yields high enough for multiple prototyping purposes, but other ion species
may offer advantages in terms of increased spatial resolution or sputter
yield, and reduced damage or chemical reactivity. Section IV.1 provides an
overview on the rich variety of subtractive fib milling applications.

##### Defect engineering:

FIB irradiation of materials at doses significantly lower than those used for
milling has been implemented in a range of applications to locally tune
material properties through the introduction of defects (vacancies and
implanted ions). For example, by varying the dose, different concentrations of
vacancy defects can be introduced into a crystalline material, thus modulating
properties such as electrical, magnetic and thermal behavior in the patterned
regions. In the case of ion implantation, this can be directed at SII, or can
be used to modify the chemical and structural properties of surfaces for
resistless patterning. An overview of defect engineering applications is given
in Section IV.2.

##### Imaging and tomography:

Just as is the case with the SEM, scanning the ion beam over a surface
generates secondary electrons that can be detected to form an image. In this
respect, there is no difference between imaging using a focused ion or a
focused electron beam. Even the same secondary electron detectors can be used.
What strongly differs, is the mass of the probe. The mass of the ions is more
than three orders of magnitude larger than that of the electrons, which
significantly influences the contrast mechanisms and interaction volumes, and
can also inflict significant damage on the sample. In this respect, the light
ions of He-FIB bring great benefit—Section IV.3 is dedicated to the
application of the helium FIB specifically for the imaging of biological
specimens. The focused ion beam can further be used in a subtractive manner as
described above to slice the sample and image the resulting cross-sections by
SEM. The images are then used for reconstruction of the full 3D information in
a so-called FIB-SEM tomography, cf. subsections IV.3.3 and IV.3.4.

##### Elemental analysis:

Upon ion beam induced physical sputtering atoms and ions originating from the
sample are ejected and can be used to study its chemical composition. In SIMS
the generated secondary ions are collected and separated by their mass in a
spectrometer, cf. Section IV.4. Other analytical techniques, like EDS or
electron backscatter diffraction (EBSD) are of minor importance for
conventional FIB system as the generation rate of X-ray quanta is negligible
and the typical penetration depth of the conventional Ga ions is too low to
receive sufficient information on the lattice orientation.

##### Gas-assisted FIB-processing:

Bottom-up prototyping of nanostructures using the FIB is known as FIBID. In
this technique, the FIB is scanned over the sample surface generating SEs that
induce the partial decomposition of precursor molecules, dissociating them
into volatile and non-volatile components. The volatile products are pumped
away, while the non-volatile products are deposited on the surface, thus
creating a nanostructure in a single-step process. The flexibility of FIBID in
terms of shape and resolution ($20\text{\,}\mathrm{nm}30\text{\,}\mathrm{nm}$
for Ga-FIBID, and 10 for He-FIBID) make it highly desirable for applications
that require unique and precise planar or 3D designs. fibid applications are
discussed further in Section IV.5.

##### Unconventional FIB-processing

Similar to gas-assisted processing, focused ion beams can be used for the
local chemical modification of lithographic resists as well as of condensed or
spin-coated metalorganic precursors. Such ‘unconventional’ FIB processing can
increase processing speed and provide new chemical reaction pathways for ion-
induced deposition of high-purity metals. Focused ions can also be used to
form self-assembled structures or combined with the wealth of other
nanofabrication techniques to obtain the best of different worlds. Recent
advances in the area of FIB-based resist lithography and further non-standard
FIB approaches are described in Section IV.6.

###  IV.1 Applications of subtractive FIB processing

As the material removal using a focused ion is local and direct, it offers an
extraordinary flexibility of both the target geometry to be realized and the
substrate materials and geometries. Often the process can be even monitored
in-operando by scanning electron microscopy for direct alignment and quality
control.

Table 5: Overview of applications of subtractive FIB-processing, in which material is locally removed by ion-beam based physical sputtering. Research area |  Application |  Ion |  Material/Device
---|---|---|---
Materials science |  TEM sample preparation |  Ga |  wide range of materials [4]
|  |  Xe |  Al and Si [436], Al alloy [437]
|  |  Ne |  Al alloy and Si [438]
|  APT sample preparation |  Ga |  wide range of materials [439]
|  |  Xe |  Al alloy [440], Ti alloy [441]
|  |  Ne |  Al alloy and AlOx thin-film structure [442]
|  3D analysis |  Ga, Xe |  slice and image [443]
|  mechanical testing |  Ga |  micro/nanopillars, notches, ‘dogbone’ tensile bar specimens [444, 445, 446, 447, 448, 4, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469], SiO2 suspended membrane beams [470]
Optics |  photonic components |  O |  optical bridge in diamond [471]
|  |  Ga |  aspherical microlens in silicon [472], solid immersion lenses in silicon [473] and around pre-localized quantum emitters in diamond [474, 475, 188], triangular nanobeam cavities in diamond [476] and in YVO [477, 478, 479]
|  |  |  Fresnel zone plates for X-ray microscopy [480]
|  |  |  photonic crystal cavity around quantum emitters in diamond [481]
|  |  |  tapered nanoantenna for single photon emission of CdSe quantum dots [482]
|  fiber-based optical components |  Ga |  lab-on-a-fiber [483], Bragg gratings and microlenses in silica nanofibers [484], superconducting single-photon detector (SSPD) on optical fiber [485, 486]
|  plasmonic antennae |  Ga |  Au bowties for extreme ultraviolet (EUV) light generation [487], inverse Ag bowties [488], ring-shaped beam patterning of Au antenna arrays [489], Yagi-Uda-type antennae [490, 491], $\lambda/2$ antennae [492], asymmetric Ag oligomers [493]
|  |  He |  Al bowtie structures [494], gaps in Au bowtie antennas [495, 496], Au coaxial nanoresonators [497], Au oligomers [190], inverse Au oligomers [498, 499]
|  plasmonic waveguides |  Ga |  Au groove waveguides [491] forming logic gates [500], two-wire waveguides in Au [501, 502] forming spin optical nanodevice [503]
Electronics |  superconductive circuitry |  Ne |  nanoSQUIDs in Nb [504]
|  |  Ga |  nanoSQUIDs in Nb [505, 506, 507, 508]
|  |  Xe |  nanoSQUIDs in Nb [509]
|  semiconductor technology |  Ga |  photo mask repair [510, 511] including deposition [512] and etching [513], circuit edit [514]
|  Au |  X-ray mask repair [515] |
|  |  He, H, N |  photo mask repair [54, 516, 517, 518, 519], circuit edit [519, 520]
Magnetism |  spintronics and magnonics |  Ne |  permalloy microstrip trimming [521], environment dependend FMR [522]
|  |  Ga |  magnetic reversal [523], spin wave phase inverter [524]
Quantum Materials |  unconventional superconductivity |  Ga |  Sr2RuO4 [525, 526]
|  Josephson-vortices |  Ga |  strongly layered high-Tc superconductors [527, 528]
|  time-reversal symmetry breaking |  Ga |  Delafossite [529]
|  topological protected surface states |  Ga |  topological semi-metals [530, 531, 532, 533]
|  critical charge and bandstructure |  Ga |  µ-crystals [534, 535, 536]
|  strain engineering |  Ga |  Sr2RuO4 [537], CeIrIn5 [538, 539]
|  control of superconducting currents |  Ga |  vortex pinning [540], directional vortex motion [541, 542, 543]
Custom-probes and sensors |  near-field microscopy |  Ga |  circular [544] and bowtie [545] nanoaperture, tip-on-aperture geometry [546, 547], Au bowtie [548] and nanocone antenna [549], nanoslit grating in Au conical taper [550]
|  |  He |  square nanopores in pyramidal Au nanocavities [551], Au nanopyramid antenna [552]
|  |  Xe |  probe shaping for nearfield scanning microwave microscope [553]
|  atomic force microscopy |  Ga |  nanoscale apertures for liquid and ion transport [554, 555, 556], tip sharpening [557], modified mechanical response [558]
|  magnetic force microscopy |  Ga |  V-shaped magnetic nanostructure at probe tip [559]
|  mechanical high Q resonators |  He |  phononic crystal [560]
|  |  Ga |  graphene trampoline [561]
Table 5: *

####  IV.1.1 FIB for materials science

Arguably the most widespread application of the FIB has been the site-
selective fabrication of cross-section samples for high-resolution imaging
using a TEM [562, 4, 563, 564, 5]. Due to the prevalence of Ga-FIB
instruments, Ga ions are most typically employed and various strategies have
been developed to mill and extract cross-sections from bulk materials and to
thin samples to electron transparency. This includes low-energy FIB milling
under glancing incidence to minimize surface amorphization, and the use of
material specific capping layers and rocking stages to avoid _curtaining_
artifacts. More recently, the use of other FIB species for TEM lamella
preparation has been demonstrated, such as the Ne-FIB [438] and the Xe-FIB
[436]. The advantage of a noble gas ion species is that it does not chemically
react with the sample or accumulate along grain boundaries, as can be the case
with Ga [565].

In the same manner FIB milling has emerged as an important tool for the
creation of needle-shaped specimens for APT [439, 6]. Similar consideration to
the case of TEM sample preparation apply. Also here, minimal damage layer, and
the possible indiffusion of in particular Ga atoms [566] has to be taken into
account. The required needle geometry is achieved via annular milling with
different currents and subsequently smaller milling areas.

Another important application is the site-specific preparation of cross-
section cuts that enable in-situ and ex-situ imaging [567] and/or other
analysis such as EDS or EBSD (e.g. Kalácska  _et al._ [467]). By automating
this process, full (destructive) tomographies can be performed by slicing the
sample, extracting the desired information from each slice, and reconstructing
the data in three dimensions (see for example Kubis  _et al._ [82] and Section
IV.3.3).

All of these techniques are part of the standard materials science repertoire
used to study the microstructure, composition, and properties of materials and
devices at specific target locations. In depth overviews on these can be found
for example in Giannuzzi and Stevie [568].

####  IV.1.2 FIB for mechanical testing

As technology miniaturizes, the external dimensions of components in devices
approach characteristic internal length scales such as dislocation
interspacing. The mechanical properties of such small volumes of material are
still not fully understood. In 2004, Uchic  _et al._ [446] suggested use of
FIB milling to machine micropillars to study size dependent mechanical
properties of metals exploiting conventional nanoindentation equipment for
microcompression experiments. In contrast to conventional cleanroom based
lithography and etching, FIB machining allows for virtually any material to be
shaped into a micropillar at a specific target location. To achieve uniform
pillar circumferences with minimal tapper lathe milling in combination with
annular milling is often applied [569]. While the former can introduce sever
levels of stress [570] which might result in cracking or destruction of the
sample during APT, it is better suited for insulating, or very inhomogeneous
samples comprising layers with very different sputter yields.

Today, most mechanical testing experiments are performed in SEM or TEM to
capture changes from almost atomic to micron scale (e.g., formation of
dislocations, stacking faults, twins, grain orientations, contraction and
expansion of volume). Complex workflows include some or all of the following
steps: (a) micropillar machining, (b) tilting of the sample towards a
mechanical testing device for in-situ SEM testing, (c) deposition of a regular
pattern of points of FIB or focused electron beam (FEB) deposits on the sample
side-walls to follow deformations via digital image correlation algorithms,
(d) in-situ mechanical testing under SEM observation, and (e) finally back-
tilting for subsequent post-mortem FIB slicing for 3D tomographic or 3D EBSD
analysis of the deformed microstructure or the fracture pattern inside the
loaded sample [467].

Figure 17: Popular FIB-machined sample geometries for micromechanical testing:
(a) micropillars [446], (b) notched micro cantilvers [465], (c) micro-tensile
bars [466] and (d) micro-shear tests [460].

FIB machining of sharp notches with a specified orientation to the loading
axis enabled a number of fracture mechanics studies [465]. For in-situ tensile
testing in TEM, milling protocols were developed to prepare electron
transparent nanospecimens [458].

To reduce ion beam-induced surface damage defects, a multistep milling
strategy is typically employed. In this approach, beam voltage and current are
sequentially stepped down to the last polishing step [4]. Among the still open
questions are how much damage (amorphization, implantation) is induced by FIB
milling into the structures and how the damaged zones affect the mechanical
behaviour of the milled structure [454]. This depends on the penetration
(implantation) depth of ions as well as the collision cascade (amorphization)
they trigger (see sections III.1.3, III.2.3, and III.4.1).

Once other ion sources, in particular He, Ne, Xe, became available the hope
was to avoid the Ga damage issues. Best  _et al._ [463] found, however, that
using either He, Xe or Ga for machining of notches would affect the measured
fracture toughness value. While He ions were demonstrated to yield suitable
sharp notches with radii below 10nm, Xe ion beams were resolution limited. In
addition, it was unclear how the penetration depth of the different ions would
affect the fracture toughness [463]. Currently combinations of FIB with other
technologies are getting more and more popular. Laser machining of large
volumes and FIB fine sculpturing have recently become available from several
manufacturers in a single setup.

####  IV.1.3 Applications in photonics and plasmonics

Miniaturized on-chip photonic components are designed to guide or focus light
while having a footprint as small as possible. The fabrication relies mostly
on conventional large-scale lithographic techniques but there are applications
where a maskless direct-write strategy has significant advantages. The prime
examples are localized light sources, with the extreme case of single photon
sources, where often the optical component has to be built around a pre-
localized (quantum) emitter. Such quantum emitters may be defects in wide-
bandgap materials (cf. Section IV.2.4) where out-coupling of the generated
quantum light is typically hindered by the large refractive index of the host
material, e.g. diamond. Here, fib milling either using Ga ions [474, 475, 188]
or, to reduce Ga-induced damage, oxygen ions [471], was successfully used to
engrave solid immersion lenses that enhance the photon collection
efficiencies. In the same manner, photonic crystal cavities with small mode
volumes have been cut into a suspended diamond layer around pre-localized
quantum emitters and proven to enhance spontaneous emission [481]. An even
further reduction of optical mode volume can be achieved using metallic
nanostructures since these have the ability to concentrate light below the
diffraction limit by collective excitations of the free electron gas [571].
Since such plasmon-polariton modes are strongly dependent on geometry, FIB-
processing is a powerful tool for rapid prototyping of nanoscale resonators,
sub-wavelength apertures [572] and optical antennas [573].

