently rendered hydrophilic using plasma clean-         ing to femtosecond laser STM63,64 and terahertz STM65,66.
                                 ing59. Carbon nanotubes have been grafted as a quasi          Examples of various time-resolved STM techniques can
                                 one-dimensional (1D) object at the end of AFM tips to         be found in Table 1.
                                 create a super-sharp, very high aspect ratio apex, but
                                 despite efforts these tips have so far had no significant     Magnetic field-sensitive SPM. Magnetic field or spin-
                                 impact in the AFM field, likely because of nanotube           sensitive SPM is very useful for characterizing local mag-
CO-functionalized tip            buckling60. Overall for biological imaging applications       netic structures and spin states in real space (Table 2).
Modification of the tip with a
single CO molecule in order to
                                 in liquid, the tip–sample interaction forces range from       The simplest method for detecting the local magnetic
enhance the spatial resolution   short range (≈1–10 nm) to long range (>10 nm) and             field is by replacing the conventional non-magnetic
of scanning probe microscopy.    can be composed of a repertoire of different physical,        probe with a magnetic probe, which is extensively used

NATURE REvIEWS | METHoDS PRimERS | Article citation ID:           (2021) 1:36                                                                                 7

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                                  Table 1 | Time-resolved scanning probe microscopy techniques
                                  Name                  Detected signal      Utility              Resolution           Disadvantages and            Refs
                                                                                                                       limitations
                                  Video-rate          Tunnelling current Fast dynamics            Atomic resolution Spatial resolution is poor        15,61

                                  scanning tunnelling                    during chemical          and millisecond   owing to short integration
                                  microscopy                             reactions, surface       temporal          time; temporal resolution
                                                                         reconstruction           resolution        is limited by the resonance
                                                                         and material                               frequency of the scanner
                                                                         growth at elevated                         and the bandwidth of the
                                                                         temperatures                               electronics
                                  Electrical pump-    Tunnelling current Fast electron spin       Atomic resolution Time resolution is limited          62

                                  probe scanning                         dynamics                 and nanosecond by the bandwidth of
                                  tunnelling                                                      temporal          advanced electronics such
                                  microscopy                                                      resolution        as the preamplifier and
                                                                                                                    pulse generators
                                  Femtosecond laser Photo-induced        Ultra-fast charge,       Atomic resolution Laser-induced thermal             63,64

                                  scanning tunnelling tunnelling current spin and phonon          and femtosecond expansion of the tip can
                                  microscopy                             dynamics at the          temporal          lead to artificial signals
                                                                         atomic scale             resolution
                                  Terahertz scanning Photo-induced       Ultra-fast charge,       Atomic resolution Introduction of                   65,66

                                  tunnelling          tunnelling current spin and phonon          and femtosecond terahertz light into
                                  microscopy                             dynamics at the          temporal          the ultra-high vacuum
                                                                         atomic scale             resolution        and low-temperature
                                                                                                                    scanning tunnelling
                                                                                                                    microscopy system is
                                                                                                                    complicated; the temporal
                                                                                                                    resolution is limited by the
                                                                                                                    wavelength and width of
                                                                                                                    the terahertz pulse

