<table><caption>TABLE VI. 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.</caption><thead><tr><th>Engineered property</th><th>Experiment</th><th>Ion</th><th>Material/device</th></tr></thead><tbody><tr><td rowspan="10">Electrical and electronic</td><td rowspan="3">Conductivity tuning</td><td>He</td><td>Graphene,<sup>681-686</sup> few-layer/monolayer MoS<sub>2</sub>,<sup>687-689</sup> epitaxial MoS<sub>2</sub>,<sup>690</sup> few-layer/monolayer WSe<sub>2</sub>,<sup>688,691</sup> monolayer WSe<sub>2</sub>,<sup>688</sup> InGaZnO thin film<sup>692</sup></td></tr><tr><td>Ne</td><td>Si nanocrystals (self-assembly of) in buried silica layer<sup>410</sup></td></tr><tr><td>Ga</td><td>AlGaAs/GaAs quantum wires,<sup>693-696</sup> GaAs quantum constrictions,<sup>697</sup> GaN nanowires,<sup>698</sup> 2D MoSe<sub>2</sub>/graphene heterostructure,<sup>699</sup> MoSi superconducting thin film,<sup>700</sup> In<sub>2</sub>O<sub>3</sub> thin film,<sup>701</sup> Al<sub>2</sub>O<sub>3</sub> film,<sup>702</sup> ZnO and VO<sub>2</sub><sup>703</sup></td></tr><tr><td rowspan="2">Formation of barriers and nanoconstrictions</td><td>Si</td><td>AlGaAs/GaAs quantum wires<sup>704</sup></td></tr><tr><td>He</td><td>Superconducting electronic circuitry including Josephson junctions and nanoSQUIDs in YBCO<sup>705-711,1198</sup> and MgB<sub>2</sub>,<sup>712</sup> nanoconstrictions in BSCCO<sup>713,714</sup></td></tr><tr><td>Tuning thermoelectric properties</td><td>He</td><td>quantum dots in single-walled CNT<sup>715</sup></td></tr><tr><td>Tuning superconductivity</td><td>He</td><td>MoSe<sub>2</sub> thin films<sup>716</sup></td></tr><tr><td>Pinning ferroelectric domains</td><td>He</td><td>Periodic arrays of artificial pinning sites in YBCO<sup>717,718</sup></td></tr><tr><td>Ferroelectric phase change</td><td>He</td><td>PbZr<sub>0.2</sub>Ti<sub>0.8</sub>O<sub>3</sub> thin film,<sup>719</sup> multilayer MoTe<sub>2</sub> flake<sup>720</sup></td></tr><tr><td rowspan="2">Magnetic</td><td rowspan="2">Tuning magnetic anisotropy</td><td>He</td><td>Co/Pt multilayers,<sup>726</sup> Ir<sub>17</sub>Mn<sub>83</sub>/Co<sub>70</sub>Fe<sub>30</sub> bilayer,<sup>727</sup> Co-based thin-film stack,<sup>728,729</sup> Co/Pt/Ru multilayer system<sup>730</sup> skyrmions in Pt/Co/MgO thin film,<sup>731</sup> and in Pt/Co<sub>60</sub>Fe<sub>25</sub>B<sub>15</sub>/MgO thin film<sup>732</sup></td></tr><tr><td>Si/Ge</td><td>Bi and Ga substituted YIG<sup>733</sup></td></tr><tr><td rowspan="2">Tuning metamagnetic transition temperature</td><td>He</td><td>CoPt multilayers,<sup>734</sup> Fe<sub>78</sub>Ni<sub>22</sub> thin film,<sup>735</sup> Ir/Co/Pt multilayers<sup>736</sup> skyrmions in FeGe thin plate,<sup>737</sup> and in Co/Pt multilayers<sup>738-740</sup></td></tr><tr><td>Ne</td><td>Fe<sub>60</sub>Al<sub>40</sub> thin film<sup>544,742</sup></td></tr><tr><td rowspan="2">Inducing ferromagnetism</td><td>Ge</td><td>Fe<sub>60</sub>Al<sub>40</sub> alloy<sup>743</sup> and Fe<sub>78</sub>Ni<sub>22</sub> on copper<sup>744</sup></td></tr><tr><td>Magnonics</td><td>Patterned Fe<sub>78</sub>Ni<sub>22</sub> films,<sup>735</sup> spin wave optical elements in YIG<sup>745</sup></td></tr><tr><td rowspan="10">Optical and quantum</td><td rowspan="2">Tuning photoluminescence</td><td>He</td><td>SiN<sub>x</sub> membrane,<sup>746</sup> monolayer MoSe<sub>2</sub>,<sup>747</sup> InGaAs/GaAs quantum well,<sup>748</sup> reducing parasitic fluorescence in hBN<sup>749</sup></td></tr><tr><td>Ge</td><td>AlGaAs/GaAs and GaInAsP/InP quantum wells<sup>750</sup></td></tr><tr><td rowspan="2">Tuning of passive optical components</td><td>He</td><td>Plasmonic resonance in graphene nanostructures,<sup>751</sup> Bragg grating in silica nanofiber<sup>752</sup></td></tr><tr><td>Li</td><td>Si microdisc nanophotonic resonator<sup>753</sup></td></tr><tr><td rowspan="2">Creation of photoluminescence, quantum emitters and qubits</td><td>He</td><td>ZnSe quantum dot micropillar cavities,<sup>754</sup> periodic poling of LiNb waveguide<sup>755</sup></td></tr><tr><td>Li</td><td>NV centers in diamond with substitutional nitrogen,<sup>756,757</sup> Si vacancy centers in SiC,<sup>758,759</sup> luminescent defects in monolayer MoS<sub>2</sub> (Refs. 760 and 761)</td></tr><tr><td rowspan="2">Si</td><td>Si vacancy centers in SiC<sup>762</sup></td></tr><tr><td>Si vacancy centers in diamond<sup>763</sup> and diamond nanostructures<sup>764</sup>, W and G centers in silicon<sup>765</sup>, isotopic enrichment of <sup>28</sup>Si to increase spin qubit coherence times<sup>766</sup></td></tr><tr><td>Ar</td><td>NV centers in diamond<sup>767</sup></td></tr><tr><td>P</td><td>Deterministic single-atom implantation of <sup>31</sup>P into Si<sup>293</sup></td></tr><tr><td>Ga</td><td>Luminescent defects in hBN,<sup>768,769</sup> monolayer WSe<sub>2</sub>,<sup>770</sup> MoS<sub>2</sub> and WS<sub>2</sub><sup>771</sup></td></tr><tr><td>Ge</td><td>Ge vacancy centers in diamond<sup>772</sup></td></tr></tbody></table>
<table><caption>TABLE VI. (Continued.)</caption><thead><tr><th>Engineered property</th><th>Experiment</th><th>Ion</th><th>Material/device</th></tr></thead><tbody><tr><td rowspan="3">Chemical</td><td>Enhancing chemical etch rates</td><td>Sb, Si</td><td>Deterministic single-atom implantation into Si<sup>773</sup></td></tr><tr><td>Enhancing catalytic activity</td><td>Xe</td><td>Recoil implantation of color centers in diamond,<sup>774</sup> spin defects in hexagonal boron nitride (hBN),<sup>775</sup> water assisted fabrication of extended defects in hexagonal boron nitride (hBN)<sup>776</sup></td></tr><tr><td>Nucleation of growth</td><td>Bi</td><td>Qubits in silicon and germanium<sup>777</sup></td></tr><tr><td rowspan="6">Thermal</td><td>Enhancing chemical etch rates</td><td>He</td><td>Si<sub>3</sub>N<sub>4</sub> thin film,<sup>778</sup> SiO<sub>2</sub> thin film,<sup>779</sup> mono-/bilayer MoS<sub>2</sub><sup>780</sup></td></tr><tr><td>Enhancing catalytic activity</td><td>He</td><td>MoS<sub>2</sub> and MoSe<sub>2</sub> flakes<sup>781</sup></td></tr><tr><td rowspan="3">Functionalization</td><td>He</td><td>Epitaxial graphene on SiC<sup>782</sup></td></tr><tr><td>Co</td><td>CoSi<sub>2</sub> nanowires in Co-saturated Si<sup>783</sup></td></tr><tr><td>Ga</td><td>InAs dots on GaAs,<sup>784</sup> Ge dots on Si<sup>785,786</sup></td></tr><tr><td rowspan="2">Tuning surface wettability</td><td>Ga</td><td>Graphene (fluorination using XeF<sub>2</sub>)<sup>787</sup></td></tr><tr><td>Ga</td><td>Molecular self-assembled monolayer<sup>788</sup></td></tr><tr><td>Reducing thermal conductivity</td><td>He</td><td>Si nanowires,<sup>789</sup> Si membrane,<sup>790</sup> VO<sub>2</sub> nanowires,<sup>791</sup> Bi<sub>2</sub>Te<sub>3</sub> nanoribbons<sup>792</sup></td></tr><tr><td rowspan="3">Mechanical</td><td>Tuning Young's modulus</td><td>He</td><td>Monolayer MoSe<sub>2</sub><sup>747</sup></td></tr><tr><td></td><td>Ga</td><td>Polymer,<sup>793</sup> hydrogels<sup>794</sup></td></tr><tr><td>Gas bubble effects</td><td>He</td><td>Nanobubble superlattice in Cu,<sup>795</sup> nanobubbles in Si,<sup>796</sup> diamond,<sup>797</sup> Eurofer steel,<sup>798</sup> W,<sup>799</sup> ultrafine-grained W and W-Cu nanocomposite<sup>800</sup></td></tr></tbody></table>