Due to the extreme plasmonic field confinement, molecular species can be
detected down to the single molecule level by surface enhanced Raman
scattering [574] as the prime example, by enhanced fluorescence [575] or by
enhanced Förster resonant energy transfer [576]. The latter two examples
employ Ga ion beam milling to fabricate an antenna-in-a-box geometry, where
the gap region of a dimer antenna provides for local electric field
enhancement and correspondingly enhanced local density of optical states. The
remaining metallic film around the antenna blocks fluorescence contributing to
the background. In general, Ga-FIB top down patterning, especially of single-
crystalline Au or Ag nanoflakes, is often employed for high-fidelity rapid
prototyping of plasmonic components [577, 502, 578, 579, 580]. When comparing
the performance and material properties of plasmonic antennas, electron beam
lithography (EBL) may lead to better results than FIB milling, depending on
the actual geometry and processing conditions, and especially in case of Ga
[581]. However, ebl fails in fabricating truly 3D profiles, as used e.g., in
the case of 3D Janus plasmonic helical nanoapertures for polarization-
encrypted data storage [582]. A particularly beautiful example of the 3D
capabilities combines the local material removal by Ga ion beam milling in a
suspended gold film with a low dose irradiation at selected edges. The latter
induces a stress distribution that lead to up- or downwards bending of the
predefined structures [583]. This nano-kirigami has been demonstrated for
various designs realizing optical chirality, polarization and phase
engineering and showing potential for opto-mechanical applications [584]. In
addition, resolution and shape fidelity of fib milling using light ions stand
out compared to any other lithographic techniques [434, 190], but they come at
the cost of the slow speed of an inherently serial process. To resolve this
issue, lithographic large area processing by ebl can be combined with the
ultimate resolution of focused ion beam processing using He. Extremely narrow
gaps between large areas of lithographically defined plasmonic gold [585] or
aluminium [494] antennas were realized using this approach. The achievable
spatial resolution can be significantly improved while keeping a reasonable
processing speed by combining Ga ion beam patterning with He patterning [495].
Another approach to increase speed of top-down FIB processing relies on
milling only the outlines of desired plasmonic features which are then
obtained by peeling off the surrounding material [586, 587, 588]. This “sketch
and peel technique” combining Ga ion beam patterning for the outlines with He
FIB for the definition of ultra-narrow gaps was used to reproducibly
demonstrate strong coupling in plasmonic dimer antennas [589].

####  IV.1.4 Fabrication of custom probes

Since FIB milling is not restricted to planar sample geometry, a vast body of
research exists on the modification of optical fibers [483], nanofibers [484]
and nano-probes.The comprehensive review by Sloyan  _et al._ [483] presents
examples for optical near-field imaging, plasmonics, beam shaping, fiber-based
photonic cavities, fiber-chip coupling and many more. He ion based
manufacturing was reviewed in detail by Allen [434]. The direct control over
precise nanostructure geometries by FIB milling is especially interesting in
near-field optical microscopy (NSOM), where a metal coated glass fiber tip
localizes the excitation and/or collection of light by making use of a
nanoaperture or antenna for plasmonic field concentration. In applications
concerned with NSOM, FIB milling has been employed to fabricate high-
definition plasmonic circular nanoapertures [544] at the tip of a metal coated
fiber glass tip. Further signal enhancement and fluorescent background
reduction can be achieved by adding a tip at the aperture rim combining the
concepts of scattering and aperture NSOM [590, 591]. While in these works the
tip was grown by FEBID and metallized afterwards, later work engraved the tip-
on-aperture geometry from the metallic (Al) fiber coating by Ga FIB milling
and tuned the tip resonance to act as a monopole antenna, thus achieving
single molecule imaging [546] and imaging of proteins on cell membranes [547].
Additional geometries realized in this way are bowtie [545] nanoapertures on
the end of metal-coated fiber tips and square plasmonic nanoapertures in
pyramidal cavity structures [551], with the latter example employing He FIB
milling. Further specific geometries of metallic tips and metal-coated fiber
tips have been fabricated to control the plasmonic response for other
purposes. These include nanocones for resonance and radiation pattern tuning
[549] by Ga FIB milling, nanopyramids for optimizing local electric near-
fields [552] by He FIB milling, and nanoslit gratings into the conical taper
of metallic tips for nanofocusing upon far-field illumination [550], again by
Ga-FIB milling.

FIB milling has also been been employed to modify AFM probes for specialized
applications. For example, nanoscale apertures have been milled into hollow
pyramidal AFM tips so that that when the tips are loaded with liquid they can
be used to dispense attoliter volumes to create droplet arrays [554]. Such
tips can also be be used for the manipulation and analysis of single cells via
so-called fluidic AFM [555]. Tips can be sharpened using FIB milling and can
also be detached from their initial substrate and mounted onto a cantilever of
choice with the help of a micro-manipulator. This technique has, for example,
been used to produce customized tips with high aspect ratios [557]. In other
work, the AFM cantilevers themselves have been fashioned with FIB-milled
apertures to enable ion implantation through those apertures aided by scanning
probe alignment [556]. fib milling of larger patterns into piezoresitive
cantilevers has been used to increase deflection sensitivity to optimize
cantilever performance [558].

####  IV.1.5 FIB processing for quantum materials

“Quantum Materials” are materials in which quantum phenomena manifest in non-
trivial ways, leading to response functions that are qualitatively distinct
from those of standard electronic materials such as silicon or copper. They
generally arise from the non-locality of quantum systems, with topology,
frustration, and correlation playing a central role in the field [592, 593].
The key goal is to refine our microscopic or phenomenological understanding of
these exotic quantum states, and develop predictors to find promising
materials candidates within the vast space of possible compounds. Here, the
FIBs excels as a versatile patterning tool that is ideal for rapid processing
of non-standard materials [594], as it a) avoids exposure to wet chemistry
compared to resist-based lithography; b) can operate with crystallites and
microparticles that do not resemble polished wafers; and c) enables 3D
structure control that is critical to many electronically 3D quantum
materials.The operational goal of this research is to fabricate hybrid
structures that join micro-/nanostructures of a quantum material to a Si chip
of conventional architecture, both to demonstrate advanced functionalities and
to probe the underlying novel physics.

Quantum systems generically respond strongly to changes in their boundary
conditions, in this case, their physical shape. FIBs enable the sculpting of
non-trivial boundary conditions in crystals, which has been used to elucidate
the unconventional superconductivity of Sr2RuO4 [525, 526], Josephson-vortices
in strongly layered high-Tc superconductors and their excitations [527, 528],
quasiparticle transport in ultra-clean metals [529], and the magnetic exchange
bias in time-reversal symmetry breaking topological semi-metals [595].
Reducing the sample size to the micron scale further enhances the contribution
of surface properties to the overall physics. This is particularly important
in the quest to probe the contribution of topologically protected surface
states which have been proposed to enable novel electronic and spintronic
applications in topological semi-metals [530, 531, 532, 533]. Controlling the
motion of Abrikosov lattices by surface structuring [541] allows the control
of the motion of the vortices and can be used to build vortex diodes [542,
543]. fib processing allows to enhance the edge quality of structures which is
a prerequisite for the fabrication of efficient SSPDs [485]. The flexibility
of FIB processing enabled this process on the top of a optical fiber [486].

Subtractive FIB processing has also been applied in the fields of spintronics
and magnonics. Examples include application to guiding and control of
propagating spin waves, which has been enabled using Ga-FIB [524] processing.
High resolution metal free FIB processing using GFIS enables the fine tuning
of the interaction of spin waves across gaps [521].

Not all applications of the FIBs aim to alter the material. There is a wide
class of experiments that aim at probing bulk properties of novel materials
which are difficult to access in their native form, for example microcrystals
that are too small for conventional measurements. This has allowed insights
into microscopic effects on critical charge transport in iron-based
superconductors [534, 535], the determination of topological bandstructures in
microcrystals [536], or the switchability of anti-ferromagnetic states under
the high current densities achievable in FIBs machined crystals [596, 597].
The rich physical responses of quantum materials tend to be rooted in the
competition of multiple electronic ground states, which leads to a strong (and
potentially discontinuous) change of their properties under weak applied
stimuli [598]. One can hardly overstate the importance of residual stress in
the samples, with a famous example being the enigma of the “3K phase” of
superconductivity in Sr2RuO4 which originated from mismatch strain [537]. Here
a crucial advantage of FIBs over mechanical techniques of sample preparation
such as polishing or wire sawing is its kinetic nature, which results in
samples of low residual stress. Alternatively, the precision control over the
physical shape of a sample has enabled microscopic control over desired strain
fields and their gradients, which imprint correlation landscapes into the
quantum materials [538, 539].

####  IV.1.6 FIB processing in the semiconductor industry

In the field of semiconductor processing, FIBs are most relevant during
debugging of new products and for identifying production errors in the context
of circuit editing and fault isolation, as well as the repair of photomasks.
Among other applications, FIBs have been used for failure analysis, fault
isolation, TEM sample preparation, mask repair and backside circuit edit [599,
568, 600]. The ongoing scaling of the transistor fin, gate, and interconnect
via linear and volumetric shrinking as well as the introduction of new
transistor technologies led to a reduction of the critical length scale from
22nm in 2012 to the current 3nm technology node to be introduced by all major
manufacturers between 2022 and 2024 [601, 602, 603].

FIBs have been used since the 1980s for mask repair, initially using LMIS and
LMAIS based Ga and Au ions [510]. However, staining from implanted ions was
quickly identified as a problem limiting the application [511]. Latter, the
application of GFIS based H+, H${}_{2}^{+}$, N${}_{2}^{+}$, and He+ for phase
shift mask and EUV mask repair was investigated by Aramaki  _et al._ [54],
Edinger  _et al._ [518], Aramaki  _et al._ [517]. For H${}_{2}^{+}$ the
minimal repairable dimension is reported to be 11nm, which is half of what
could be achieved using electron beams [516]. The application of FIBID was
investigated early on for adding missing material to masks and repairing pin
holes by Cleaver  _et al._ [512] using Ga ions and a carbon deposit. This has
been extended to other precursors for deposition and the application of
etching gases such as Br2 and Cl2 for accelerated material removal [513] in
eUV masks.

For circuit edit and fault isolation applications, gallium was used initially
[514] but later Ne-GFIS based FIB processing was employed and resulted in
minimal trench widths for high aspect ratio vias of 14nm [519] and comparable
or less collateral damage compared to Ga as measured via changes to ring
oscillator timing [520]. Recently, also hydrogen GFIS based delayering has
been used successfully [604]. However, other source technologies, e.g.,
Chromium based MOTIS [605], also show potential for circuit edit applications
[606]. In general it is found that lower energies will be required while still
maintaining a suitably high resolution beam.

To better understand the effects of the beam profile on the achievable mill
resolution, in particular for the important case of via fabrication,
approaches have been developed to elucidate the probe current distribution
[607, 608]. The latter is of importance for the fabrication of the high aspect
holes created by milling—in many cases with a stationary beam. For via
formation applications during which a good signal to noise ratio is required
for reliable endpoint detection, a new figure of merit—SE yield per sputtered
atom—can be defined. Here, GFIS based He and Ne based milling promises a
spatial and temporal precision compared to Ga based FIB processing [609].
However, GFIS based milling suffers from the formation of gas bubbles and the
creation of defects far below the milled surface [610].

####  IV.1.7 Summary and outlook

As an all-in-one processing tool, it has been shown how FIBs can provide a
versatile method for flexible and fast prototyping of nanostructures and
devices by top-down fabrication.

To further advance these developments, FIB technology needs to improve not
only lateral resolution but also the in-situ control over the material removal
process itself. Critical issues include material selectivity and increasing
the signal to noise ratio of the SE monitoring during milling of high aspect
ratio structures. However, FIB top-down nanofabrication is intrinsically
limited by the fact that the associated chemical species and energetic
particles cause structural and chemical damage or changes, such as
amorphization or poisoning. While traditional Ga-FIB still represents the FIB
standard, some of the above mentioned fundamental limitations may be resolved
by using other ion sources such as GFIS, MOTIS, LOTIS, multicusp plasma ion
sources [72] or LMAIS (see e.g. Section II.1).

Additionally, leveraging FIB-based top-down nanofabrication as a practical
option will only be achieved when increased reproducibility and throughput are
consolidated.

These challenges can be addressed by advances in software and hardware tools
that enable, for example, modeling-informed automated operation, thus allowing
scale up or in line integration of FIB processing in the whole
(nano)-fabrication routine. Theoretical knowledge, modelling and simulation
tools that provide precise descriptions of FIB modifications to materials,
from the atomic to the microscopic scale, are a prerequisite for predictive
design and realization of tailored properties and functionalities in
nanostructured surfaces and operating devices. At the same time, there are
opportunities for coordinated FIB system development based on the experimental
needs.

The strong interest within emerging fields such as quantum technology, as well
as novel miniaturized platforms in the fields of microfluidics for lab-on-a-
chip or organ-on-a-chip developments would benefit from synergies of theory
groups and tool makers within the FIB application community.

###  IV.2 Engineering materials properties through defects

In addition to the subtractive nanofabrication applications described above,
site-specific and dose-controlled irradiation of samples with the FIB is used
to tune material properties in spatially defined regions down to the nanoscale
and even down to the single-atom level, without surface erosion or deposition.
These applications are based on the local introduction of varying
concentrations of defects (vacancies, dopants, and dopant-vacancy complexes),
controlled by the dose.

####  IV.2.1 Basics of irradiation-induced defect creation

A common technique used to create defects in crystals relies on bombardment
with high energy ions or electrons [611, 211, 612], and in some cases photons,
protons or neutrons [613]. For example, tuning the fluorescence properties or
the refractive index of a material for optical applications by bombardment
with ions is a well-established technique [614, 615]. Ion implanters are often
employed for such applications. Since these deliver broad beams with spot
sizes in the millimeter regime, a lithographically defined mask is needed when
higher spatial resolution is required. However, the large collision cascades
that are inherent to both high energy ion beams and light ion bombardment make
mask design rather challenging. This is where FIB processing comes into play.