                                 in magnetic force microscopy67,68, magnetic exchange           for use in aqueous environments. The self-assembly and
                                 force microscopy 69 and spin-polarized STM 70,71 .             reactivity of supramolecular systems inside non-ionic
                                 Another avenue is grafting a micro-magnetic sensor             organic liquids has been investigated by liquid-phase
                                 such as a superconducting quantum interference device          STM85–87. Meanwhile, working at the solid–electrolyte
                                 (SQUID) or Hall probe on the tip, constructing scan-           interfaces, electrochemical STM (EC-STM) is developed
                                 ning SQUID microscopy72,73 and scanning Hall probe             with four electrodes including the tip, working elec-
                                 microscopy74. In addition, by incorporating microwaves         trode, counter electrode and reference electrode, which
                                 into SPM to excite magnetic resonance, the magnetic            are controlled by a bipotentiostat17,88. As EC-STM only
                                 sensitivity of SPM can be enhanced up to single electron       works on conductive surfaces, liquid-phase non-contact
                                 or nuclear spin, such as electron spin resonance (ESR)         AFM was developed for imaging the local structures on
                                 STM75–77, magnetic resonant force microscopy78 and             insulator–liquid interfaces89,90. In order to characterize
                                 nitrogen vacancy-based SPM79.                                  complex biological systems such as living cells in phys-
                                                                                                iological buffers with high spatial resolution, scanning
                                 Electric field-sensitive SPM. To map out the surface           ion conductance microscopy should be chosen91. In this
                                 potential or charge with high resolution, typically a          system, the ion current flow from the tip to the refer-
                                 conductive SPM tip biased with variable voltage is             ence electrodes in the solution is monitored and used for
                                 used (Table 3). One form of electric field-sensitive SPM       feedback to control the tip–surface distance. Compared
                                 is scanning capacitance microscopy80, where the local          with EC-STM and liquid-phase AFM mentioned above,
                                 capacitive coupling between the tip and the sample is          scanning ion conductance microscopy provides the
                                 detected for deriving the local dielectric and electrical      unique possibility of locally probing the ion transport
                                 properties. Another option for sensing local potential         of biological systems by monitoring the ion current92.
                                 is the integration of a microelectric sensor such as a         Similarly, AFM can scan a hollow microcantilever to
                                 single-electron transistor onto the tip81. For single charge   perform scanning ion conductance microscopy mea­
Hall probe
A micron-sized device for
                                 detection, the tip should be brought as close as possible      surements, which is also called fluid force microscopy,
detecting the external           to the sample, which requires a sharp metal tip instead        to patch clamp or to manipulate living cells93,94. Examples
magnetic field through           of a microelectric sensor, such as in Kelvin probe force       of liquid-phase SPM can be found in Table 4.
the Hall effect.                 microscopy82. Piezoresponse force microscopy (PFM)
                                 is another important electric-field sensitive SPM83,84,        Electrical transport-compatible SPM. In order to make
Bipotentiostat
An electronic system             in which a modulated pressure is applied locally on            SPM suitable for investigating local electron transport
capable of controlling two       the sample by the tip and its piezoelectric response is        properties both on the surface and the interface of sam-
potentiostats, which include     monitored during scanning.                                     ples such as 2D material-based novel electronic devices,
two working electrodes, one                                                                     various electrodes should be fabricated on the surface
shared reference electrode
and one shared counter
                                 Liquid-phase SPM. Although surface characterization            in addition to the bias electrode, acting as source, drain
electrode for electrochemical    with atomic resolution is ever-present in UHV and              and electric gates. Immediately after the appearance of
measurements.                    low-temperature experiments, it remains challenging            STM, scanning tunnelling potentiometry was invented

8 | Article citation ID:    (2021) 1:36                                                                                             www.nature.com/nrmp

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                             Table 2 | Magnetic field-sensitive scanning probe microscopy techniques
                             Name                  Detected signal         Utility                Resolution         Disadvantages and         Refs
                                                                                                  and                limitations
                                                                                                  sensitivity
                             Spin-polarized        Spin-polarized          Nanoscale              Atomic             High-energy resolution     70,71

                             scanning tunnelling   tunnelling current      spin texture           resolution         only works on
                             microscopy                                    or long-range          with sensitivity   conductive samples
                                                                           spin ordering of       of single          under low temperature
                                                                           magnetic materials     electron spin      and ultra-high vacuum
                             Electron spin         Spin-polarized          Spin identification,   Atomic             The spin-polarized        75–77

                             resonance             tunnelling current      electron spin          resolution         tip is not only a probe
                             scanning tunnelling                           resonance spectra/     with sensitivity   but has an effect on
                             microscopy                                    imaging and            of single          the coherence of the
                                                                           quantum sensing        electron spin      target spin
                             Magnetic force        Dipolar magnetic        Magnetic structures    Spatial            The magnetic tip           67,68