FIB processing is serial and the penetration depth is limited, the use of the FIB in this area is mostly of interest in cases where a small number of ions needs to be placed with high spatial accuracy. A particularly beautiful example is the tuning and imaging of resonant optical modes in a silicon disk resonator using Li-FIB.<sup>753</sup> A low beam current of 1 pA at 3.9 kV acceleration voltage was used to radially raster scan in pulses of ≈ 3000 ions while the transmitted light passing through a critically coupled waveguide was monitored. The optical shifts observed could be attributed to ion damage and a rapid thermal (and thus reversible) response. Knowledge of this time-varying response was used to enable imaging of different optical modes with minimum device degradation.

The spatial accuracy of defect creation using the mask-less FIB approach becomes especially beneficial in the field of quantum technology. Here, a defect in an otherwise ideally perfect crystal can take the role of an artificial atom emitting quantum light. Furthermore, the defect may exhibit electronic and nuclear spin degrees of freedom that may be coherently coupled to the emitted quantum light, turning the defect into a solid state quantum bit (qubit). The most popular example of a defect-based quantum emitter, or qubit, is the nitrogen vacancy (NV) center in diamond. Diamond NV centers are routinely fabricated using ion implanters,<sup>811</sup> but have also been realized using He-FIB processing.<sup>756,757</sup> FIB implantation of Si ions has been used to realize nearly lifetime-limited single Si vacancy (SiV) quantum emitters in diamond nanostructures.<sup>764</sup> This maskless approach achieved ≈ 32 nm lateral precision and <50 nm positioning accuracy and is thus promising for the development of scalable solid-state quantum