As described in Section III, the incident ion induces a collision cascade in
the solid with a size that is determined by the target material and the ion’s
kinetic energy, as defined by the primary beam voltage. In a simplified
picture, when a recoil is generated, it leaves behind a vacancy and forms an
interstitial when it comes to rest[616]. In reality, defect clusters and
amorphous pockets may form depending on the target material[617] and the ion
mass and energy [618]. Such larger defects are usually undesirable for defect
engineering as their properties are less well defined than those of simple
defects. They are best avoided by using light ions which cause more dilute
collision cascades than heavier ions due to the lower nuclear stopping power,
and the recoils are less energetic because of the unequal masses of ion and
target atoms. In addition, light ions cause less sputtering, which is
considered an unwanted effect in defect engineering. Still, the applied ion
doses and beam parameters have to be carefully adjusted. Considering the
example of He+ ion irradiation of silicon and copper substrates, Livengood
_et al._ [610] differentiate the various defect regimes according to dose,
ranging from individual point defects at low fluence, to extended subsurface
microbubbles at very high fluence. While the picture will vary somewhat for
other ion-substrate combinations, the same overall trends apply.

Table LABEL:table:property_engineering gives the reader a flavor of the
breadth of FIB-based defect engineering applications, categorized according to
the specific materials property engineered (electrical, ferroelectric,
magnetic, optical, quantum optical, chemical, thermal, and mechanical).
Further examples can be found in the review articles from Gierak [619], Orús,
Córdoba, and De Teresa [620], and Allen [434]. In the remainder of this
section we focus on those applications in Table
LABEL:table:property_engineering that are concerned with engineering of
electronic, magnetic, optical and quantum(-optical) properties, as well as
tuning of low-dimensional materials (in particular, thin films and 2D
materials), and the study of irradiation damage mechanisms (e.g. the formation
of gas nanobubbles).

Table 6: Overview of FIB-based property engineering applications, in which fine control over the ion dose, beam energy, and irradiated regions enables local tuning of material properties. Engineered Property |  Experiment |  Ion |  Material/Device
---|---|---|---
Electrical & electronic |  Conductivity tuning |  He |  graphene [621, 622, 623, 624, 625], few-layer/monolayer MoS2 [626, 627, 628], epitaxial MoS2 [629], few-layer/monolayer WSe2 [630, 627], monolayer WSe2 [627], InGaZnO thin film [631]
|  |  Ga |  AlGaAs/GaAs quantum wires [632, 633, 634], GaAs quantum constrictions [635] GaN nanowires [636], 2D MoSe2/graphene heterostructure [637], MoSi superconducting thin film [638], In2O3 thin film [639], Al2O3 film [640], ZnO and VO2 [641]
|  Formation of tunnel barriers |  He |  superconducting electronic circuitry including nanoSQUIDs in YBCO [642, 643, 644, 645, 646], MgB2 [647]
|  |  Ga |  single-walled CNT [648], nanoSQUID in Nb [505]
|  Tuning thermoelectric properties |  He |  MoSe2 thin films [649]
|  Tuning superconductivity |  He |  pinning vortices [650]
|  Pinning ferroelectric domains |  He |  PbZr0.2Ti0.8O3 thin film [651], multilayer MoTe2 flake [652]
|  ferroelectric phase change |  He |  induced ferroelectricity in HfO2 [653], conversion to paraelectric phase [654]
|  |  Ga |  HfO2 thin film [655], damage in ferroelectric capacitors [656, 657]
Magnetic |  Tuning magnetic anisotropy |  He |  Co/Pt multilayers [658], Ir17Mn83/Co70Fe30 bilayer [659], Co-based thin-film stack [660, 661], Co/Pt/Ru multilayer system [662]
|  |  |  skyrmions in Pt/Co/MgO thin film [663], and in Pt/Co60Fe25B15/MgO thin film [664]
|  |  Ga |  CoPt multilayers [665], Fe78Ni22 thin film [666], Ir/Co/Pt multilayers [667]
|  |  |  skyrmions in FeGe thin plate [668], and in Co/Pt multilayers [669, 670, 671]
|  |  Si/Ge |  Bi and Ga substituted YIG [672]
|  Tuning metamagnetic transition temp. |  He |  FeRh thin film [673]
|  FIB-induced ferromagnetism |  Ga |  Fe60Al40 alloy [674] and Fe78Ni22 on copper [675]
|  |  Ne |  Fe60Al40 thin film [676, 522]
|  Magnonic |  Ga |  patterned Fe78Ni22 films [666], spin wave optical elements in YIG [677]
Optical |  Tuning photoluminescence |  He |  SiNx membrane [678], monolayer MoSe2 [679], InGaAs/GaAs quantum well [680], reducing parasitic fluorescence in hBN [681]
|  |  Ga |  AlGaAs/GaAs and GaInAsP/InP quantum wells [682]
|  Tuning of passive optical components |  He |  plasmonic resonance in graphene nanostructures [683], Bragg grating in silica nanofiber [684]
|  |  Li |  Si microdisc nanophotonic resonator [685]
|  |  Ga |  ZnSe quantum dot micropillar cavitities [686], periodic poling of LiNb waveguide [687]
Quantum |  Creation of quantum emitters |  He |  NVcenters in diamond with substitutional nitrogen [688, 689], Si vacancy centers in SiC [690, 691], luminescent defects in monolayer MoS2 [692, 693]
|  |  Bi |  qubits in silicon and germanium [694]
|  |  Li |  Si vacancy centers in SiC [695]
|  |  Si |  Si vacancy centers in diamond [696] and diamond nanostructures [697], W and G centers in silicon [698]
|  |  Ge |  Ge vacancy centers in diamond [699]
|  |  Ga |  luminescent defects in hBN [700, 701], monolayer WSe2 [702], MoS2 and WS2 [703]
|  |  Sb, Si |  deterministic single-atom doping [704]
|  |  Xe |  recoil implantation of color centers into diamond [705], spin defects in hBN [706], water assisted fabrication of extended defects in hBN [707]
Chemical |  Enhancing chemical etch rates |  He |  Si3N4 thin film [708], SiO2 thin film [709], mono-/bilayer MoS2 [710]
|  Enhancing catalytic activity |  He |  MoS2 and MoSe2 flakes [711]
|  Nucleation of growth |  He |  epitaxial graphene on SiC [712]
|  |  Ga |  InAs dots on GaAs [713], Ge dots on Si [714, 715]
|  |  Co |  CoSi2 nanowires in Co-saturated silicon [716]
|  Functionalization |  Ga |  graphene (fluorination using XeF2) [717]
|  Tuning surface wettability |  Ga |  molecular self-assembled monolayer [718]
Thermal |  Reducing thermal conductivity |  He |  Si nanowires [719], Si membrane [720], VO2 nanowires [721], Bi2Te3 nanoribbons [722]
Mechanical |  Tuning Young’s modulus |  He |  monolayer MoSe2 [679]
|  |  Ga |  polymer [723], hydrogels [724]
|  Gas bubble effects |  He |  nanobubble superlattice in Cu [725], nanobubbles in Si [726], diamond [727], Eurofer steel [728], W [729], ultrafine-grained W and W-Cu nanocomposite [730]
Table 6: *

####  IV.2.2 Electronic applications

FIBs have been used from the beginning to manufacture electronic devices at
the nanoscale. An early example is the fabrication of GaAs quantum wires [632]
and the slightly later fabrication of a quantum wire transistor [634] by Ga-
FIB. Recently, a focused Ga ion beam was employed for the fabrication of a
lateral diode based on a 2D heterostructure from MoSe2 and graphene [637]. The
preferential sputtering of Se transformed the top MoSe2 locally into a
quasimetallic state generating a pn junction with rectification performance
comparable to that of a vertical diode. The above examples have in common that
material needed to be removed by the FIB beam. Indeed, subtractive materials
modification was more prevalent initially, but the engineering of electrical
materials properties without intentional surface modification has recently
become more and more important.

Here, light—and possibly—inert ion beams are of relevance due to their high
resolution for creating defect based devices. Furthermore, ion beams of
electronically active elements (e.g., P, Sb, As, …) have the potential for
interesting applications. A prime example is the fabrication of nanometer-
sized insulating tunnel junctions in the thin-film high-temperature
superconductor yttrium barium copper oxide (YBCO) using line irradiation with
the He+ FIB [642]. Similar tunneling junctions have also been created in other
materials such as Nb [505] and MgB2 [647].

Due to the nanoscale beam diameter achievable with FIBs and in particular with
GFIS based FIBs, they are the ideal tools for the fabrication of single
quantum dots, tunneling devices and single electron transistors. This has been
demonstrated by the fabrication of single electron transistors in Si/SiO2
stacks [375] and the fabrication of single quantum dots in carbon nanotubes
[648].

The fabrication of single electrically active quantum dots in Si is a new
challenge where some progress has been recently achieved [704, 258]. While
these works are a clear demonstration of the placement accuracy for single or
a few ions achievable with FIB, both approaches rely on the implantation of
the donor atoms (Sb or P) into an active detector which also doubles as the
host for the quantum device.

####  IV.2.3 Modification of magnetic materials

Ions have been used for many decades for the modification of magnetic
materials [731]. To achieve this sort of modification complex and expensive
masking processes have to be used unless one employs a focused beams of ions
which can modify the magnetic properties locally with nm precision. In 1989
Ishii, Nonaka, and Hatakeyama [672] used Si and Ge from a LMAIS FIB to create
nucleation sites for controlled switching of the magnetization in Bi and Ga
substituted yttrium iron garnet (YIG) films. Ga FIB processing was used for
the read/write heads [732] required for magnetic hard disks but also for
modern approaches such as magnetic random access memories composed of magnetic
multilayer structures [733]. The FIB-induced local change in magnetic
anisotropy was used to create isolated tracks of single domain islands in
recording media [734] and to control injection location and field dependency
of magnetic domain walls in multilayers with perpendicular magnetic anisotropy
using focused Ga and He ions [658]. In the case of Co nanowires fabricated by
FEBID, irradiation with focused Ga ions allowed modification of the
propagation speed of the magnetic domain wall [735]. In some materials,
focused ion-beams can be used to generate ferromagnetism in selected regions,
such as in paramagnetic FeAl alloys. The spatially resolved creation of
disorder-induced ferromagnetism by focused Ga-FIB beam modification has been
demonstrated by Menéndez  _et al._ [674]. A spatial resolution of below 100nm
could thus be achieved with the possibility of erasing the pattern by
annealing. Later Fe60Al40 was studied in depth for order-disorder phase
transitions and ferromagnetic resonance (FMR) in magnetically written single
objects [522] induced by focused Ne irradiation [676].

Paramagnetic regions in non-magnetic materials can also be created by FIB
processing as done for InGaAs using a focused Ga ion beam to create a spin
filter device [736]. The continued quest for an increase in storage density in
combination with novel data processing approaches (i.e. neuromorphic
computing) triggered the development of advanced patterning of complex
magnetic alloys and multilayer systems [737, 738, 739]. In these systems
various interactions due to the intrinsic anisotropy or lattice and system
geometry may lead to topologically protected spin configurations such as
skyrmions or controlled formation and transport of spin waves. Here, FIB
stands out as it enables tuning of magnetic anisotropy landscapes without any
topographical changes of the devices. This was demonstrated for the nucleation
control of skyrmions in Co/Pt multilayers using Ga+ FIB [670] and He+ FIB
[669], and the patterning of skyrmion racetracks in a Pt/Co/MgO thin film
using the He+ FIB [663]. Patterning dots as nucleation sites within a low-dose
racetrack using He+ FIB processing could realize both deterministic generation
and movement of skyrmions with nanometric precision [664]. Finally, spin-wave
optical components such as graded-index lenses for applications in magnonics
can be created by ion-induced modification of the local magnetization in YIG,
which corresponds to an effective refractive index for spin wave propagation.
Here, focused Ga ions of 50 keV were employed and the penetration depth of
about 100 nm allowed for an effective index of up to 1.8 comparable to light-
based optics. Since this depth was only one third of the actual device
thickness the much lighter He is expected to significantly improve the optical
device performance [677].

####  IV.2.4 Optical applications

Typical applications of ion implantation in optics comprise the local change
of refractive index and the creation of fluorescence [740]. However, since FIB
processing is serial and the penetration depth is limited, it is mostly
interesting in cases where a small number of ions needs to be placed with high
spatial accuracy. One especially interesting example in that respect is the
tuning and imaging of resonant optical modes in a silicon disc resonator with
focused Li ion beams [685]. Here, an extremely low beam current of 1pA at
3.9kV acceleration voltage was used to radially raster scan in ion pulses of
$\approx 3000$ ions while the transmitted light through a critically coupled
waveguide was monitored. The optical shifts could be attributed to an ion
damage related contribution and a rapid thermal and, thus, reversal response.
Using the knowledge about this time-varying response, imaging of different
optical modes could be achieved with minimum device degradation [685].

The spatial accuracy of defect creation of the mask-less process becomes
especially beneficial in the field of quantum optics. Here, a defect in an
otherwise ideally perfect crystal can take the role of an artificial atom
emitting quantum light. The most popular example for this kind of a defect-
based quantum emitter is the nitrogen vacancy (NV) center in diamond that are
routinely fabricated using ion implanters [741] but were also realized by He
ion beam processing [688, 689]. FIB implantation of Si ions has been used to
realize nearly lifetime-limited single silicon vacancy (SiV) quantum emitters
in diamond nanostructures [697]. This maskless creation of SiV centres in
diamond nanocavities has been proven to occur with ≈32nm lateral precision and
<50nm positioning accuracy, and has been envisioned as promising for the
development of scalable solid-state quantum information processors. Focused Si
ions at 35keV with
$5\text{\,}\mathrm{n}\mathrm{m}10\text{\,}\mathrm{n}\mathrm{m}$ beam diameter
were also used to fabricate V${}_{Si}^{-}$ defects in 4H-SiC. Starting from 40
ions per spot single emitters were found [742]. A comparative study by the
same author using hydrogen, helium and carbon showed that helium produced the
highest defect concentration, while the lowest brightness of the emitters was
observed for carbon [743]. In additions Li ions have been employed for the
creation of silicon vacancies in silicon carbide [695]. Recently an electron
beam ion source with focusing capability was shown to induce Ar8+ ion
implantation for NV-creation in diamond [744]. A particularly interesting
study made use of focused Xe ion for recoil implantation of targeted group IV
dopants in a deposited surface layer [705]. Thereby, Pb, Sn, Ge and Si color
centers in diamond could be fabricated with a spatial accuracy of better than
50nm in combination with an ultra-shallow doping profile. In the case of
silicon Si and C FIB implantation has been employed very recently to create
single defects in a spatially resolved way for their application as quantum
emitters in the telecom window [698].