                             microscopy            interaction             of sample surfaces     resolution of      will disturb the
                                                                                                  several tens       magnetic state of
                                                                                                  of nanometres      the sample, and vice
                                                                                                                     versa, complicating
                                                                                                                     quantitative
                                                                                                                     interpretation
                                                                                                                     of the magnetic
                                                                                                                     force microscopy
                                                                                                                     measurement; atomic
                                                                                                                     resolution cannot be
                                                                                                                     achieved owing to the
                                                                                                                     long-range magnetic
                                                                                                                     forces between tip
                                                                                                                     and sample
                             Scanning              Magnetic flux and       Scanning               Spatial            Only works under low       72,73

                             superconducting       superconducting         magnetometry and       resolution of      temperature; spatial
                             quantum               current                 thermometry at low     several tens       resolution is limited
                             interference device                           temperature            of nanometres      by the size of the
                             microscopy                                                           and magnetic       superconducting loop
                                                                                                  sensitivity
                                                                                                  up to single
                                                                                                  electron spin
                             Nitrogen vacancy      Fluorescence of the     Scanning               Spatial            The quantum sensor           79

                             centre scanning       nitrogen vacancy        magnetometry of        resolution of      is buried underneath
                             probe microscopy      centre                  nanoscale magnetic     ~10 nm and         the diamond surface,
                                                                           textures at various    magnetic           which makes atomic
                                                                           temperatures;          sensitivity        resolution challenging;
                                                                           compatible             up to single       the shallower nitrogen
                                                                           with an ambient        nuclear spin       vacancy has poorer
                                                                           environment and                           quantum coherence,
                                                                           biological systems                        which decreases the
                                                                                                                     signal to noise ratio
                                                                                                                     and sensitivity
                             Magnetic resonance    Magnetic dipolar        Nanoscale electron     Resolution         Only works under             78

                             force microscopy      interaction             and nuclear
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                                   Table 3 | Electric field-sensitive scanning probe microscopy techniques
                                   Name               Detected signal        Utility                    Resolution and       Disadvantages and          Refs
                                                                                                        sensitivity          limitations
                                   Scanning           Tunnelling current     Local electric field and   Spatial resolution   Only works under low           81

                                   single-electron                           potential caused by        of several tens of   temperature; spatial
                                   transistor                                the local charges,         nanometres and       resolution is limited by
                                   microscopy                                especially the local       electric field       the size of the device
                                                                             electronic states of       sensitivity up to
                                                                             strongly correlated        2 μV Hz–1/2
                                                                             materials
                                   Scanning           Capacitance            Dielectric and             Spatial resolution   Spatial resolution             80

                                   capacitance                               electrical properties      of several           is limited by the
                                   microscopy                                of semiconductors          nanometres with      long-range capacitance
                                                                             and buried                 capacitance          coupling
                                                                             two-dimensional            sensitivity of
                                                                             electron gas               attofarad
                                   Kelvin probe     Contact potential        Local work function        Nanoscale spatial    Unsuitable for                 82

                                   force microscopy difference               and electric dipole        resolution with      characterization of
                                                                             distribution of various    sensitivity up to    voltage-sensitive
                                                                             samples                    a single charge      samples; spatial
                                                                                                                             resolution is limited
                                                                                                                             by the long-range
                                                                                                                             electrostatic force
                                   Piezoresponse    Piezoelectric            Ferroelectric ordering, Spatial resolution Tip wear can modify the           83,84

                                   force microscopy response of the          piezo coefficient and   with several       tip–surface interaction,
                                                    sample                   energy dissipation      nanometres         affecting imaging
                                                                                                                        contrast; the acquired
                                                                                                                        force signals may not
                                                                                                                        always arise from
                                                                                                                        piezo/ferro electricity
                                                                                                                        phenomena