information processors. Focused Si ions at 35 keV with beam diameters of 5–10 nm have also been used to fabricate negatively charged silicon vacancies ($V_{Si}^{-}$) in 4H-SiC with single emitters observed starting from 40 ions per irradiated spot.<sup>812</sup> A comparative study by the same author using H, He, and C ions showed that He ions produced the highest defect concentration, while the lowest brightness emitters were observed for C ions.<sup>813</sup> In addition, Li-FIB has been employed for the creation of Si vacancies in SiC.<sup>762</sup> Recently, focused Ar<sup>8+</sup> ions from an EBIT were also used for NV-creation in diamond.<sup>767</sup> A particularly interesting study made use of Xe-FIB for recoil implantation of targeted group IV dopants in a deposited surface layer.<sup>774</sup> In this work, Pb, Sn, Ge, and Si color centers in diamond were fabricated with a spatial accuracy of better than 50 nm in combination with an ultra-shallow doping profile. So-called G and W centers in Si have recently been demonstrated using Si-FIB to create spatially resolved single defect centers of this type for application as quantum emitters in the telecom band.<sup>765</sup> In a very recent approach, a dedicated FIB system equipped with a ultrahigh vacuum (UHV) sample chamber<sup>814</sup> was used to suppress unwanted isotopes in Si that would otherwise limit coherence times and therewith the performance of solid-state spin qubits. This was achieved using a LMAIS source to implant <sup>28</sup>Si<sup>++</sup> into natural Si, lowering the level of unwanted <sup>29</sup>Si to the single-digit ppm range without introducing contamination from the FIB processing.<sup>766</sup> The deterministic placement of single atoms (e.g., Sb or P) into Si to act as qubits is another challenge where progress has recently been made.<sup>293,773</sup> While the two cited works are a clear demonstration
of the placement accuracy of single (or few) atoms using a FIB, the approaches rely on implantation into a host material that can also double as an active detector of the ion impacts.

In parallel, 2D materials have been heavily explored as hosts for usable quantum emitters, e.g., sources of single photons.⁸¹⁵ Here, ion irradiation can be used to both tailor the optical properties of the 2D system⁸¹⁶ as well as to produce defects that introduce novel optical activity.⁸¹⁷,⁸¹⁸ He-FIB processing, in particular, has been used for the site-selective creation of defects in, e.g., 2D MoS₂.⁷⁶¹ While the exact type of defects being introduced is still under investigation (true for most luminescent defects in 2D materials), they are expected to cause highly localized trapping potentials for exciton emission. Encapsulation with hBN leads to very narrow linewidths of the emission lines in the visible range, 100–220 meV below the neutral exciton.⁷⁶¹ He irradiation has also been shown to result in a fivefold reduction in background and parasitic fluorescence, enabling the isolation of bright and stable quantum emitters in hBN.⁷⁴⁹ Recent results using Ga-FIB patterning indicate that the formation of luminescent defects is positively correlated with material swelling rather than material removal by milling.⁷⁶⁹ This helps to explain earlier results on the generation of defects by 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.⁷⁶⁸

## 5. Engineering of low-dimensional materials

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 VI, 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 30 keV Ga ion beam is around 60 nm, which severely limits possibilities for property engineering of bulk materials. While lighter ions of the same energy penetrate more deeply, for many defect engineering applications implantation of the ion into the material is not actually desired. Rather, it is the local damage created by the ion in transit that is leveraged. Therefore, low-dimensional materials are often the ideal testbed material for defect engineering using the FIB. Notably, an increase in ion energy typically causes a decrease in defect production in 2D materials,⁸¹⁹ such that lower beam energies are in fact better suited for efficient materials modification in these cases.

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 MoS₂.⁶⁸⁷ 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 the electrical conductivity in spatially defined regions at the nanoscale. For example, using the He-FIB and a line irradiation strategy on 2D MoS₂, a neuromorphic mem-transistor device has been demonstrated.⁶⁹⁰ Similarly, Ga-FIB has been used for defect creation in supported graphene with MD simulations

providing insight into the effect of irradiation angle on the lateral damage distribution.⁸²⁰ He-FIB line irradiation of graphene has also been used to create graphene nanoribbons,⁶⁸⁶ which opens up a bandgap in graphene due to quantum confinement. Tuning of the ribbon width and, hence, the size of the bandgap is a key step toward the use of graphene in electronic applications. As discussed in Sec. III B 3, for supported graphene, the minimum achievable nanoribbon width is limited by the influence of the backscattered ions from the substrate.³⁷⁰

Other defect engineering applications concerning 2D materials include the use of Ga-FIB in combination with the simultaneous flow of XeF₂ gas for the localized fluorination of graphene⁷⁸⁷ and the use of the He-FIB to create localized defects in graphene to serve as nucleation points for the epitaxial growth of hBN.⁷⁸² An example of defect engineering of a 1D structure is the employment of localized He-FIB irradiation to induce regions of disorder in a silicon nanowire in order to tune the thermal conductivity along its length.⁷⁸⁹

## 6. Study of irradiation damage mechanisms

Fundamental curiosity and the need for experimentally straightforward replacements for long-duration 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 α particles, for example, He⁺ ions are a convenient species to use. A further advantage of using an inert species such as He 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.⁶²¹

A phenomenon that was discovered several decades ago is the formation of He nanobubbles upon He ion irradiation of various metal targets. These nanobubbles form as a result of vacancy defects and He interstitials that diffuse and recombine to produce gas clusters. However, fundamental experimental 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 Si targets, mostly driven by the need of the semiconductor industry to evaluate the invasiveness of He-FIB processing.⁶⁴⁴ Later studies included the investigation of He gas-bubble superlattices, using single-crystal Cu 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.⁷⁹⁵ Since samples are irradiated with the He-FIB on the nanoscale, individual grains and grain boundaries can be targeted in polycrystalline samples.⁸²¹ By increasing the dose, the coalescence of nanobubbles forming crack planes that ultimately result in blistering and delamination can also be studied with a level of control that was previously unattainable.⁷⁹⁹ 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 combined with nanoindentation, e.g., in studies of Eurofer steel,⁷⁹⁸ W,⁸²² ultrafine-grained W, and a W-Cu nanocomposite.⁸⁰⁰