In parallel, 2D materials have been heavily explored for usable quantum
emitters e.g. sources of single photons [745]. In that context, ion
irradiation can be used to not only tailor the optical properties of 2D
systems [746], but also to produce defects which possess the desired
characteristics [747, 748]. In particular, He ion beam processing was
successfully used for the site-selective creation of defects in MoS2. While
the actual type of the defects is still to be investigated (being true for
most of the luminescent defects in 2D materials) they are expected to cause
highly localized trapping potentials for exciton emission. Encapsulation with
hBN led to very narrow linewidths of the emission lines in the visible range
$100\text{\,}\mathrm{m}\mathrm{e}\mathrm{V}220\text{\,}\mathrm{m}\mathrm{e}\mathrm{V}$
below the neutral exciton [693]. He irradiation was also shown to result in a
five-fold reduction of background and parasitic fluorescence resulting in
isolation of bright and stable quantum emitters in hBN [681]. Recent results
on Ga ion beam patterning indicate that the luminescent defect formation is
positively correlated to material swelling instead of material removal by
milling [701]. This helps to explain earlier results on the generation of
defects based on Ga FIB where it was not clear whether the single photon
emission was actually generated inside the milled holes, at their edges or in
the damaged region near the edges [700].

####  IV.2.5 Property engineering of low-dimensional materials

In general, 2D materials such as graphene and atomically thin transition-metal
dichalcogenides are expected to play an important role in the realization of
future electronic and optoelectronic devices and there exists a significant
body of work in which FIB-based defect engineering has been used to tune the
unique properties of these materials. In fact, as can be seen in Table
LABEL:table:property_engineering, the majority of materials that are used in
FIB-based defect engineering work are indeed low-dimensional (thin films, 2D
materials, and nanowires). The simple reason for this is that typical FIB
instruments deliver beams with energies of several tens of keV, which limits
the ion penetration depth. For example, in most materials the maximum
penetration depth of the ubiquitous 30keV Ga+ ion beam is around 60nm, which
severely limits possibilities for property engineering of bulk materials.
Here, light ions such as He+ and Ne+ bring benefit, as these ions can travel
deeper into the sample while leaving the surface largely intact due to
significantly reduced surface sputtering. In contrast, increase in ion energy
normally gives rise to a drop in defect production in 2D materials [749], so
that lower energies are more suitable for efficient modification of 2D
materials.

An example of FIB-based defect engineering of a low-dimensional material is
the use of the He+ FIB to tune the electrical resistivity of 2D MoS2 [626]. In
the cited work, the electrical resistivity of the MoS2 monolayer was tuned
from semiconducting to insulating depending on the vacancy defect
concentration, as controlled by the irradiation dose. Above a certain
threshold dose, total amorphization (i.e. disordering) of the material occurs.
By irradiating samples locally in specific patterns with fluences below the
total amorphization threshold, the FIB can be used to tune the defect density
and hence electrical conductivity in spatially defined regions at the
nanoscale. For example, using the He+ FIB and a line irradiation strategy,
also on a 2D MoS2 sample, a neuromorphic memtransistor device has been
demonstrated [628]. Similarly, Ga-FIB has been used for defect creation in
supported graphene with MD simulations providing a pathway for reducing the
extension of the damage region by irradiation under an angle [750]. He+ FIB
line irradiation has been used to isolate narrow widths of graphene, thus
creating graphene nanoribbons [751]. This enables the opening up of a bandgap
in graphene, where tuning of the bandgap size (directly related to the
nanoribbon width) is a key step towards the use of graphene in electronic
applications. It should be noted that the minimum achievable nanoribbon width
is limited by the influence of the backscattered ions from the substrate
[335], as discussed in Section III.2.3.

Other defect engineering applications concerning 2D materials include use of
the He+ FIB to create localized defects in graphene to serve as nucleation
points for epitaxial growth of hexagonal boron nitride [712] and localized
fluorination of graphene using Ga+ FIB irradiation with the simultaneous flow
of XeF2 gas [717]. An example of defect engineering of a 1D structure is the
use of the He+ FIB to induce regions of local disorder in a silicon nanowire
in order to tune the thermal conductivity along its length [719].

####  IV.2.6 Study of irradiation damage mechanisms

Fundamental curiosity and the need for experimentally straightforward
replacements for long-term reactor-based irradiation experiments have resulted
in FIB instruments being used for the systematic study of irradiation effects
on structural materials. In order to simulate irradiation damage caused by
$\alpha$ particles, for example, He+ ions are a convenient species to use. A
further advantage of using He+ ions is that fundamental studies of irradiation
effects can be made while avoiding alloying effects and grain boundary
embrittlement, as can occur with a metallic ion species such as gallium [565].

A phenomenon that was discovered several decades ago is the formation of
helium nanobubbles upon He+ ion irradiation of various metal targets. These
nanobubbles form as a result of vacancy defects and helium interstitials that
diffuse and recombine to produce gas clusters. However, fundamental studies of
the resulting changes in the mechanical properties of the target material were
for a long time confined to the use of large-scale ion accelerators and plasma
devices. The introduction of the He+ FIB changed this, enabling the first
systematic dose-controlled irradiation studies. Using the He+ FIB, gas bubble
phenomena that had been observed in large-scale experiments have been
reproduced with much greater control over the experimental conditions. Initial
He+ FIB studies in this area used silicon targets, mostly driven by the need
of the semiconductor industry to evaluate the invasiveness of He+ FIB
processing [610]. Later studies have included the investigation of helium gas-
bubble superlattices, using single-crystal copper as a simple model system and
probing the effect of the superlattice on the mechanical properties of the
host material using in-situ TEM nanoindentation [725]. Since samples are
irradiated with the He+ FIB on the nanoscale, individual grains and grain
boundaries can be targeted in polycrystalline samples [752]. By increasing the
dose, the coalescence of nanobubbles to form crack planes that ultimately
result in blistering and delamination can also be studied with a level of
control that was previously unattainable [753]. Furthermore, irradiation-
induced mechanical property changes of a number of materials that are directly
relevant for nuclear applications have been investigated using the He+ FIB
method combined with nanoindentation, for example in studies of Eurofer steel
[728], tungsten [729], ultrafine-grained tungsten and a tungsten-copper
nanocomposite [730].

Finally, helium gas bubble effects have also been employed for nanofabrication
tasks, using patterning with the He+ FIB at high dose for localized subsurface
swelling to deform surfaces and thereby create 3D nanostructures such as
nanopyramids and nanohemispheres [754, 755, 756].

####  IV.2.7 Outlook

Ion beam processing is well-established for material modification and property
engineering at the microscopic scale. Recently, strong efforts are underway to
further down-scaling with the ultimate goal of creating single defects or
implanting single impurity atoms for quantum technology applications. The
intrinsically stochastic nature of both ion creation from most source types
and of ion-solid interaction in the sample poses a severe challenge. Hence,
the deterministic implantation of single ions either in the bulk or at a
surface pushes the technique to its fundamental limits in terms of spatial
resolution and controllability.

There are two fundamentally different approaches. One is to count the ions
that are incident on the surface, the other is to reliability detect the ion
impact event, ideally in an universal manner. The first approach can be
realized by using an Paul ion trap as a deterministic source of a single ion
[757, 758]. While the presence of the ion can be unambiguously proven,
ejecting the ion and loading the trap again is time-consuming and using ion-
optical elements to spatially localize the impact event causes significant
losses. Given that the probabilities for the creation of specific defects is
usually low and highly material dependent (see also Section III.2) this
approach is appealing but technologically extremely demanding. Alternatively,
ion columns may be equipped with image charge detectors that count ions from
different types of ion sources. The beam is directed towards the sample only
if an ion is detected. Thereby, limited detection efficiencies can be
mitigated since all non-detected ions are blanked [166, 759]. The drawback of
this technique is the large charge state that is necessary for detection such
as e.g. 18+ for the case of Ar ions created by an electron beam ion trap
(EBIT) source [759]. This requirement excludes light ions by construction and
represents severe technological challenges for column design. The second
approach, the detection of the ion impact event, could in principle work for
any ion source. Promising attempts combine an on-chip IBIC detector with a
plasma ion source and a near-surface aperture realized into an AFM cantilever
[258]. Here, the aperture scanning realizes the spatial localization [760,
761, 762] and thus allows use of various types of ion sources, including broad
beam implanters. While this is an important step for all quantum devices that
tolerate a nearby pn-junction and amplifier, other device concepts e.g. in
photonic quantum technology require truly sample agnostic detector concepts.
The conventional SE detectors (Everhart-Thornley, CMOS, see also Section II.3)
may work as such but suffer from their strong dependence on the SE yield which
is unknown for most materials and is, in addition, very surface dependent.
These quests are combined with the need for a better understanding and
prediction of SE generation and expected detection yields, and for advancing
SE detectors exceeding 97% detection efficiency [763, 694]. Instead of
detecting all ion impact events (that come with a small probability of
creating the target defect) one may instead detect device function in-situ
while shooting ions at the target locations. A combination of short dwell
times at extremely low current results in a Poissonian probability of either
one or zero ions per shot and the process may be stopped once the device is
operable. Here, the technological challenge comprises the co-integration of an
extremely sensitive fluorescence detection setup [764]. In conclusion, several
promising development routes are currently pursued showing first exciting
results. Which of the approaches, either modifying the ion supply towards
being deterministic or enhancing the detection capabilities towards single-ion
sensitivity or even a combined technology, will finally succeed is still open.

###  IV.3 FIB-based imaging and tomography

In addition to imaging ever smaller features in samples down to atomic
resolution as achieved by aberration-corrected TEM, imaging complex systems is
becoming increasingly important. To understand data transmission in a brain or
chemical energy storage in a battery, one needs to capture the “big picture”
ideally in three dimensions rather than resolving individual atoms. This is
where FIB-based techniques come into play, either by imaging of radiation-
sensitive biological samples by light ions or 3D imaging by tomography where
focused ion beam slicing is typically combined with SEM imaging.

####  IV.3.1 A brief history of FIB-based imaging and analysis

The enormous potential of electron microscopy for imaging the structure of
matter became clear immediately after the invention of the TEM in 1932 [765]
and soon thereafter first images of bacteria [766, 767] and virus particles
[768] proved the same for the life-sciences. The introduction of ion
microscopy for structural imaging, however, took much longer. Pioneering work
was done in the 1970s by the Levi-Setti group who experimented with a scanning
transmission ion microscope using up to 65keV H${}_{2}^{+}$ ions from a GFIS
and published images of myofibrils from rabbit muscle [36]. However, since the
achievable lateral resolution of ion microscopy had always been inferior to
that of electron microscopy, ion microscopy had not been used for high-
resolution imaging until the early 2000s when the HIM was invented [19, 23]
(see Section IV.3.2).

The breakthrough, or in Ballerini  _et al._ [769]’s words, “the revolution in
ultra-microscopy” occurred around the same time when ion microscopic
techniques finally became well accepted means for sub-cellular
(chemical-)imaging. On one hand, ion beams from liquid metal based sources
could now be focused down to better than 10nm [770]. On the other hand, the
idea to use the ion beam “like a tiny scalpel which slices away layers of the
sample [and] to exploit this destruction to gain high-resolution three-
dimensional structural, morphological, and chemical information” [769] was
brought to the life sciences [769] and other fields, like energy materials
[771]. The following years saw the commercialisation of dual beam systems, in
the following referred to as FIB-SEM. These usually consist of a field
emission SEMs used for high-resolution imaging coupled with a Ga FIB column
for sectioning. At the same time significant progress in 3D image segmentation
and reconstruction was made [772] which paved the way for 3D structural
imaging of complex specimens. One of the first reported FIB tomography
investigations was presented by Inkson, Mulvihill, and Möbus [771] in the year
2001 on the “3D characterization of a metallic nanocomposite”. After that, FIB
tomography became a more and more common tool in various fields of research
such as metallurgy [773, 82, 567], energy research [774], geology [775],
biology, and medicine [776]. Especially in the latter fields a major step
forward in the preservation of ultra-structure was to develop cryo-workflows
for cryo-FIB-SEM tomography [777, 778]. Recently FIB has even been applied to
paleontology samples [779].

####  IV.3.2 HIM—A tool for imaging of the tiniest living objects

SEM is a standard method for imaging biological specimens. Samples are usually
coated with a conductive layer to prevent charging under the beam.
Technically, SEM imaging without a conductive layer is possible if the
accelerating voltage of the electron beam is reduced below 1kV. However, the
downside of using lower electron voltages is increased chromatic aberration
and reduced depth of field [780]. Basically, HIM and SEM are comparable in
function and application, so HIM can be considered complementary to SEM in the
field of life science. However, compared to the SEM, HIM has some significant
advantages: a larger depth of field, less sample damage, higher surface
contrast (especially for light elements like carbon) and sub-nanometer image
resolution. A particularly important advantage of HIM is the built-in charge
compensation with an electron flood gun which allows for investigating non-
conductive biological samples without having to coat them with a conductive
layer. This is important as metallic coatings can alter and conceal nanoscopic
sample features such as virus particles or the cell membrane topography. FIB
images can also be generated by the detection of back-scattered ions, to make
material contrasts visible. However, He backscattering in a HIM is
particularly well-suited as it provides sufficient back scattering yields and
minimizes damage (see also Section II.3). So far, this has rarely been used in
the life sciences. However, Bidlack  _et al._ [160] stated, that backscattered
ion (BI) imaging could improve the visualization of immuno-gold labels in
cells as they show the same contrast using the ETD. Ma  _et al._ [159] used BI
imaging to detect different concentrations of colloidal nanoparticles in
cells.

##### Preparation of the specimen

Since the sample requirements of HIM—samples should be dry and vacuum-
compatible—are almost identical to those of electron microscopy, established
protocols from SEM provide a good basis for HIM as well. In general the
preparation involves 1) chemical fixation with aldehydes (e.g. formaldehyde or
glutaraldehyde) 2) optional post-fixation with strong oxidising agents (e.g.
osmium tetroxide), 3) dehydration in a graded series of an organic solvent
(e.g. methanol, ethanol or acetone) and finally 4) drying (e.g. critical point
drying). Instead of dehydration and drying of the sample, the application of
ionic liquids has been proposed as an alternative [781] and successfully
applied for imaging bacterial bio-films with the HIM [782]. As mentioned
before, because of the possibility to compensate charging in the HIM no
metallisation of the sample surface is needed. This allows for analysing the
sample in a more pristine state.