                                  for investigating the local distribution of potential and      tip-enhanced Raman spectroscopy (TERS)9,48. Recently,
                                  inhomogeneous conductivity of metals and semiconduc-           TERS has demonstrated its ability in identifying and
                                  tors95. Without the need for detecting the tunnelling cur-     resolving chemical structures of single molecules with
                                  rent, scanning gate microscopy uses a conductive tip as the    sub-nanometre resolution9. Benefiting from the local
                                  movable electric gate and is capable of revealing the local    plasmon confined within the tunnelling junction, scan-
                                  gating effects on the transport currents from the source       ning tunnelling microscope-induced luminescence was
                                  and drain96,97. As the electrodes for transport measure-       also developed and applied for detecting the optical
                                  ments are usually fixed by nanofabrication, much more          emission from the electronic and vibrational transition
                                  precise and flexible positioning of such electrodes was        at the single-molecule level103. Apart from working within
                                  realized by multi-probe STM98,99 (Table 5).                    the range of visible light, it is also attractive for investi-
                                                                                                 gating the dielectric response of materials in the mega-
                                  Near-field SPM. To optically probe the structural, dielec-     hertz to gigahertz regime, such as microwave impedance
                                  tric and chemical properties with visible sub-wavelength       microscopy, where a sharp metallic tip extended from
                                  resolution, scanning near-field optical microscopy             a high-frequency resonator was used as the antenna to
                                  (SNOM) was developed and has been widely used in the           emit and collect microwave photons104,105. In contrast
                                  past decades100 (Table 6). SNOM makes use of the eva-          to conventional near-field SPM, photo-induced force
                                  nescent components of the light highly confined near the       microscopy106 directly detects the near-field signal
                                  surface, thus overcoming the diffraction limit of far-field    based on photo-induced dipolar forces, which efficiently
                                  optics. Generally, a sharpened optical fibre with a metal      suppress the overwhelming background signals.
                                  shield and a nanoscale aperture is used as the light
                                  source or detector for scanning. However, the spatial          Results
                                  resolution is limited by the aperture size of the optical      SPM images are always acquired as a 2D matrix, whereas
                                  fibre, with a typical value of 30–50 nm. By contrast, aper-    spectroscopic curves are saved in the form of arrays.
                                  tureless SNOM such as scattering-type SNOM101 uses a           The main steps for data analysis include image inspec-
                                  metallic AFM tip as the near-field scatterer and works         tion, noise analysis, filtering and image reconstruction.
Scanning gate microscopy          in a dynamical mode for suppressing the background             For the curves of SPM spectra and the line profiles of
A kind of scanning probe          far-field signals, which improves the spatial resolution       topographic images, a fitting procedure is usually nec-
microscopy capable of             up to 1 nm (ref.102). Furthermore, making use of a sharp       essary for interpretation of the underlying quantities
probing electrical transport      noble tip and highly confined surface plasmon101, the          and parameters. In this section, we showcase several
at the nanoscale, where a
conductive tip is used as the
                                  efficiency of Raman scattering in the tip–sample gap           representative examples to discuss how to analyse SPM
local gate capacitively coupled   is enhanced several orders of magnitude as compared            images and spectra. The popular software for processing
to the sample.                    with conventional far-field Raman experiments, such as         the SPM data are briefly introduced.

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                            Representative results                                            biomolecules, the interaction force is detected and used
                            SPM imaging provides pseudo-3D data. As a surface                 to describe the deformations of the sample33 (Fig. 5c).
                            probing technique, it does not deliver information about          On the other hand, upon withdrawing the tip, the force–
                            the inside volume of the object under investigation but           distance curve can be used to infer multi-mechanical
                            provides an x–y grid of data points to each of which a sin-       parameters such as adhesion, Young’s modulus, plas-
                            gle z height is associated. SPM data are thus most often          tic deformation and energy dissipation of the sample
                            represented as an x–y 2D image, where a false-colour              through fittings.
                            scale represents the z height107 (Fig. 5a). Sometimes, SPM            STS is suitable for investigating the local density
                            data are represented as a 3D surface shown in perspec-            of states of a sample. In Fig. 5d, a typical dI/dV curve
                            tive (Fig. 5b) that is visually attractive but scientifically     acquired on a single pentacene molecule shows prom-
                            less precise because at least one of the in-plane axes is         inent peaks at both the positive and negative biases,
                            skewed, the z height sometimes increased and some                 which are attributed to the highest and lowest molecular
                            structural features obstructed by the perspective view.           orbitals (HOMO and LUMO, respectively)37. By fixing
                            In the SPM field, unfortunately, no stringent standards           the bias at the LUMO or HOMO and spatially mapping
                            have been established regarding the representation of             out the dI/dV intensity, the frontier orbitals of the sin-
                            SPM data in publications, and sometimes filters are               gle pentacene molecule can be directly visualized in real
                            used to display images. Specifically, the application of          space37 (Fig. 5f). Whereas the STM mode is only sensitive
                            short-range median filters in the y dimension, which              to the electronic states near the Fermi level, non-contact
                            cancel lines from the fast scan axis (x dimension) of the         AFM working under the frequency modulation mode
                            image acquisition, is common.                                     is able to probe the total electron density of the sample
                               Force–distance curves are acquired by recording                by entering into the region of short-range Pauli repul-
                            the deflection signal of the AFM cantilever while con-            sion108. In Fig. 5g, a CO-functionalized tip clearly resolves
                            trolling the tip–sample distance. For example, when               the chemical skeleton of the single pentacene molecule,
                            the tip approaches the surface and interacts with the             where the short-range Pauli repulsion dominates the