Finally, He gas bubble effects have also been employed for nano-fabrication 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.⁸²³⁻⁸²⁶
## 7. Outlook

The use of the FIB for property engineering down to the nanoscale is now well established. Recently, strong efforts have been under way to increase the spatial resolution and control of the technique even further with the ultimate goal of creating single defect centers or implanting single impurity atoms for applications in quantum technology. Here, a significant challenge is posed by the intrinsically stochastic nature of both the production of ions from most FIB sources and of the ion-solid interaction itself. The deterministic placement of single ions either into the bulk or at a surface thus pushes the FIB technique to its fundamental limits.

There are two distinct approaches that are being pursued for realizing deterministic SII using the FIB. One is to count the ions as they travel to the sample and the other is to detect individual ion impact events, ideally in an universal manner. The first approach can be realized by using a Paul ion trap as a deterministic source of single ions.<sup>827,828</sup> While the presence of the ion can be unambiguously proven, ejecting the ion and re-loading the trap is time-consuming and the spatial localization of the eventual impact event using ion-optical elements causes significant losses. Given that the probabilities for the creation of specific defects are usually low and highly material dependent (see also Sec. III B), this deterministic ion source approach is appealing, but technologically extremely demanding. Alternatively, ion columns can be equipped with image-charge detectors that count ions produced from different types of ion sources. The beam is directed toward the sample only if an ion is detected. In this way, imperfect detection efficiencies can be mitigated since all non-detected ions are automatically blanked.<sup>193</sup> The drawback of this technique is the large charge state (at least 10<sup>+</sup>) that is necessary for detection of the image charge, requiring ion sources such as an EBIT. Here, Ar<sup>18+</sup> ions created by an EBIT have been successfully used.<sup>194</sup> Light ions are excluded from this technique, unless the sensitivity of the image-charge detectors can be significantly increased, and this method also presents significant technological challenges for column design.

The second approach, i.e., the detection of individual ion impacts on the sample, could in principle work for any ion source. Promising attempts combine an on-chip IBIC detector<sup>199,829</sup> with a plasma ion source and a near-surface aperture in an AFM cantilever.<sup>293</sup> Here, scanning of the aperture realizes the spatial localization<sup>830-832</sup> and thus allows use of various types of ion source, 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 agnostic sample detector concepts. Conventional SE detectors (Everhart-Thornley, see also Sec. II C) or novel detector types (e.g., channeltrons<sup>777</sup>) may work as such, but suffer from their strong dependence on the SE yield, which is unknown for most materials and is very surface dependent. There is also a need for a better understanding and prediction of SE generation and expected detection yields, and for the development of advanced SE detection schemes with detection efficiencies approaching 100%.<sup>777,833</sup> Instead of detecting all ion impact events (that may each come with a small probability of creating the target defect), one may instead detect device function *in situ* while delivering ions to 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 desired device operation is achieved. Here, the technological challenge of these implementations involves the co-integration of an extremely sensitive fluorescence detection setup.<sup>834,835</sup>

In conclusion, several promising development routes for SII are currently being pursued that are showing first promising results. Whether modifying the ion supply toward being deterministic or enhancing the detection capabilities toward single-ion sensitivity (or a combination of both) will finally lead to success is still an open question.

## C. FIB-based imaging and tomography

Multiscale imaging of complex systems is becoming increasingly important. For example, to understand data transmission in the brain or chemical energy storage in a battery, one needs to capture the “big picture,” ideally in three dimensions, as well as resolve features down to individual atoms. This is where FIB based techniques play a central role, by direct imaging using light ions such as He, by 3D volume imaging combining FIB slicing with SEM, and by preparing thinned cross sections and specialized geometries for TEM and APT.

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

The enormous potential of electron microscopy for imaging the structure of condensed matter became clear with the invention of the TEM in 1932<sup>836</sup> and soon thereafter first images of bacteria<sup>837,838</sup> and virus particles<sup>839</sup> proved the same for the life sciences. The introduction of ion microscopy for imaging, however, took much longer. Pioneering work was carried out in the 1970s by Levi-Setti and co-workers, who experimented with a scanning transmission ion microscope using up to 65 keV H<sub>2</sub><sup>+</sup> ions from a GFIS and published images of myofibrils from rabbit muscle.<sup>26</sup> However, since the achievable lateral resolution of ion microscopy had always been inferior to that of electron microscopy, ion microscopy was not used for nanoscale imaging until the early 2000s with the invention of the HIM<sup>21,25</sup> (see Sec. IV C 2).