##### Viruses

Sharma  _et al._ [783] investigated the interactions of viruses and their
hosts in sediment and microbial mat samples. In the same manner, HIM has been
shown to be a powerful tool to investigate bacteriophages (i.e. viruses that
attack bacteria) and their interactions with their host cells. Both Leppänen
_et al._ [784] and You  _et al._ [785] published high-resolution HIM images of
T4-phage infected E. coli bacteria and Vinner  _et al._ [786] visualized phage
Felix O1 infected Salmonella bacteria. How those and other microscope images
contributed to our understanding of bacteriophages was recently reviewed in
more detail by Almeida  _et al._ [787]. Frese  _et al._ [788] and Barreto-
Vieira  _et al._ [789] recently reported the first visualization of SARS-CoV-2
virus particles by HIM, demonstrating significant topographical differences
from previously published SEM images of sputter-coated samples. Looking ahead,
the HIM could be used, for example, to examine phage-infected cells by milling
inside them or to create 3D images by projections. In addition, the HIM can be
used to better understand the spread of viral particles through other
organisms, as it is possible to easily wash away, for example, lightly
attached phages through the preparation.

Figure 18:  (a) SARS-CoV-2 virus particles on the cell membrane of a vero E6
cell. (b) T4-phage infected E. coli bacteria on a fibrous agar surface. (a)
Copyright ©2021 Frese  _et al._ [788], distributed under the terms and
conditions of the Creative Commons Attribution License.

##### Single-celled organisms

HIM is an excellent tool for viewing single-celled organisms such as bacteria,
archea, yeast, micro-algea, protozoa and the like at a resolution close to
that of TEM without having to embed and section the samples. In their 2013
paper Joens  _et al._ [780] employed HIM for the first time for imaging of
microbes, namely iron-oxidising bacteria. In particular for viewing bacteria
on non-conductive surfaces with a strong topography, charge-compensation and
large depth-of-field render HIM an excellent tool. The first HIM images of a
culture of archea were published by Chen  _et al._ [790] where HIM proved
particularly useful for investigation of alleged cell budding of Ca. A.
ethanivorans. Furthermore, HIM has been utilized by Said, Chatzinotas, and
Schmidt [791] to image infections of bacteria with the bacterial predator
Bdellovibrio bacteriovorus. Owing to its “large depth of field, the efficient
charge compensation and strong edge contrast” HIM is particularly suitable for
imaging biofilms which often show strong topography and tend to charge up
under charged particle beams [782]. HIM of bacterial biofilms was published by
LeTourneau  _et al._ [792] (rhizobacteria), by Belianinov  _et al._ [793]
(Geobacter sulfurreducens) and Schmidt, Byrne, and Maasilta [782] (Pseudomonas
putida). Further HIM studies on biofilms comprise imaging of microbial mats
from hot springs in the Indian Himalayans by Sharma  _et al._ [783] and
investigations of micro-algal biofilms with regard to architecture and
phosphorus distribution by Moreno Osorio  _et al._ [794]. Other potential
applications of HIM imaging of microbiological objects include investigations
of biofilms in different environments, for example on medical implants or in
bio-reactors, to name a few. Furthermore, HIM will be an excellent technique
to study phage-infection or predation by protists or bacteria in environmental
bacterial biofilms. One can also perceive HIM investigations into the complex
interplay of microbes with plants or fungii. A recent example of such a
complex system is given by You  _et al._ [785] where HIM was used to analyse
phage co-transport on hyphal-riding bacteria.

##### Cells, tissues, immuno-gold labelling

To date, the HIM has been used in many studies to investigate whole cells and
nanoscopic cell structures, including plant [794], animal [795] and human
cells [796, 797]. In the study of nanoscopic cell structures, which are
usually distorted or obscured by metallic coatings, charge compensation allows
visualization of topographical structures that would not be observable in SEM.
For the first time, Schürmann  _et al._ [798] visualized lipid nanodomains in
cell membranes of neurons, which were demonstrated to be concealed under a
10nm gold coating. Sato, Sato, and Ogawa [799] have shown that immuno-gold-
tagged antibodies can be resolved within cells to identify specific
organelles. For the first time, they demonstrated the detection of
ionoluminescence from ZnO nanoparticles in biological specimens using HIM.
When imaging animal nanostructures such as insect wings, the superior depth of
field of the HIM has proven advantageous [800, 801]. Joens  _et al._ [780]
demonstrated that the mouth cavity of a nematode can be dissected using the
focused neon beam in HIM with minimal thermal damage to the cutting surface.

#####  HIM in correlative workflows

Besides structural analysis the life science applications also require tools
for investigations into the chemical composition on the subcellular level. In
general there are two possibilities to overcome the chemical blindness of the
HIM. On the one hand detectors such as SIMS (cf. Subsection II.3) can be
installed directly on the tool and be used for in-situ correlative
investigations as has been shown for _E.coli_ cells incubated with TiO2
nanoparticles [156]. On the other hand HIM can be embedded into correlative
work-flows with micro-analytical tools such as SIMS and EDS or fluorescence
microscopy in combination with fluorescent markers (see also Section II.6). A
recently published example shows how HIM in correlation with the
aforementioned techniques was used to analyse a resin-embedded soil sample
with regard to roots, sediments, soil-organic matter and bacteria [802]. In
the future we expect to see applications of correlative microscopy with the
HIM for instance to analyze bio-mineralization processes, to solve ecological
questions in environmental microbiology, in plant- and soil science and many
more. Owing to its possibility to image non-conductive samples almost
destruction-free HIM may also become a central high-resolution technique in
correlative workflows for structural and chemical analysis of biological
specimens.

####  IV.3.3 FIB-based tomography in the life sciences

Three-dimensional nano-imaging of biological objects has become more and more
important with respect to, for instance, structural investigations into 3D
cell-architecture, the ultra-structure of cell components, cell-to-cell
interactions, analysis of tissues and the structure of bio-films, to name a
few. Until the early 2000s investigations into the ultra-structure of
micrometer-sized biological objects such as resin-embedded tissues or cells in
three dimensions were carried out by serial block-face SEM[803] or serial
sectioning TEM[804]. Whilst a very high lateral resolution can be achieved by
this approach, depth resolution is limited by the achievable thickness of the
slices. Alternatively serial block-face SEMs with a microtome fitted into the
analysis chamber can be used for tomographic imaging of resin-embedded
samples. However, in this technique the depth resolution is also limited by
the minimal thickness of the removed material.

With the advent of fine-focused ion beams (mainly $\mathrm{Ga}^{+}$-based),
micro-tomography of biological objects made a great leap as it allows for
better controlled and much finer removal of material from the blocks [805]. As
one of the first examples of FIB micro-tomography, Ballerini  _et al._ [769]
investigated the internal structure of yeast cells by _in-situ_ FIB-sectioning
followed by FIB-imaging using (negatively charged) secondary ions and
secondary electrons. Soon thereafter the image resolution could be further
improved by employing dual-beam FIB-SEM systems where the specimen is FIB-
sectioned and electron-imaged. The use of oxygen ions from an PFIB seems to
reduce curtaining and other artifacts, allowing the faster fabrication of
smoother surfaces for the imaging step [806]. The basic workflow for FIB-SEM
analysis of a resin-embedded biological specimen consists of repeated FIB-
milling of a trench and SEM-imaging of the facet followed by 2D image-stack
registration and finally 3D reconstruction as depicted in Figure 19.

Figure 19:  Illustration of the basic workflow for FIB-SEM: a) repeated FIB-
milling of a trench followed by SEM imaging, image-stack registration and
reconstruction reproduced from Narayan and Subramaniam [805]b-d) Example of a
mouse intestinal sample, reproduced from Hartnell  _et al._ [807]

In order to obtain sufficient contrast in the SEM images the sample is usually
stained with heavy metals. Pioneering work was done by Drobne  _et al._ [808]
who investigated the digestive system of a crustacean by FIB-SEM and discussed
the possible imaging modes. In order to achieve better contrast, Leser  _et
al._ [809] systematically investigated different $\mathrm{OsO}_{4}$ and
uranylacetate staining techniques and concluded that for plastic resin
embedded samples the OTOTO method ($\mathrm{OsO}_{4}$ / thiocarbohydrazide /
$\mathrm{OsO}_{4}$ / thiocarbohydrazide / $\mathrm{OsO}_{4}$) in combination
with back-scattered electron imaging provides best results. Other protocols
involve a combination of potassium ferrocyanide, $\mathrm{OsO}_{4}$ and
uranylacetate and were successfully applied on brain [810] and bone tissue
[811] as well as for the investigation of the interaction of CNTs with lung
tissue [812]. A detailed description of standard protocols for FIB-SEM on
dried as well as plastic resin embedded (tissue) samples can be found in the
work of Drobne [813]. An alternative preparation method for FIB-SEM
investigation of cells on surfaces does not require resin embedding and full
impregnation but is based on thin layer plastification of the samples [811].

It is well known that dehydration and embedding in plastic resins introduces
artifacts and may destroy the ultra-structure of cell components. These can be
partially avoided by high-pressure or plunge freezing of the sample followed
by cryo-substitution of water and slow infiltration with an epoxy-resin. fib-
SEM imaging of the embedded sample, however, is then done at room temperature,
as described, for instance, by Schmid  _et al._ [814] for samples of the
nitrate-reducing and iron-oxidising bacteria BoFeN1333This is the same culture
as used by Joens  _et al._ [780] for HIM imaging, see Section IV.3.2. However,
by the early 2000s it became clear that the ultra-structure of cells could be
preserved even better if full cryo-workflows, where a plunge- or high-pressure
frozen specimen (still hydrated) is imaged at cryogenic temperatures, were
employed. As a first step towards cryo-FIB-SEM Marko  _et al._ [815] explored
the possibilities of “thinning of vitreously frozen biological specimens for
[…] TEM” by cryo-FIB milling of plunge-frozen water at different temperatures
and concluded that A) the experiments will have to be done below -135 to avoid
devitrification and B) that “FIB-milling of vitreous ice does not induce
heating sufficient to cause devitrification”.In 2006, Heymann  _et al._ [777]
published SEM data of plunge-frozen and FIB-milled yeast cells as well as SEM
and TEM images of FIB-milled lamella of plunge-frozen tumor tissue. Although
the frozen samples were not stained at all sufficient contrast for SEM imaging
with secondary electrons was gained “by a combination of sublimation at the
surface and metal deposition on the exposed surface”. Similar work was done by
Hayles  _et al._ [778] who used a GIS system to deposit platinum onto frozen
samples of yeast cells and a petal epidermis sample of _Nicotinia tabaccum_. A
recent overview over techniques for “cryo-FIB-SEM cross-sectioning of frozen,
hydrated life science samples” was published by Hayles and De Winter [816].

Another leap forward was the development of correlative confocal laser
scanning and FIB-SEM tomography using fluorescent dyes, high-pressure freezing
and cryo-substitution embedding[817] which has paved the way for promising
3D-correlative light-electron microscopy techniques. One of those is the
location of protein complexes in living cells at ultra-high resolution. For
that Gorelick  _et al._ [818] developed the photon ion electron microscope
(PIE-scope) which employs “integrated cryo-correlative light and FIB-SEM
microscopy” and “enables direct and rapid isolation of cellular regions
containing protein complexes of interest”. Another example is the recently
published 3D-correlative workflow combining super-resolution light microscopy
and FIB-SEM using reactive oxygen FIB spin milling to study embedded cultured
cells [819].

Driven by questions in cell biology and connectomics, strategies have been
developed to scan large volumes at high spatial resolution using FIB-SEM. For
that, Xu  _et al._ [820] developed an improved FIB-SEM analysis technique with
automated recovery from beam/system malfunctions that allowed them to image
one third of a fruit fly’s brain at a depth resolution of 8nm. In order to
scan large volumes of hard materials such as bone heavier ions with stronger
milling capacity can be used as demonstrated by Binkley  _et al._ [821] who
employed Xe-ions from a plasma source to obtain a tomogram of human bone by
FIB-SEM.

In the context of the CoVid-19 pandemic FIB-SEM tomography proved a valuable
tool to understand the microscopic mechanisms of the disease. Baena  _et al._
[822] employed FIB-SEM to analyse how SARS-CoV-2 spreads from infected cells
to new hosts as shown in Figure 20. Using a combination of TEM-tomography and
FIB-SEM Cortese  _et al._ [823] were able to visualise morphological changes
of SARS-CoV-2-infected lung cells. In a recent study on the frequently
observed infection of the human kidney by SARS-CoV-2 FIB-SEM was used to image
virus-particles in vacuoles[824].