                             Table 4 | Liquid-phase scanning probe microscopy techniques
                             Name               Detected signal         Utility                    Resolution            Disadvantages and          Refs
                                                                                                                         limitations
                             Scanning ion       Ion current             Non-invasive imaging       Spatial resolution    Spatial resolution is        91,92

                             conductance                                of the tomography          with several tens     limited by the size of
                             microscopy                                 and investigation          of nanometres         the microchannel
                                                                        of the physiological
                                                                        properties of complex
                                                                        biological systems
                                                                        such as living cells
                                                                        in solutions
                             Fluidic force      Deflection of           Single-cell                Sub-micrometre        Spatial resolution is        93,94

                             microscope         the cantilever          manipulation and                                 limited by the size of
                                                                        controlled delivery                              the microchannel
                                                                        of bioactive agents
                             Liquid-phase       Tunnelling current      Investigation of        Atomic resolution        Tip condition is not         85–87

                             scanning                                   supramolecular                                   well controllable
                             tunnelling                                 systems and their                                compared with
                             microscope                                 self-assembly,                                   scanning tunnelling
                                                                        dynamics and reactivity                          microscopy in an
                                                                                                                         ultra-high vacuum;
                                                                                                                         only a conductive
                                                                                                                         surface could be
                                                                                                                         investigated
                             Electrochemical Tunnelling current         In situ detection          Atomic resolution     Tip condition is not         17,88

                             scanning                                   of various                                       easily controllable
                             tunnelling                                 electrochemical                                  for electrochemical
                             microscopy                                 processes, such                                  reactions; Faraday
                                                                        as formation of an                               currents interfere with
                                                                        electrochemical                                  the tunnelling current
                                                                        double layer, metal
                                                                        corrosion and
                                                                        electrodeposition
                             Liquid-phase       Frequency shift         In situ detection of       Atomic resolution     Three-dimensional            89,90

                             non-contact                                the structure of the                             force mapping for
                             atomic force                               hydration layer and                              structural analyses on
                             microscopy                                 electrochemical                                  solid–liquid interfaces
                                                                        double layer on a solid–                         is time consuming; only
                                                                        liquid interface with                            local liquid density can
                                                                        atomic resolution                                be probed

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                                 Table 5 | Transport-compatible scanning probe microscopy techniques
                                 Name             Detected signal       Utility                 Resolution           Disadvantages and               Refs
                                                                                                                     limitations
                                 Scanning      Tunnelling current       Imaging of the          Atomic resolution    Interpretation of the              95

                                 tunnelling                             spatial distribution    in principle         signal is difficult because
                                 potentiometry                          of electrostatic                             distinguishing tomography
                                                                        potential                                    from potentiometry is
                                                                                                                     challenging
                                 Scanning gate Conductance              Spatial mapping of      Spatial resolution   As the capacitive coupling       96,97

                                 microscopy    between source           electron flows in       of several tens of   between tip and sample
                                               and drain                two-dimensional         nanometres           is long range, the spatial
                                               electrodes               materials and                                resolution is largely limited
                                                                        semiconducting                               by the sharpness of the tip
                                                                        materials                                    apex and the tip–sample
                                                                                                                     distance
                                 Four-probe       Tunnelling current    Local and in situ       Atomic resolution    Closest distance (10–20 nm)      98,99