The breakthrough in the use of ion microscopy for sub-cellular imaging in biology, or “the revolution in ultra-microscopy” as stated by Ballerini *et al.*,<sup>840</sup> occurred once Ga ion beams from LMIS-based sources could be focused down to better than 10 nm.<sup>841</sup> It was recognized that the ion beam could be used “like a tiny scalpel which slices away layers of the sample (and that one could) exploit this destruction to gain high-resolution three-dimensional structural, morphological, and chemical information.”<sup>840</sup> Thus, the FIB based microscopy and machining that had until the turn of the century mainly been used in the semiconductor industry was brought to the life sciences.<sup>840,842</sup> Various other fields also adopted the technique. For example, one of the first reports of FIB tomography was presented in 2001 by Inkson *et al.*<sup>843</sup> on the 3D characterization of a metallic nanocomposite, and FIB based tomography also became increasingly common in, e.g., metallurgy,<sup>103,626,844</sup> energy research,<sup>845</sup> and geology.<sup>846</sup> Recently, FIB tomography has even been applied to paleontology samples.<sup>847</sup> While early work sometimes used the Ga-FIB for the imaging as well as the sectioning, the most common implementation of FIB tomography uses the dual beam FIB-SEM, comprising a Ga-FIB column for the milling coupled with a SEM for high-resolution surface imaging of the exposed faces. Significant progress in 3D image segmentation and reconstruction<sup>848</sup> was also key to enabling 3D structural imaging of complex specimens by the FIB-SEM technique. Furthermore, the development of cryo-workflows for cryo-FIB-SEM tomography was a major step forward allowing preservation of cell ultra-structure.<sup>849,850</sup> Such cryo workflows are now used for other beam-sensitive samples as well (see Sec. IV C 4).
<table><caption>TABLE VII. Overview of FIB based imaging and analysis in the life sciences.</caption><thead><tr><th></th><th>Application</th><th>Technique</th><th>Experiment</th></tr></thead><tbody><tr><td rowspan="3">Molecules</td><td>Localization of proteins</td><td>cryo-FIB-SEM</td><td>Protein detection in vitrified HeLa-cells using Au-conjugated antibodies against RNA polymerase II<sup>853</sup></td></tr><tr><td></td><td>HIM and fluorescence microscopy</td><td>Detection of quantum-dot labeled proteins<sup>854</sup></td></tr><tr><td>Metabolic imaging</td><td>ToF-SIMS<br>OrbiSIMS</td><td>Detection of proteins on DNA bio-sensor chip<sup>855</sup><br>Imaging of the distribution of neurotransmitters in mouse hippocampus<sup>856</sup></td></tr><tr><td rowspan="3">Viruses and nanoparticles</td><td>Virus imaging</td><td>HIM</td><td>3D metabolic imaging of Paramecium caudatum using orbitrap-MS coupled to TOF-SIMS<sup>857</sup><br>Imaging of bacteriophage infection,<sup>858,859</sup> and transport by bacteria<sup>860</sup></td></tr><tr><td>Nanoparticle-cell interactions</td><td>FIB-SEM<br>HIM<br>HIM-SIMS<br>ToF-SIMS</td><td>Imaging of SARS-CoV-2 infected Vero cells<sup>861,862</sup><br>Investigations into SARS-CoV-2 viral density at cell-cell contacts<sup>863</sup><br>Investigation of biogenic nanoparticles by HIM-SIMS<sup>864</sup><br>3D-imaging of nanoparticles in an algal biofilm<sup>865</sup></td></tr><tr><td>Imaging of microbial cells</td><td>HIM</td><td>Imaging of nitrate-reducing bacteria with spiky minerals,<sup>866,867</sup> archea<sup>868</sup>,<br>predatory bacteria<sup>869</sup></td></tr><tr><td>Imaging of biofilms</td><td>HIM</td><td>Geobacter sulfurreducens,<sup>870</sup> microbial mats from Himalayan hot springs,<sup>859</sup><br>chlorella micro-algae<sup>871</sup></td></tr><tr><td>Imaging of mammalian cells and tissues</td><td>HIM</td><td>Imaging of mitotic HeLa cells,<sup>866</sup> visualization of lipid nanodomains in human neural stem-cells,<sup>872</sup> imaging of kidney<sup>873</sup></td></tr><tr><td>3D imaging and remodeling of microbial cells</td><td>(cryo-)FIB-SEM</td><td>FIB-SEM of yeast cells,<sup>840,849</sup> 3D remodeling of Acantharia-microalgae<sup>874</sup></td></tr><tr><td>3D imaging of cells and tissues</td><td>(cryo-)FIB-SEM</td><td>Imaging of FIB-sectioned gland cells,<sup>875</sup> lymphoid tumor tissue,<sup>849</sup> carbon nanotubes (CNTs) in mouse lung tissue,<sup>876</sup> tobacco petal epidermis,<sup>850</sup> human bone<sup>877</sup></td></tr><tr><td rowspan="6">Cell-level</td><td>Sub-cellular elemental mapping</td><td>nanoSIMS,<br>ToF-SIMS</td><td>Element distribution in E.coli exposed to natural antibacterial clay,<sup>878</sup> mapping of N/P ratio in a photosymbiotic Acantharia-microalgae system,<sup>874</sup> identification of TiO<sub>2</sub> in an algal biofilm<sup>865</sup></td></tr><tr><td>Metabolic activity measurements</td><td>nanoSIMS</td><td>Elemental analysis of hair, skin, nervous tissue<sup>879</sup><br>Identification of Ni-U-phosphate deposits in bacteria<sup>880</sup></td></tr><tr><td>Biomarker imaging of single cells</td><td>ToF-SIMS</td><td>nanoSIMS and stable isotope labeling to measure metabolic activity of microbial cells<sup>881,882</sup> and heterogeneity in isogenic microbial populations<sup>883,884</sup></td></tr><tr><td>Chemical analysis of biofilms</td><td>ToF-SIMS</td><td>Biomarker imaging of diatom cells in a microbial mat<sup>885</sup></td></tr><tr><td>Bacterial predators</td><td>HIM</td><td>Localization of P in micro-algae biofilms<sup>886</sup></td></tr><tr><td>Geomicrobiology</td><td>HIM</td><td>Imaging of iron-oxidizing bacteria,<sup>866,867</sup> structure of Geobacter sulfurreducens biofilm<sup>870</sup></td></tr><tr><td></td><td></td><td>ToF-SIMS</td><td>Microaerophilic Fe(II) oxidizing Zetaproteobacteria,<sup>887</sup> iron corrosion by methanogens<sup>888</sup></td></tr><tr><td></td><td>Anti-microbial properties of surfaces</td><td>HIM milling</td><td>Investigation of the anti-bacterial properties of the nanostructures on drag-onfly wings<sup>889</sup></td></tr></tbody></table>
An overview of the various FIB based imaging and analysis modal-
ities used in the life sciences is given in Table VII. In all of the examples
given, the imaging and analysis was primarily performed in situ, i.e.,
inside the FIB-(SEM) instrument. Key works on cryo-FIB milling for
the site-selective preparation of electron transparent biological speci-
mens for analysis by cryo-TEM can be found in Refs. 851 and 852.