Figure 20:  (a) FIB-SEM images of two 8nm slices showing two contacted (yellow) Vero E6 cells (green, brown) and SARS-CoV-2 particles in the extracellular space (arrows). Inset scale bar: 200nm. (b) 3D reconstruction of the plasma membranes of the two cells shown in (a). The junction-mediated contact between the cells is coloured in yellow. The virus particles are depicted in red and show a different density on either side of the junction. Data reproduced from Baena  _et al._ [822]. Table 7: Overview of FIB based imaging and analysis in the life sciences. |  Application |  Technique |  Experiment
---|---|---|---
molecules |  localisation of proteins |  cryo-FIB-SEM |  protein-detection in vitrified HeLa-cells using gold-conjugated antibodies against RNA polymerase II [825]
|  |  HIM & LSM |  detection of quantum-dot labelled proteins[826]
|  |  ToF-SIMS |  detection of proteins on DNA bio-sensor chip[827]
|  metabolic imaging |  OrbiSIMS |  imaging of the distribution of neurotransmitters in mouse hippocampus[828]
|  |  |  3D metabolic imaging of _Paramecium caudatum_ using orbitrap-MS coupled to TOF-SIMS[829]
virus- & nano-particles |  virus imaging |  HIM |  imaging of bacteriophage-infection[784, 783], and transport by bacteria[785]
|  |  |  imaging of SARS-CoV-2 infected vero-cells[788, 830]
|  |  FIB-SEM |  investigations into SARS-CoV-2 viral density at cell-cell contacts [822]
|  nano-particle – |  HIM |
|  cell interactions |  HIM-SIMS |  investigation of biogenic nanoparticles by HIM-SIMS[831]
|  |  ToF-SIMS |  3D-imaging of nanoparticles in an algal bio-film[832]
cell-level |  imaging of microbial cells |  HIM |  Joens  _et al._ [780], Chen  _et al._ [790]
|  & 3D remodelling |  FIB-SEM |  Ballerini  _et al._ [769], Drobne  _et al._ [808], Decelle  _et al._ [833]
|  |  cryo-FIB-SEM |  Heymann  _et al._ [777], Hayles  _et al._ [778]
|  imaging of mammalian cells |  HIM |  imaging of mitotic HeLa cells[780], visualisation of lipid nanodomains in human neural stem-cells [798]
|  sub-cellular element mapping |  nanoSIMS, ToF-SIMS |  mapping of nitrogen/phosphorus ratio in a photosymbiotic _Acantharia_ -microalgae system [833]
|  |  PIXE |  elemental analysis of hair, skin, nervous tissue [834]
|  |  |  identification of Ni-U-phosphate deposits in bacteria [835]
|  metabolic activity measurements |  nanoSIMS |  Musat  _et al._ [836], Calabrese  _et al._ [837]
|  biomarker imaging of single cells |  ToF-SIMS |  Leefmann  _et al._ [838]
|  bio-films |  HIM |
|  chemical analysis of bio-films |  ToF-SIMS |  Moreno  _et al._ [839]
|  bacterial predators |  HIM |  imaging of the different stages of the life-cycle of _Bdellovibrio bacteriovorus_ [791]
|  geomicrobiology |  HIM |  imaging of iron-oxidising bacteria [780, 840]
|  |  HIM & ToF-SIMS |  iron corrosion by methanogens [841]
|  bio-mineralisation |  ToF-SIMS |  Laufer  _et al._ [842]
|  anti-microbial properties of surfaces |  HIM milling |  investigation of the anti-bacterial properties of the nanostructures on dragonfly wings [801]

####  IV.3.4 FIB-based tomography of energy materials

One of the very first applications of FIB tomography in energy materials
research was presented by Wilson  _et al._ [843] in 2006. They investigated a
solid oxide fuel cell anode based on yttrium stabilized zirconia (YSZ) and
demonstrated how to separate the YSZ from the Ni and pore structure in a
three-dimensional reconstruction of their sample. The presented detail of the
3D structure enabled them to quantify important structural features such as
volume fractions, surfaces and even information about the so-called three-
phase boundary.

In 2010, Ostadi  _et al._ [774] investigated a microporous layer (MPL) used in
a hydrogen-powered proton exchange membrane fuel cell (PEMFC). FIB tomography
was used to complement the X-ray tomographic investigations of the fuel cell
electrode structure in order to record the nanostructure of the microporous
layer (MPL), which can hardly be resolved with standard X-ray imaging
equipment due to the limited spatial resolutions of ≈1 compared to FIB
tomography (≈10nm). The porous MPL structure was reconstructed three-
dimensionally and the porosity and pore size distribution analyzed. The
obtained 3D data set were used as input for simulation of a single-phase flow
through the MPL with lattice Boltzmann techniques.

In the same year Zils  _et al._ [844] have demonstrated how FIB tomography can
be used to study fabrication-structure-properties relationships (i.e. how
material manufacturing parameters are related to the 3D features in the
structure). For the development of catalyst electrode materials for PEMFC,
they compared the pore size distribution and porosity for different catalyst
electrode materials and related the 3D structural features to the performance
of the materials. Schulenburg  _et al._ [845] have used FIB tomography to
study the degradation effects in the 3D structure of carbon based fuel cell
electrodes after several start-stop cycles. They found a breakdown of the
entire nanoporous structure, which could lead to a significant reduction in
the supply of reaction gases to the catalyst. In combination with other (X-ray
based) tomographic imaging techniques and structural modelling, FIB tomography
can also be used for correlative tomographic imaging [846] to fill in missing
information at the nanometer scale and to produce multiscale 3D data covering
structural features at a broad length scale. Zielke  _et al._ [847] have shown
how FIB tomography can be used to supplement the information missing in
synchrotron tomography data due to the limited spatial resolution. The high-
resolution 3D data obtained with FIB was used to create a structural model at
the nanometer scale, which was used to fill the synchrotron data set with
nanometer detail [847]. In a recent study Paulisch  _et al._ [848] used FIB
tomography to analyze the complex three-dimensional path network inside silver
gas diffusion electrodes (Figure 21). 3D data acquired with FIB tomography can
also be used for mathematical modeling of 3D structures of energy materials
[849]. The artificially computer created (modelled) 3D structures can be later
used for the development of digital twins and for future virtual materials
design.

Today, FIB tomography can be seen as an established tool for the study of
materials in energy research, especially for battery materials [850, 851, 852,
853, 854, 855, 856, 857, 858, 859, 860], fuel cells [861, 862, 863, 864],
electrolyzers [865, 866, 867, 868] and catalytic materials [869, 870, 871,
872].

Figure 21:  FIB tomography of a silver electrode: grey: silver gas diffusion
electrode, green: binder/PTFE. Only the 3D image can reveal the complex paths
inside the pore system (Paulisch  _et al._ [848])

FIB tomography is also useful to study materials that are relatively sensitive
to ion beam damage. For example Dong et al were recently able to resolve the
inner structure of Lithium dendrites with FIB tomography [873]. The study
revealed new details about the correlation between Li dendrite growth
conditions and their 3D morphology. For such sensitive samples, cryo-FIB
tomography has recently become increasingly popular as radiation damage can be
significantly reduced at low temperatures [874, 875, 876, 873].

####  IV.3.5 Data processing of FIB-based tomographies

With the growing volume of data, the analysis of large tensors containing
mostly grey scale information is becoming increasingly challenging.
Sophisticated analysis requires data classification, i.e. assigning a class to
each point. This is particularly challenging for FIB-based tomography, where a
measurement contains a large number of classes, but in addition artefacts need
to be detected and addressed.

Here, machine learning approaches, especially easy-to-use mostly random forest
based tools such as Ilastik [877] or the trainable Weka segmentation [878],
become more and more established for image annotation and classification.

One of the major issues in tomographic imaging of porous materials is the
problem of separating the foreground from the background. If possible, pore
infiltration using carbon-based resins is therefore carried out. Silicone-
based resins are frequently used for energy materials due to their generally
high carbon content [879]. Due to sample alteration or inaccessibility of pore
systems, sample infiltration is often either impossible or undesirable. Thus,
when the ion beam cuts through a pore, the electron beam always also
illuminates the background of the pore. In such cases a 3D reconstruction can
no longer be done in a simple way, because only the foreground around the pore
edges of the samples represents the actual material distribution. To address
this issue the optimized algorithm of Salzer  _et al._ [880] incorporates
information from all sequentially measured layers, resulting in the first good
reconstructions on suitable single phase porous samples. Meanwhile, numerous
other techniques have been developed, resulting in better and more reliable
results [881, 882, 883]. Machine learning tools have recently been developed
for this purpose [884, 885, 886]. Osenberg  _et al._ [887] have shown a way to
combine two different signals (InLens and back scattering) together with a
machine learning algorithm to obtain better results for the separation of
foreground and background in case of NMC battery electrode materials. However,
despite much progress, the general problem is still not completely solved for
all types of material structures.

####  IV.3.6 Outlook

During the past twenty years FIB-SEM has become a well established technique
for investigations into the three-dimensional structure of complex specimens,
often with fully established cryo-workflows.

Further improvements in sample preparation and control of heat generation
under the ion beam could enable precise nanometer-scale cutting with the ion
beam to study the internal structure of biological samples, but also reduce
artefacts in tomography of energy materials, as these may consist of fine and
heat-sensitive components such as polymers.

In parallel, the ever growing and complex data volumes demand more and more
automated analysis pipelines. To make this possible, standardised data and
metadata formats are needed. The combination of standardised data sets and
high quality individual image classifications, generated e.g. based on random
forest models, would then allow for the compilation of diverse training sets
to train deep learning models.

With sufficient training data, neural networks such as the U-Nets [888] can be
trained and applied to data that is very different from the original training
set itself [779].

On the instrument side, great progress has been made in increasing the
accessible volumes in FIB-based tomographies through the use of plasma sources
for heavy noble gases, especially xenon. Together with advances in automation
of data acquisition and analysis, tomographies of cubic millimeter volumes
with a spatial resolution of several 10 nm are now possible. Finally, complex
data from different experimental sources with different lateral resolution and
complementary information can be made available to the research community in
large multiscale atlases. This is celebrated in a particularly impressive way
in the life sciences, where, for example, Ga FIB-SEM was used to map and
reconstruct the connectome of the Drosophila fly brain[820, 889]. Also in
terms of open data, life science offers the prime example with the virtual fly
brain [890] and the fly brain atlas [891], a digital twin of Drosophila’s
brain combining huge amounts of data from different sources and methods in an
easily accessible way. Creating and analyzing such massive data in an
automated way is based on the rapid development of machine learning, which
will be one of the key factors for the future evolution of FIB technologies.

###  IV.4 Elemental Analysis using SIMS

While many correlative imaging approaches—mostly based on FIB–SEM
instruments—do exist, SIMS in the FIB is the only relevant ion beam based
analysis method used to date. However, the combination of SIMS and FIB is also
often found in dedicated SIMS instruments [892, 893]. These implementations
may provide better SIMS performance (mass resolution, sensitivity, …) due to
the use of—often two—dedicated FIB beams and a highly optimized mass
spectrometer but lack the versatility that a FIB instrument equipped with a
SIMS add-on can provide. Today GFIS based FIB instruments provide the highest
spatial resolution for SIMS applications [83, 894]. However, recently also a
LOTIS based FIB-SIMS instrument has been introduced [895].

####  IV.4.1 Overview

sims consists in irradiating the sample with a finely focused beam of ions
(the so-called primary ions) and extracting, mass-filtering and detecting the
ions sputtered from the sample surface (the so-called secondary ions). sims is
a powerful technique for analysing surfaces owing in particular to its ability
to detect all elements from hydrogen (H) to uranium (U), its excellent
sensitivity, its high dynamic range and its ability to differentiate between
isotopes. sims offers four main analysis modes, namely mass spectrum
acquisition, depth profiling, 2D imaging and 3D imaging. In addition, SIMS
does not require any complex sample preparation (in contrast to techniques
such as EDS or electron energy loss spectroscopy (EELS) performed on TEM or
APT).

Therefore, equipping FIB-based instruments with a SIMS system adds unique
analytical capabilities for 3D chemical characterisation. Furthermore, the
availability of SIMS on FIB instruments offers unique workflows for multimodal
analytics by correlating the SIMS data with other imaging/analytical
techniques available on these FIB platforms (e.g. SE-imaging, EDS, EBSD,
etc.).

####  IV.4.2 Applications in materials science

sims on FIB(-SEM) instruments has been applied to a number of topics in
materials science, in particular for the nano-characterization of complex 3D
architectures and compositions. Microelectronic devices are a typical example
in this context, where 2D or even 3D SIMS imaging provide the required
information with unique lateral and depth resolution [896]. Figure 22 shows as
an example a 3D analysis of a fin field-effect transistor (FinFET) [86]. The
spatial resolution of this 3D SIMS map obtained with a magnetic sector SIMS
system installed on a HIM is better than 15. Such 3D maps can be used for end
pointing and circuit editing applications.

Figure 22: SE and SIMS images of a FinFET obtained on a HIM equipped with a
magnetic sector SIMS system. The SE image was taken with a 25 He+ beam (a) and
the SIMS images of the 28Si and 63Cu were acquired with a 20 Ne+ beam (b to e)
in the zone identified by the white square on the SE image (a). Eight
successive SIMS images (noted 1 to 8, (c)) were taken on the same area (FOV
3x3) allowing to determine the 3D composition of the FinFET. Image (b)
corresponds to the top surface (first slice) and the images (d) and (e)
correspond to the 7${}^{\text{th}}$ slice; reproduced from [86]

There are also a number of examples where FIB based SIMS has been used as a
major asset in the development of technologies in the fields of photovoltaics
and battery materials. The latest advances in photovoltaic conversion
technologies are based on thin films, whether second generation, such as
copper indium gallium selenide (CIGS), or third generation dye-based, such as
lead halide perovskites, and their development requires a very comprehensive
understanding in order to correlate structure and chemical composition with
performance and ageing. FIB based SIMS studies allowed addressing many
questions related to the chemical heterogeneity of grains [897] and grain
boundaries [97, 898], precipitation of secondary phases (e.g. PbI2), or
chemical and structural modification at the interfaces with charge-collecting
electrodes [899, 900, 901]. These optimizations have helped realize new
photovoltaic cells with an efficiency approaching 25%.

In batteries, SIMS technology allows the detection of lithium (in addition to
any other elements of interest) with a very high sensitivity. Therefore the Li
gradient can be mapped over several orders of magnitude and at highest spatial
resolution across the different surfaces and interfaces in batteries [97, 902,
903, 904, 151, 905, 906].

Further examples of application of FIB-SIMS in materials science include
petroleum based polyolefin plastics [88], polyester and melamine resins [907],
the investigation of alloys and superalloys [908, 909, 910], the study of
nanoparticles [911, 912, 913, 914], the investigation of chemical
inhomogeneities in grain sizes between 50 and 200 in Delafossite materials
[915], oxygen diffusion in grain boundaries [916] the distribution of rare
earths in optical fibres [917, 918] and characterizing thin films [150, 919].