                                 scanning                               investigation of        in principle         between the probes is limited
                                 tunnelling                             in-plane electronic                          by the curvature radius of
                                 microscopy                             transport properties                         the tip apex; performance is
                                                                                                                     generally poorer than that
                                                                                                                     of conventional scanning
                                                                                                                     tunnelling microscopy
                                                                                                                     owing to the complex
                                                                                                                     scanner design

                                tip–molecular interaction108. The sharp lines arise from            Here, we take the application of AFM in biology as
                                the electron density build-up across the covalent bonds         an example. When AFM is used for cellular imaging,
                                between the carbon atoms.                                       either proprietary software is used for analysis or images
                                    In some cases, inelastic electron tunnelling signals        are exported in various file formats such as .tiff, .raw,
                                may be superimposed on the large background of elas-            .png, .sxm and .gwy to be analysed by laboratory-written
                                tic tunnelling conductance during STS measurements.             routines in the software packages mentioned above or in
                                For example, the dI/dV curve taken on the bilayer               MATLAB112. Analysis of data from the above-described
                                NaCl(001) film grown on Au(111) demonstrates a broad            hybrid imaging/nanomechanical mapping modes113 is
                                peak (grey), which corresponds to the interfacial elec-         often done in proprietary application mode software;
                                tronic states109 (Fig. 5e). When the tip is positioned on the   in this case, not only the data encoding but also the
                                water molecule adsorbed on the surface, distinct kinks          acquisition process is system-dependent. When AFM
                                appear in addition to the interfacial electronic states         is used for molecular imaging and analysis of protein
                                (red). Such kinks are more clearly resolved as dips and         structures and conformations, AFM users often borrow
                                peaks in d2I/dV2 spectra, which are point-symmetrical           methods from electron microscopy. The recent progress
                                with respect to the zero bias. The energy positions of          in electron microscopy to solve protein structures114 is
                                those features reflect the energies of different vibrational    directly associated with image analysis developments.
                                modes of the single water molecule.                             To this end, there is a plethora of such programs for
                                                                                                analysis of macromolecular structures, such as EMAN115,
                                Visualization and analysis software                             IMAGIC 116, SPIDER 117 and RELION118. Given that
                                The major problem of image visualization and image              the contrast transfer function and the noise distribu-
                                analysis originates from the fact that, so far, no com-         tion of AFM are very different from those of electron
                                mon SPM file format has been established. Each SPM              microscopy, these programs must be adapted with care.
                                company has a specific proprietary file format and              SEMPER and MRC are most powerful to analyse 2D
                                microscope-associated software for image data analysis.         crystalline data58, and most other programs are adapted
                                Among others, Gwyddion110, WSxM111 and ImageJ are               to analyse single particles119.
                                free and open source software. They are likely the most
                                powerful SPM data visualization and analysis platforms,         Analysis of biological data
                                as they provide a large number of data processing func-         When using AFM for the analysis of images of pro-
                                tions. These include standard statistical characterization,     teins, one particle is used for a cross-correlation
                                data correction, filtering and grain marking functions.         search of all other molecules in the image. Next, cross-
                                Gwyddion and WSxM are compatible with most stand-               correlation-based lateral and rotational alignment of
                                ard file formats (such as .dat, .txt and .sxm) acquired         the particles is performed. Particle selection based on
                                from commercial SPM programs such as Nanonis,                   cross-correlation values can be performed to calculate
                                Omicron and RHK. ImageJ has the advantage that it is            an average of the most common particle structure120.
                                widely used by the optical fluorescence microscopy com-         During the averaging process, a standard deviation
                                munity and, thus, features a large variety of functions         map can be calculated that highlights the most flexi-
                                that can be adapted for SPM data, and its capabilities are      ble parts in the molecule121. From the stack of particle
                                rapidly growing through contributions of analysis tools         images that one has extracted using cross-correlation
                                from a large scientific community.                              searches, one can statistically assess any parameter of