## 2. HIM–A tool for imaging of the tiniest living objects

SEM is a standard method for imaging biological specimens, in which samples are typically coated with a conductive layer to prevent charging under the beam. SEM imaging of uncoated samples without charging becomes possible if the accelerating voltage of the electron beam is reduced below 1 kV, but at the expense of increased chromatic aberration and a reduced depth of field.⁸⁶⁶ In contrast, with HIM, in situ charge compensation with an electron flood gun allows the investigation of non-conductive biological samples without conductive coatings while maintaining good spatial resolution. This is important, as metallic coatings can alter and conceal nanoscopic samples and features, such as virus particles or the cell membrane topography. Furthermore, compared to SEM, HIM delivers a larger depth of field, enhanced topographic contrast, and greater surface sensitivity.¹⁸⁷,⁸⁹⁰ Typically, HIM imaging relies on the detection of SEs, but backscattered ions (BIs) can also be detected, which enhances material contrast. (This is comparable to SE vs backscattered electron detection in SEM.) Since backscatter detection in HIM is also sensitive to the neutrals that are generated, detection yields are relatively high meaning that images can be collected at lower dose (see also Sec. II C). Bidlack et al.¹⁸³ pointed out that BI imaging could improve the visualization of immuno-gold labels in cells and Ma et al.¹⁸² used BI imaging to detect different concentrations of colloidal nanoparticles in cells. However, in general, the use of BI detection for HIM in the life sciences is still underexplored.

a. *Preparation of the specimen.* Since the sample requirements for room-temperature HIM (dry and vacuum-compatible) are almost identical to those of electron microscopy, established protocols from the SEM community provide a good basis for HIM sample preparation. In general, the sample preparation steps involve:

1. chemical fixation with aldehydes (e.g., formaldehyde or glutaraldehyde),

2. optional post-fixation with strong oxidizing agents (e.g., osmium tetroxide),

3. dehydration in a graded series of an organic solvent (e.g., methanol, ethanol or acetone),

4. drying (e.g., critical point drying).

Instead of the final dehydration and drying of the sample, the application of ionic liquids has been proposed as an alternative⁸⁹¹ and successfully applied for imaging bacterial biofilms using HIM.⁸⁹² In all cases, no final metallization of the sample is required (due to the *in situ* charge compensation mentioned previously); hence, samples can be visualized in a more pristine state.

b. *Viruses.* Sharma *et al.*<sup>859</sup> used HIM in investigations of 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.<sup>858</sup> and You et al.<sup>860</sup> published high-resolution HIM images of T4-phage infected *E. coli* bacteria, and Vinner at al.<sup>893</sup> visualized phage Felix O1 infected Salmonella bacteria. The contributions that HIM and other microscopies have made to our understanding of bacteriophages have been reviewed in more detail by Almeida et al.<sup>894</sup> Furthermore, Frese et al.<sup>861</sup> and Barreto-Vieira<sup>895</sup> recently reported the first visualization of SARS-CoV-2 virus particles by HIM, demonstrating significant topographical differences compared to previously published SEM images of sputter-coated samples. Examples of HIM imaging of virus are shown in Fig. 18. In the future, HIM could be used, for example, to examine the internal structure of phage-infected cells by milling cross sections. In addition, HIM could be used to better understand the spread of viral particles through other organisms, since it is possible to remove lightly attached phages during a washing step in the sample preparation and image what remains.

c. *Single-celled organisms.* HIM is an excellent tool for viewing single-celled organisms such as bacteria, archea, yeast, micro-algea, protzoa, etc., at a resolution approaching that of TEM without needing to embed and section the samples. Here, it is important to note that the HIM technique primarily enables imaging of the cell surface. In their 2013 paper, Joens et al.<sup>866</sup> employed HIM for the first time for the imaging of microbes, namely, iron-oxidizing bacteria. The ability to view highly texturized biological specimens on non-conductive surfaces with strong topographic contrast, charge-compensation, and large depth-of-field renders the HIM an excellent tool for this work. The first HIM images of a culture of archea were published by Chen et al.,<sup>868</sup> where HIM proved particularly useful for investigation of the alleged cell budding of Ca. A. ethanivorans. Furthermore, HIM has been utilized by Said et al.<sup>869</sup> to image bacterial infections by the bacterial predator Bdellovibrio bacteriovorus. HIM of bacterial biofilms (also often highly texturized) was published by LeTourneau et al.<sup>896</sup> (rhizobacteria), Belianinov et al.<sup>870</sup> (*Geobacter sulfurreducens*), and Schmidt et al.<sup>892</sup> (*Pseudomonas putida*). Further HIM studies of biofilms include imaging of microbial mats from hot springs in the Indian Himalayans by Sharma et al.<sup>859</sup> and investigations of micro-algal biofilms with regard to architecture and P distribution by Moreno Osorio et al.<sup>871</sup> Other potential applications of HIM imaging of microbiological objects