####  IV.4.3 Applications in life sciences

Ion-microscopy has been used for chemical micro-analytics and imaging of
biological specimens since the 1970s when high-energy PIXE was found to be a
valuable application of ion-beams to determine trace elements in tissue
section [920]. By the beginning of the 1990s accelerator-based proton beams
could be focused down to 1 and were ready for elemental mapping of trace
elements in biological specimens [834]. The development of high-brightness
LMIS in the second-half of the 1970s [31] also allowed for introducing medium-
energy (<100keV) ion-beam microprobe-techniques to bio-imaging and micro-
analysis; in particular in the field of SIMS [921, 922]. Already at that time
it turned out that SIMS is advantageous for biological applications because of
its low detection limits but also its sensitivity to different isotopes of
chemical elements.
Hence, In the life sciences numerous exciting studies based on imaging SIMS
exist [923]. For example, FIB-SIMS has been used to study the spatially
resolved chemical signatures of the surface and the interior of mammalian
individual cells [924] and bone tissue [925]. The Cameca nanoSIMS—a sector-
field secondary ion mass spectrometer with about 50 lateral resolution—is an
important tool for sub-cellular chemical and isotopic micro-analysis in the
analytical toolbox of the life sciences [926]. It was designed to achieve a
mass resolution high enough to detect the stable isotopes of elements such as
carbon and nitrogen (${}^{13}\mathrm{C}$ and ${}^{15}\mathrm{N}$) which are
commonly used for isotope-labelling experiments [836]. Furthermore, time-of-
flight mass spectrometer based SIMS techniques for 2D and 3D imaging are
becoming increasingly important in the life sciences [923, 794]. Metabolic
imaging on a sub-cellular level and a mass-resolution of 240,000 was recently
achieved by combining TOF-SIMS with an orbitrap mass-analyzer [828]. It was
the application of gas field-ionization source that allowed to focus ion beams
to sub-nanometer spots. HIMs equipped with SIMS spectrometers are not
chemically-blind anymore and provide a new possibility to study bio-
mineralisation processes such as tooth or bone formation as well as microbial
corrosion, and many others in FIB-SIMS. Being implemented in the scanning
helium ion microscope this technique paved the way for numerous high-
resolution analyses of micro-organisms, viruses, cells, small animals, plants
etc. [782]. The development of SIMS spectrometers for the HIM not only added
micro-analytical capabilities to the HIM but also significantly improved the
lateral resolution of SIMS in general.

Recent examples of such applications include the localisation and
identification of silver nanoparticles and nanowires in intestinal or alveolar
cell cultures [927, 912] and the characterisation of biogenic nanoparticles
produced by bacteria [831].

A recently developed GFIS based variant of the standard HIM enables
correlative imaging using SE, STIM [109], and SIMS signals [156].

This was used to perform a correlative SE, STIM [109] and SIMS investigation
of thin tissue sections of Daphnia magna exposed to TiO2 nanoparticles (Figure
23) [156]. In this nano-toxicological test study the machine demonstrated
excellent contrast on biological structures as well as on the incorporated
inorganic nanoparticles, e.g. the particles were shown to accumulate in the
gut without penetration of the epithelial barrier [156].

Figure 23: npSCOPE correlative high resolution imaging and nano-analytics on
keratinocyte cell cultures exposed to 30 Si-Al-TiO2 nanoparticles. (a) SE
imaging (HeSE), (b) HeSTIM bright field imaging, (c) SIMS false color image of
CN (green) and Ti-species (red), (d) SIMS spectrum (NeSIMS). SE: FOV [product-
units=single]15x15, [product-units=brackets]1024x1024, dwell time 1; STIM: FOV
[product-units=single]8x8, beam current 2, dwell time 400, [product-
units=brackets]512x512; SIMS negative mode: FOV [product-units=single]8x8,
magnetic field 300, dwell time 9000, [product-units=brackets]256x256; SIMS
positive mode: FOV [product-units=single]8x8, magnetic field 325, dwell time
4000, [product-units=brackets]256x256.

In future one may anticipate novel SIMS approaches for biological questions.
On the one hand the very high mass resolution of OrbiSIMS does allow for
chemical micro-mapping of complex bio-molecules in cells and tissues, albeit
with a very limited lateral resolution in the µm range. On the other hand
LOTIS systems provide high brightness ion beams with extremely low spot sizes
that enable high speed SIMS at high sensitivity such that relatively large
volumes of biological samples can be chemically mapped.

Considering the prospects offered by novel highest brightness ion sources
delivering reactive species such as Cs+ and cryo-capabilities on the FIB
platforms, one of the most exciting applications of FIB based SIMS in life
sciences will become subcellular imaging, allowing for instance the
investigation of accumulations of metals, ingulfed nanoparticles or drugs in
the different cellular structures.

FIB-SIMS providing high spatial resolution analytical and structural data can
be a valuable tool in various fields beyond materials and life sciences, such
as soil science [928], geology [87] and cosmochemistry [929, 930]. It has been
also used for the analysis of cultural heritage objects [931, 932, 933].

####  IV.4.4 Outlook

Elemental analysis using FIB-SIMS can still continue the trend towards even
higher lateral and spatial resolutions. The resolution is no longer mainly
limited by the pure beam size. In HIM, lateral resolution is mainly limited by
the low signal yield and destructive nature of SIMS. To obtain the smallest
possible detection limits, as much signal as possible must be extracted from
the sputtered volume. One possibility is the use of other projectile ions
which achieve a higher useful yield of sputtered ions. However, most ions only
achieve a higher yield of either positive or negative ions. Higher yields of
positive ions, which are particularly suitable for the detection of metal
elements, are achieved by projectiles on ions with high electro-negativity
such as oxygen or halogen ions. Future developments could therefore be
achieved by smaller spot sizes from plasma FIBs or the use of ILIS for FIBs.
Higher yields of negative ions are achieved by using projectiles that lower
the work function of the sample surface. Recent developments in the direction
will already be possible in the near future by using SIMS spectrometers on
FIBs using LOTIS [895]. Alternatively, the use of precursor gases could also
increase the yield of ions.

One obvious approach to increase the ion yield and therefore also the spatial
resolution is to further develop SNMS for FIBs. A major drawback of SIMS is
the difficult quantification due to the matrix effect. The use of lasers for
post-ionization reduces the dependence of the ionization process at the sample
surface to controlled, sample-independent ionization by photons. Due to the
required high laser intensity, SNMS is only possible in pulsed operation. This
inevitably requires pulsing of the primary ion beam. For this reason, a
combination with TOF spectrometers is advantageous and obvious. Post-
ionization with focused electron beams is also conceivable, although
experimental preliminary work in this area remains rare.

Another problem of elemental analysis in FIBs is the sample intermixing
behavior from the primary ions used. To achieve the highest possible beam
resolutions, comparatively high energies in the range of
$20\text{\,}\mathrm{keV}50\text{\,}\mathrm{keV}$ are typically used. The high
energy has the disadvantage of a long range of ions in the target compared to
low energy argon, which is commonly used for depth profiling with SIMS. This
quickly leads to mixing of deeper layers and therefore to decreasing depth
resolution with increasing sputter depth [934]. High spatial resolution could
be achieved in the future by using projectile ions with high atomic number
and/or small projectile energy per nucleon. Cs from LOTIS FIBs or Xe from GFIS
FIBs could provide both small beam sizes and good depth resolutions.
Alternatively, the energy per nucleon is also reduced by using cluster ions
such as bismuth or gold clusters from LMAIS.

Small cluster ions [935], reactive projectile ions, or laser post-ionization
can also reduce fragmentation of molecules—another aim for future
developments. The fragmentation of molecules would need to be understood both
theoretically and experimentally in order to deduce the molecular composition
of the sample from measured spectra. The creation of molecular fragmentation
databases for typically used ion energies and projectiles would enable
fingerprinting in the future.

Another focus is of course the further development of spectrometers. Important
is the complete detection of all sputtered ions which is currently already
possible by the use of TOF spectrometers or magnetic sectors with large area
MCP. A possible further development would be the combination of fib with
spectrometers that can separate isobars. The results already shown with
Orbitraps, for example, are very promising [828].

What has already been shown individually, in the perfect machine all
parameters such as spatial resolution, mass resolution, detection limit as
well as measurement time should be optimized simultaneously. In addition, an
in-situ combination of elemental analysis in the FIB with other, for example,
electron beam-based analytical methods would be beneficial. The combination
with focused electron beams would also be possible for charge compensation of
insulating sample surfaces. In-situ AFM would allow the correlation of the
acquired signal versus fluence with true sputtering depths. The reconstruction
of measured signals from three-dimensional volumes will continue to be a very
difficult task in the future, which could be facilitated by the use of
electron beams and AFM.

Last but not least, most element analysis methods like SIMS require vacuum
levels better than ultra-high vacuum (UHV) in the FIB. This is a prerequisite
that is not always given so far and that should be considered by all
manufacturers in the future because of its high relevance.

###  IV.5 Applications of gas-assisted FIB processing

Table 8: Overview of applications of gas-assisted FIB-processing, in which gaseous precursor compounds are locally dissociated by the ion beam to grow nanostructures. Property |  Target Application |  Ion |  Deposit Geometry & Precursor
---|---|---|---
Electrical & electronic |  Electrical connections |  He |  semiconducting nanowires from CpPtMe3 [936], metallic Co lines from Co2(CO)8 [937]
|  |  Ne |  metallic nanowires from CpPtMe3 [936]
|  |  Ga |  conducting nanowires from CpPtMe3 [938, 939] and MeCpPtMe3 [940, 941, 942], C7H7F6O2Au [943, 944], Co(CO)3NO [945], C10H13CuF6O2Si [946], W(CO)6 contacts to Co and Cu nanowires [947, 948, 949], Pt based sidewall contacts using MeCpPtMe3 to MoSi layer stack [950]
|  Insulating barriers |  Si |  thin layer from tetramethoxysilane (Si(OCH3)4) [951]
|  |  Ga |  thin layer from tetramethoxysilane [952, 953] and pentamethylcyclopentasiloxane [954]
|  Superconductivity |  He |  planar and 3D superconducting wires from W(CO)6 [955, 956, 957, 958]
|  |  Ga |  planar nanowires W(CO)6 [959, 960, 961, 962, 963, 964, 965, 966, 967, 968, 969] and Nb(NMe2)3(N-t-Bu)[970, 971], arrays of JJs from Nb(NMe2)3(N-t-Bu) [972], 3D SQUID from W(CO)6 [973], WC nanoSQUID [974]
Magnetic |  Nanomagnets |  He |  nanowires from Co2(CO)8[937]
|  |  Ga |  nanoparticles from Co2(CO)8 [975], nanowires from Co(CO)3NO [945] and from Co2(CO)8 [976]
|  Tips for magnetic force microscopy |  Ga |  deposition of thin layer by milling Co71Cr17Pt12 target [977]
|  Nanomagnetic probes |  Ga |  filling FIB milled trenches with tungsten [978], Hall-probes from Co2(CO)8 [979]
Optical |  Photonic cavities / waveguides |  Ga |  deposition of defects in etch mask for photonic crystal [980]
|  Fresnel zone plates |  Ga |  Deposition of the central Pt beamstop [480]
|  Chiral photonic nano-antennas |  Ga |  helices from MeCpPtMe3 [981, 982, 983] and from phenanthrene [984]
|  Chiral plasmonic nano-antennas |  Ga |  helices from phenanthrene covered with gold [985, 986]
|  Chiral biosensing |  Ga |  helix arrays from MeCpPtMe3 coated with poly o-phenylediamine [987]
Mechanical |  AFM tips |  He |  hammerhead probes from MeCpPtMe3 [988]
|  Tunable elastic moduli |  Ga |  core-shell pillars and springs from phenanthrene [989, 990]
|  |  |  metal containing pillars and springs from phenanthrene and ferrocene [991], MeCpPtMe3 [992], W(CO)6 [993], tetramethylcyclotetrasiloxane (TMCTS) and oxygen (O2) [994]

Direct bottom-up writing of nanostructures with a focused ion beam is
powerful, flexible, and conceptually simple, but at the same time extremely
complex in the chemical and physical processes involved. In addition to the
surface processes and electron-driven chemistry that also occur in direct
writing with electron beams, competition with physical sputtering, and thermal
or ion-induced structural changes contribute here to the shape and
microstructure of the deposit. Hence, fibid strongly depends on multiple
growth conditions such as ion species, acceleration voltage, ion beam current,
ion dose, beam dwell time, scanning strategy, substrate type (insulating or
conductive), GIS nozzle position, precursor molecule (vapour pressure,
sticking coefficient to the surface, residence time, non-hazardous), precursor
temperature, base and process pressure in the vacuum chamber among others.
This makes fibid of functional nanostructures highly dependent on the
experience of the particular user and calls for both, better theoretical
understanding and empirical modeling tools that generate patterns based on few
calibration routines, thus enabling also less experienced users to fabricate
complex nanostructures. Table 8 provides an overview on the fields where gas-
assisted FIB processing has been employed so far.

####  IV.5.1 Basics of ion-induced chemistry

Ion-molecule reactions have been studied in the context of FIBID, which
involves decomposition of the precursor on the substrate surface during ion
bombardment. In FIBID of metal nanostructures from organometallic precursors,
the deposited material is composed of the metal(s) and contamination from
nonvolatile ligand-derived decomposition byproducts. Ion-induced chemistry
during FIBID is only partially understood but has been postulated to involve
ion-molecule collisions with the precursor, reactions with low energy
secondary electrons produced by impact of ions with the substrate, and thermal
processes driven by dissipation of collision energy (see also Figure 14).[396,
995]. An additional feature of FIBID is the concomitant sputtering of material
from the surface that competes with deposition. Although preferential
sputtering of ligand-derived atoms can purify the material under appropriate
conditions,[996, 413] etching of the metal will also occur and the choice of
reaction conditions is critical to obtaining deposits with high metal content.
Broad application of FIBID will require development of custom precursors that
undergo well-understood and efficient ion-induced decomposition to metal atoms
and volatile byproducts. In addition to the standard physical properties
common to all deposition methods that involve gas phase delivery of reactants
to the substrate (volatility, thermal stability, ready availability, etc.),
mechanism-based design [995, 997] of FIBID precursors will require a
fundamental understanding of ion-molecule reactions on the surface. Much of
the current understanding of these processes comes from model studies of FIBID
carried out by ion bombardment of a few monolayers of precursor molecules on a
substrate in ultra-high vacuum (UHV) [995, 997]. Although there are
differences between FIBID and its UHV models (the UHV environment is cleaner
than standard HV FIBID deposition conditions, the UHV studies are carried out
at lower temperatures, and the ion source is more diffuse), UHV studies can be
used to identify ligands that dissociate from the complex and ultimately
desorb cleanly from the surface during ion-molecule reactions. Purification of
deposits by sputtering away ligand-derived contaminants can also be modeled in
UHV. Additional mechanistic information has been obtained in gas phase studies
of ion-molecule collisions between organometallic precursors and ions of
different masses and energies [998].