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                            interest characterizing the molecule, such as the height      representations accompanied with statistical data, as is
                            and volume distribution of the particles122, or molecular     done in the electron microscopy field.
                            symmetry123. For example, the complete perforin 2 rings
                            shown in Fig. 5a can be distinguished from incomplete         Applications
                            arcs using cross-correlation-based selection and later-       SPM has found a multitude of applications in the natural
                            ally and rotationally aligned to calculate an ensemble        sciences. In the following, we divide those applications
                            average (Fig. 5a, insets). For the analysis of filamentous    into physics, chemistry, materials science and biology,
                            structures, such as DNA or filamentous proteins, auto-        although they are often closely linked to each other and
                            mated particle detection based on the height above the        have strong overlap.
                            background, followed by tracing of the filaments, allows
                            direct extraction of the physical properties of the fila-     Examples from physics
                            ment, such as its persistence length124. Unfortunately,       Surface science. The initial application for STM was in
                            structural analysis using automated programs is not           the field of surface science, where atomic-scale arrange-
                            utilized enough in the AFM field, and it is still rather      ment as well as the electronic properties of materials
                            common to place arrows on image panels to high-               needed investigation. The key initial experimental
                            light features instead of calculating relevant molecular      evidence for the power of STM in this regard was the

                             Table 6 | Near-field scanning probe microscopy
                             Name                    Detected signal       Utility                  Resolution and       Disadvantages and      Refs
                                                                                                    sensitivity          limitations
                             Scanning near-field     Emission of           Local fluorescence       Spatial resolution   Spatial resolution        100

                             optical microscopy      fluorescence or       imaging of biological    with tens of         is largely limited
                                                     adsorption of         molecules and            nanometres           by the size of the
                                                     excitation lights     photoluminescent                              nanofibres used as
                                                                           spectroscopy of                               probes; near-field
                                                                           semiconductors                                signal is weak and
                                                                                                                         easily disturbed by
                                                                                                                         metallic coatings
                             Scattering-type         Elastic scattering    Local dielectric         Spatial resolution   Requires cantilevers   101,102

                             scanning near-field     of lights             response from optical    up to 1 nm and       to work under
                             optical microscopy                            light and plasmonic      monolayer            large amplitude to
                                                                           structures               sensitivity          eliminate far-field
                                                                                                                         background,
                                                                                                                         making the method
                                                                                                                         insensitive to
                                                                                                                         short-range tip–
                                                                                                                         sample interactions
                             Tip-enhanced            Raman scattering Analysis and                  Single-molecule      High spatial              9,48

                                                     of lights        identification of             sensitivity and      resolution relies on
                             Raman scattering
                                                                      the local chemical            sub-nanometre        the electromagnetic
                                                                      structure of                  spatial resolution   coupling between
                                                                      small molecules,                                   the tip and a
                                                                      biomolecules,                                      plasmonic substrate,
                                                                      living cells and                                   thus limiting the
                                                                      two-dimensional                                    systems that can
                                                                      materials                                          be studied
                             Scanning tunnelling     Photon emission Photon yield images            Single-molecule      High spatial              103

                             microscope-induced      from sample      and energy-resolved           sensitivity and      resolution relies on
                             luminescence                             spectroscopic images          sub-nanometre        the electromagnetic
                                                                                                    spatial resolution   coupling between
                                                                                                                         the tip and a
                                                                                                                         plasmonic substrate,
                                                                                                                         thus limiting the
                                                                                                                         systems that can
                                                                                                                         be studied
                             Microwave impedance Reflection or             Local dielectric         Spatial resolution   Spatial resolution     104,105

                             microscopy          transmission              properties and           of several tens of   is limited by the
                                                 parameters of             conductivities;          nanometres           long wavelength of
                                                 microwaves                suitable for obtaining                        microwave photons
                                                                           information from a
                                                                           buried interface
                             Photo-induced force     Photo-induced         Detection of both        Spatial resolution   Quantitative              106

                             microscopy              dipolar               topography and           of sub-10 nm         interpretation of
                                                     interactions          chemical signature on    and monolayer        the imaging contrast
                                                                           organic and inorganic    sensitivity          is difficult; only
                                                                           samples                                       works with the
                                                                                                                         narrow band of
                                                                                                                         infrared lights

NATURE REvIEWS | METHoDS PRimERS | Article citation ID:      (2021) 1:36                                                                             13

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