<figure><img src="image_29.png" /><figcaption>**FIG. 18.** (a) SARS-CoV-2 virus particles on the cell membrane of a Vero E6 cell,<sup>861</sup> reproduced with permission from Frese et al., Beilstein J. Nanotechnol.<b>12</b>, 172–179 (2021). Copyright 2021 Authors, licensed under a Creative Commons Attribution (CC BY) license. (b) T4-phage infected *E. coli* bacteria on a fibrous agar surface.<sup>858</sup> Reproduced with permission from Leppänen et al., Adv. Biosyst.<b>1</b>, 1700070 (2017). Copyright 2017 John Wiley and Sons.</figcaption></figure>
include investigations of biofilms in different environments, e.g., on
medical implants or in bio-reactors. HIM also holds great promise for
studying phage-infection or predation by protists or bacteria in environ-
mental bacterial biofilms. Furthermore, one can conceive of HIM inves-
tigations into the complex interplay of microbes with plants or fungi. A
recent example in this area is given by You *et al.*,⁸⁶⁰ where HIM was
used to analyze phage co-transport on hyphal-riding bacteria.

d. Cells, tissues, immuno-gold labeling. The HIM has been used in many studies to investigate whole cells of multicellular organisms, including plant,⁸⁷¹ animal,⁸⁹⁷ and human cells.⁸⁹⁸,⁸⁹⁹ 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 by SEM. For example, Schürmann et al.⁸⁷² visualized lipid nanodomains in the cell membranes of neurons, which were demonstrated to otherwise be concealed under a 10 nm metallic coating. Sato et al.⁹⁰⁰ have shown that immuno-gold-tagged antibodies can be resolved within cells to identify specific organelles, demonstrating 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.⁸⁸⁹,⁹⁰¹ In addition, Joens et al.⁸⁶⁶ demonstrated that the mouth cavity of a nematode can be dissected using Ne-FIB milling with subsequent imaging by HIM, with minimal thermal damage during the milling process.

e. *HIM in correlative workflows.* In addition to structural analysis, the ability to investigate chemical compositions on the subcellular level is also needed. In order to achieve this with a HIM-based platform, detectors such as for SIMS (cf. Subsection II C) can be installed and used for *in situ* chemical investigations, as has been shown for *E. coli* cells incubated with TiO₂ nanoparticles.¹⁴⁰ Alternatively, HIM imaging can be integrated into correlative workflows *ex situ* with SIMS, EDS, or fluorescence microscopy using fluorescent markers (see also Sec. II F). A recently published example shows how HIM in correlation with the aforementioned techniques was used to analyze a resin-embedded soil sample with regard to roots, sediments, soil-organic matter, and bacteria.⁹⁰² Further correlative studies that make use of the unique charge-free high-resolution imaging capabilities of HIM can be expected, e.g., to analyze biomineralization processes, and to address ecological questions in environmental microbiology, plant and soil science, etc.

**3. FIB tomography in the life sciences**

Three-dimensional nano-imaging of biological samples has become increasingly important, e.g., for investigations of cell architecture, the ultra-structure of cell components, cell-cell interactions, structural analysis of tissues and biofilms, etc.⁹⁰³ Until the early 2000s, investigations into the 3D ultra-structure of samples such as resin-embedded tissue or cells were carried out by serial block-face SEM⁹⁰⁴ or by serial sectioning for TEM.⁹⁰⁵ While a very high lateral resolution can be achieved by these approaches, depth resolution is limited by the achievable thickness of the slices. Alternatively, serial block-face SEMs with an ultramicrotome fitted into the analysis chamber can be used for tomographic imaging of resin-embedded samples. However, the depth resolution is still limited by the minimum about of material that can be removed in each slice.

The advent of FIBs (principally the Ga-FIB) propelled the field of biological micro-tomography, allowing much better control and much finer removal of material.⁹⁰⁶ In one of the first examples of FIB based tomography in the life sciences, Ballerini et al.⁸⁴⁰ investigated the internal structure of yeast cells using Ga-FIB sectioning followed by a sample tilt to allow FIB based imaging of the cross section via secondary electrons and (negatively charged) secondary ions. Soon thereafter, the image resolution and efficiency of the technique were improved using dual-beam FIB-SEM systems where the specimen is Ga-FIB-sectioned and imaged by SEM. The use of oxygen ions from a PFIB appears to reduce curtaining and other artifacts, allowing faster preparation of smoother surfaces for the imaging step.⁹⁰⁷ The basic workflow for FIB-SEM analysis of a resin-embedded biological specimen consists of repeated FIB-milling and SEM imaging of the exposed face followed by 2D image-stack registration and finally 3D reconstruction, as summarized in Fig. 19.

In order to obtain sufficient contrast in the SEM images, the sample is usually stained with heavy metals. Pioneering work was carried out by Drobne et al.,⁸⁷⁵ who investigated the digestive system of a crustacean by FIB-SEM and compared imaging modes. In order to achieve better contrast, Leser et al.⁹⁰⁸ systematically investigated different OsO₄ and uranylacetate staining techniques and concluded that for plastic resin embedded samples, the OTOTO method (OsO₄/thiocarbohydrazide/OsO₄/thiocarbohydrazide/OsO₄) in combination with backscattered electron imaging provides best results. Other protocols involve a combination of potassium ferrocyanide, OsO₄, and uranylacetate, and were successfully applied to brain⁹⁰⁹ and bone tissue,⁹¹⁰ as well as for the investigation of the interaction of CNTs with lung tissue.⁸⁷⁶ A detailed description of standard protocols for FIB-SEM of dried as well as plastic resin embedded (tissue) samples can be found in the work of Drobne.⁹¹¹ An alternative preparation method for FIB-SEM investigation of cells on surfaces uses thin layer plastification of the samples in place of resin embedding and full impregnation.⁹¹⁰