As an example, a study of the reactions of Ru(CO)4I2 with 860eV Ar+ ions on a
surface in UHV demonstrated that the initial reaction was loss of all four CO
ligands to form adsorbed RuI2 [413]. Additional ion exposure resulted in
sputtering of iodine from the surface at a rate five times faster than
sputtering of Ru. These results suggest that proper optimization of FIBID
conditions could result in deposition of high metal content Ru from this
precursor. This study also highlights the difference in the charged-particle
induced reactivity between FIBID and FEBID, as modeling of the FEBID process
in UHV with 500eV electrons results in loss of the CO ligands, but not the
iodide, to afford RuI2 as the final product [999]. Rapid loss of all of the
carbonyl ligands was also observed upon ion bombardment (860eV) in a UHV model
study of the heterobimetallic precursor ($\eta^{5}$-C5H5)Fe(CO)2Re(CO)5 [996].
In contrast to the electron-induced chemistry of this complex under the same
conditions, the ion beam slowly removed the remaining carbon from the
cyclopentadienyl ligand by sputtering, leaving behind non-stoichiometric Fe/Re
material.

Additional information on ion-molecule reactions was obtained during studies
of FIBID of gold from (CH3)2Au(hfac) (hfac = hexafluoroacetylacetonate) with
He+, Ne+, Ar+, Kr+, or Xe+ at energies of
$2\text{\,}\mathrm{k}\mathrm{e}\mathrm{V}100\text{\,}\mathrm{k}\mathrm{e}\mathrm{V}$
[414, 1000]. The decomposition yield from the precursor increased with
increasing ion mass and energy, consistent with a binary collision model for
decomposition. The authors concluded that the FIBID process was driven by
energy deposition from ion-surface collisions. These results have implications
for ion source choice in FIBID, because the mass variation in ions impacts the
deposition chemistry through differences in secondary electron yields, sputter
yields and ion implantation yields. Ar+ and Ne+ generate sufficient secondary
electrons at low beam energies (30eV) but have a shallower beam penetration
depth than He+, leading to lower ion-substrate interactions. Heavier ions have
higher sputtering yields, which can remove light atom impurities but at the
cost of deposition rates, as the target material will also be sputtered away
[1001, 53].

Gas phase studies of reactions of Fe(CO)5 with He, Ne, Ar and Kr ions of
varying charge and energy [998] also demonstrated facile loss of CO ligands
upon ion-molecule collision. The distribution of fragment ions from CO loss,
Fe(CO)5-x where x=$15$, was dependent on the ion mass and the energy transfer
in the collision. Under these conditions, light ions such as He+ resulted in
electronic excitation with low fragmentation efficiency. Heavier ions yielded
more extensive CO dissociation from energy transfer and nuclear stopping. The
highest extent of CO loss occurred upon collision with Ne+, where both
electron transfer and energy transfer were significant. It was pointed out
that the gas phase results may not accurately predict behavior on a surface
during FIBID due to the heat sink behavior of the substrate. However, more
efficient fragmentation upon impact with heavier ions is to be expected.
Although there is not yet an extensive set of privileged ligands for FIBID,
some preliminary conclusions about ion-molecule chemistry of organometallic
precursors on substrate surfaces can be drawn from the mechanistic studies
described above: [995] 1) to minimize ligand-derived contamination in
deposits, ligands should be small and few in number; 2) CO ligands can be
removed quite easily by ions; 3) halide ligands can be removed by sputtering,
but more slowly than CO; 4) carbon derived from anionic $\pi$-facial ligands
such as cyclopentadienyl and allyl can be removed by sputtering but it is also
slow and competes with removal of metal.

####  IV.5.2 Nanostructures for electronics

Table 9: Overview on various precursor ion combinations and the resulting electrical properties. Material |  | Precursor
---
material
Ion | Shape |  | Composition
---
($\mathrm{mol}\text{\,}\mathrm{\char 37\relax}$)
Microstructure |  | Electric
---
behavior
| $\rho_{RT}$
---
($\mathrm{\SIUnitSymbolMicro\SIUnitSymbolOhm}\text{\,}\mathrm{cm}$)
| $\rho_{RT}$
---
bulk
($\mathrm{\SIUnitSymbolMicro\SIUnitSymbolOhm}\text{\,}\mathrm{cm}$)
Ref.
Platinum | MeCpPtMe3 | Ga+ | planar |  | Pt:C:Ga:O
---
22:60:11:7
|  $510\text{\,}\mathrm{n}\mathrm{m}$ sized
---
nanocrystals
Metal | 700 | 10.4 | 941
| CpPtMe3 | Ga+ | planar |  | Pt:C:Ga:O
---
46:24:28:2
Amorphous | Metal | 70–700 |  | 940
| MeCpPtMe3 | Ga+ | planar |  | Pt:C:Ga
---
17:72:11
|  ≈3nm sized
---
nanocrystals
Metal | 800 |  | 942
| MeCpPtMe3 | Ne+ | planar |  | Pt:C
---
17:83
|  ≈4.5nm sized
---
nanocrystals
Metal | 600 |  | 936
| MeCpPtMe3 | He+ | planar |  | Pt:C
---
16:84
|  ≈3nm sized
---
nanocrystals
Semiconductor | 180000 |  | 936
Gold | C7H7F6O2Au | Ga+ | planar |  | Au:C:Ga
---
50:35:15
— | Metal | 500–1500 | 2.4 | 943
| C7H7F6O2Au | Ga+ | planar |  | Au:C:Ga:O
---
75:<5:20:<5
— | Metal | 500–1300 |  | 944
Cobalt | Co2(CO)8 | Ga+ | planar | — | — | Metal | 189 | 6 | 975
| Co2(CO)8 | Ga+ | planar | — | amorphous | Metal | 19–38 |  | 976
| Co(CO)3NO | Ga+ | planar |  | Co:C:Ga:N:O
---
54:7:9:13:17
|  >20nm sized
---
nanocrystals
Metal | 189 |  | 945
| Co2(CO)8 | He+ | planar | — |  |  6nm sized
---
nanocrystals
Metal | 64–116 |  | 937
Copper | C10H13CuF6O2Si | Ga+ | planar |  | Cu:C
---
55:45
|  20nm sized
---
nanocrystals
Metal | 50 | 1.7 | 946
Tungsten | W(CO)6 | Ga+ | planar |  | W:C:Ga
---
40:40:20
Amorphous |  | Superconductor
---
below 5.2K
200 | 5.6 | 959, 960
| W(CO)6 | Ga+ | planar |  | W:C:Ga:O
---
40:43:10:7
|  $12\text{\,}\mathrm{n}\mathrm{m}$ sized
---
nanocrystals
| Superconductor
---
below $4.25.1\text{\,}\mathrm{K}$
275 |  | 967
| W(CO)6 | Ga+ | planar |  | W:C:Ga:O
---
53:34:11:2
|  ≈1nm sized
---
nanocrystals
| Superconductor
---
below $55.5\text{\,}\mathrm{K}$
100–350 |  | 964
| W(CO)6 | He+ | 3D |  | W:C:O
---
72:20:8
|  $2030\text{\,}\mathrm{n}\mathrm{m}$ sized
---
nanocrystals
| Superconductor
---
below $6.27.1\text{\,}\mathrm{K}$
398 |  | 955, 956, 957
Niobium | Nb(NMe2)3(N-t-Bu) | Ga+ | planar |  | Nb:C:Ga:N
---
29:43:15:13
| 1$520\text{\,}\mathrm{n}\mathrm{m}$ sized
---
nanocrystals
| Superconductor
---
below 5.0K
550 | 15 | 970
| Nb(NMe2)3(N-t-Bu) | Ga+ | 3D | — |  |  $1520\text{\,}\mathrm{n}\mathrm{m}$ sized
---
nanocrystals
| Superconductor
---
below 8.1K
380 |  | 970

The ease to directly write functional structures with different conductivity
regimes render fibid a powerful tool in electronic applications. At least
three different electric conductivity regimes are reported for materials grown
using fibid: semiconducting, metallic and superconducting at low temperature.
In this regard, semiconducting and metallic platinum (Pt), gold (Au), cobalt
(Co) and copper (Cu) based deposits were grown using a variety of precursor
compounds (cf. Table 9) mostly under use of Ga ions. Thus, Ga+ FIB is the
ionic species used in the process when no other is mentioned. As the actual
content of carbon as well as the micro-structure of the deposit depends on the
actual growth conditions, this offers an efficient way to tune electrical and
electronic behavior. Examples include Pt [941] and Au [943, 944] for which the
conductivity increases with thickness for the as-grown material. Pt-based
deposits below 50 in thickness behave as semiconductors; for 50 in thickness
and above, they behave as metals [940] (reaching the threshold of 3000 for
metallic conduction [1002]) with metallic content <33at.% and exhibiting fcc
Pt nanocrystals with diameters from
$5\text{\,}\mathrm{nm}10\text{\,}\mathrm{nm}$ embedded in an amorphous carbon
matrix [942]. Additionally, using Ne+ FIB, Pt deposits behave as metals
whereas they behave as semiconductors using He+ FIB [936]. In the case of
gold-based deposits, its high gold content (75 at. % Au) allows obtaining
metallic deposits with $\rho_{RT}$ around 500 but still two orders of
magnitude above the bulk resistivity.

As-grown [975, 1003] and annealed [945] Co deposits (50at.% Co) are
ferromagnetic with $\rho_{RT}=$189 and 62 ($\rho_{RT}$ Co bulk=6),
respectively. Using He+ FIB, metallic Co 10-wide lines were grown with similar
$\rho_{RT}$ values [937]. Cu deposits behave as metals with 55at.% Cu and
20-sized crystals embedded in an amorphous C matrix and their conductivity
increasing with the ion beam current [946].

Other interesting materials deposited with FIBID exhibited metallic behavior
at room temperature, while at low temperature they transitioned to the
superconducting state. This is the case for superconducting tungsten (W) and
niobium (Nb) based nanostructures grown using W(CO)6 and Nb(Nme2)3(N-t-Bu) as
precursor materials, respectively. Particularly, WC- and NbC- deposits behave
as superconductors below $4.2\text{\,}\mathrm{K}5.1\text{\,}\mathrm{K}$ [959,
960, 967, 964] (Tc W bulk=15) and 5[970] (Tc Nb bulk=9.7), respectively.

On the other hand, freestanding 3D NbC nanowires exhibit a broadened
superconducting transition between
$4\text{\,}\mathrm{K}11\text{\,}\mathrm{K}$. The composition is around
$40\text{\,}\mathrm{a}\mathrm{t}\,\%50\text{\,}\mathrm{a}\mathrm{t}\,\%$ W for
WC deposits, and 29at.% Nb for NbC deposits and their microstructure has
short-range order (1-sized crystals) for the former and
$15\text{\,}\mathrm{nm}20\text{\,}\mathrm{nm}$-sized crystals of fcc NbC phase
for the latter. It is worth mentioning that reasonably high values of the
superconducting parameters are found for WC nanostructures, such as the upper
critical magnetic field Bc2(2K)=$7\text{\,}\mathrm{T}8.5\text{\,}\mathrm{T}$
[967, 965] and critical current density
Jc(2K)=$0.01\text{\,}\mathrm{MA}\text{\,}{\mathrm{cm}}^{-2}0.1\text{\,}\mathrm{MA}\text{\,}{\mathrm{cm}}^{-2}$
[959, 967, 962, 961, 963]. For narrower nanostructures (≤50 in width), finite
size effects which are key to their application to superconducting circuits,
have been studied. This includes a magnetic field-driven reentrance of the
superconductivity [966]; the occurrence of non-local voltages [968, 969], and
electric field-induced control of superconductivity [958]. He+ FIB enabled the
growth of fancied shaped 3D WC nanosuperconductors with outstanding
capabilities (Tc=$6.2\text{\,}\mathrm{K}7.1\text{\,}\mathrm{K}$,
Bc2(0)=$12\text{\,}\mathrm{T}15\text{\,}\mathrm{T}$), such as hollow nanowires
(32 in diameter and an aspect ratio of $\approx 200$) [955, 957] and nano-
helices (100 in diameter, and an aspect ratio of $\approx 65$) [956](Figure
24), cf. Fig. 24. These nanostructures exhibit a metallic content of 70at.% W
and consist of $20\text{\,}\mathrm{nm}30\text{\,}\mathrm{nm}$-sized fcc
WC1$-$x  crystals.

Figure 24: fibid. (a) SEMimage of a hollow crystalline W-C 3D superconducting
nanopillar grown by He+ FIBID. (b) Cross-sectional TEM image of the hollow
nanowire. (c) High-magnification SEM image of (a). Adapted with permission
from Córdoba  _et al._ [955] ©(2018) American Chemical Society. (d)
Superconducting W-C 3D nano-helix grown by He+ FIBID. Inset shows its top
view. (e) Superconducting transition of the nano-helix. Inset shows the nano-
helix contacted for the electrical transport measurements. Adapted with
permission from Córdoba  _et al._ [968] ©(2019) American Chemical Society.

####  IV.5.3 Nanostructures for mechanics

One of the main advantages of FIBID is the capability of directly writing
high-aspect ratio structures onto any substrate topography. When it comes to
mechanical applications, this would allow to place dedicated tips on top of
AFM cantilevers and place springs into prefabricated mechanical devices. A a
recent review by Utke  _et al._ [1004], summarizes the mechanical properties
of all bottom-up grown FIBID pillars and springs. All were deposited by Ga+
ions (mostly within the range of
$10\text{\,}\mathrm{keV}30\text{\,}\mathrm{keV}$ ion energy,
$0.5\text{\,}\mathrm{pA}9\text{\,}\mathrm{pA}$ beam current). The most
interesting finding was that the gallium-FIBID pillars tend to grow as core-
shell structures. Using phenenthrene (C14H10), the elastic moduli of the
hydrogenated carbonaceous material were ≈300 (stiff core with Ga implantation,
low H content) and ≈30 (soft shell, presumably high H content) [989, 990].
Depending on the inner diameter of the core and the thickness of the shell,
the total elastic modulus ranges between these boundary values. Metal
containing pillars with <40at.%, i.e. below percolation, are dominated in
their mechanical properties by the co-deposited carbonaceous matrix [1004].
Larger metal contents in pillars and elastic moduli sum up as follows (metal
at.% / elastic modulus normalized to pure metal): Fe (21 at.% / 0.4) [991], Pt
(60 at.% / 0.8) [992], W (80 at.% / 0.4) [993], SiO2 (95 at.% / 0.8) [994].
The non-correlation between metal content and elastic pillar modulus may be
due to Ga implantation, which softens the metals. Furthermore, the
carbonaceous matrix stiffens or softens the pillar depending on its sp2 vs.