It is well known that dehydration and embedding in plastic resins introduces artifacts and may destroy the ultra-structure of cell components. These effects 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. However, FIB-SEM imaging of the embedded sample is then done at room temperature, as described, e.g., by Schmid et al.⁹¹² for samples of the nitrate-reducing and Fe-oxidizing bacteria BoFeN1. (This is the same cell culture as used by Joens et al.,⁸⁶⁶ see Sec. IV C 2 c.) By the early 2000s, it became clear that the ultra-structure of cells could be preserved even better if full cryo-workflows are employed, where a plunge- or high-pressure frozen specimen (still hydrated) is imaged at cryogenic temperatures. Marko et al.⁹¹³ explored the possibilities of thinning vitrified biological specimens by cryo-FIB milling plunge-frozen water and concluded that (a) cryo FIB-milling of vitreous ice does not induce heating sufficient to cause devitrification, and (b) subsequent experiments should be performed below -135°C to maintain a vitreous state. In 2006, Heymann et al.⁸⁴⁹ published SEM data of plunge-frozen and FIB-milled yeast cells, as well as SEM and TEM images of FIB-milled lamellae of plunge-frozen tumor tissue. Although the frozen samples were not stained, sufficient contrast for SEM imaging with SEs was achieved through a combination of sublimation and metal deposition on the exposed surface. Similar work was performed by Heyles et al.,⁸⁵⁰ who used a GIS system to deposit platinum onto frozen yeast cells and onto a petal epidermis sample of Nicotinia tabaccum. A
<figure><img src="image_30.png" /><figcaption>**FIG. 19.** Illustration of the basic workflow for volume imaging by FIB-SEM tomography:⁹⁰⁶ (a) Repeated FIB milling followed by SEM imaging, image-stack registration and reconstruction. (b)–(d) Example of a mouse intestine sample. Reproduced with permission from Narayan and Subramaniam, Nat. Methods **12**, 1021–1031 (2015). Copyright 2016 Springer Nature America.</figcaption></figure>

recent overview of cryo-FIB-SEM techniques for frozen, hydrated bio-
logical samples is given by Hayles and De Winter.⁹¹⁴

Another leap forward was the development of correlative confo-
cal laser scanning and FIB-SEM tomography using fluorescent dyes,
high-pressure freezing, and cryo-substitution embedding.⁹¹⁵ For exam-
ple, Gorelick *et al*.⁹¹⁶ developed a photon-ion-electron microscope
(PIE-scope), which employs correlative cryogenic fluorescent light
microscopy and FIB-SEM enabling the rapid and precise location of
protein complexes in cells. Another example is the recently published
(non-cryo) 3D-correlative workflow combining super-resolution light
microscopy and FIB-SEM using reactive oxygen ion PFIB milling and
a rotating sample stage to study embedded cultured cells.⁹¹⁷

Driven by questions in cell biology and connectomics, strategies have also been developed to enable FIB-SEM analysis of large volumes at high spatial resolution. Pivotal work in this area by Xu *et al.*,⁹¹⁸ involving automated recovery from beam/system malfunctions, enabled enhanced large-volume 3D FIB-SEM analysis of one third of a fruit fly brain at a depth resolution of 8 nm. In order to analyze large volumes of hard materials such as bone, FIB-SEM using high-current beams of Xe ions available from PFIB sources has been demonstrated.⁸⁷⁷

In the context of the COVID-19 pandemic, FIB-SEM tomogra-
phy proved valuable for gaining insight into the microscopic mecha-
nisms of the disease. Baena *et al*.⁸⁶³ employed FIB-SEM to analyze
how SARS-CoV-2 spreads from infected cells to new hosts, as shown

<figure><img src="image_31.png" /><figcaption>**FIG. 20.** (a) FIB-SEM images of two 8 nm slices showing two contacted Vero E6 cells (green, brown) and SARS-CoV-2 particles in the extracellular space (arrows).⁸⁶³ Inset scale bar: 200 nm. (b) 3D reconstruction of the plasma membranes of the two cells shown in (a). The junction-mediated contact between the cells is colored in yellow. The virus particles are depicted in red and show a different density on either side of the junction. Reproduced with permission from Baena *et al.*, Viruses **13**, 611 (2021). Copyright 2021 Authors, licensed under a Creative Commons Attribution (CC BY) license.</figcaption></figure>
in Fig. 20. Using a combination of TEM-tomography and FIB-SEM, Cortese *et al.*⁹¹⁹ were able to visualize morphological changes in 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 also used to image virus particles in vacuoles.⁹²⁰

### 4. FIB tomography of energy materials

One of the very first applications of FIB-SEM tomography in energy materials research was presented by Wilson *et al.*⁹²¹ in 2006. The authors investigated a solid oxide fuel cell anode based on yttrium stabilized zirconia (YSZ) and used 3D reconstruction to differentiate the YSZ, Ni, and pore phases. This enabled quantification of important structural features, such as volume fractions, surfaces, and even information on the so-called three-phase boundary.

In 2010, Ostadi *et al.*⁸⁴⁵ investigated a microporous layer used in a hydrogen-powered proton exchange membrane fuel cell (PEMFC). FIB tomography was used to complement the X-ray tomography investigations of the fuel cell electrode structure in order to capture the nanostructure of the microporous layer, which cannot be resolved using standard X-ray imaging equipment due to the limited spatial resolution of ≈ 1 µm compared to the FIB-SEM tomography resolution of ≈ 10 nm. The porous structure was reconstructed in 3D and the porosity and pore size distribution analyzed.

In the same year, Zils *et al.*⁹²² demonstrated how FIB tomography can be used to study the effects of manufacturing parameters on the 3D structure and resulting properties of the fabricated material. For various catalyst electrode materials intended for use in PEMFCs, the authors compared porosity and pore size distributions made with air-brushing and a fast spray coating technique, and related the 3D structural features to the performance of the materials. Schulenburg *et al.*⁹²³ used FIB tomography to study degradation effects in the 3D structure of carbon-based fuel cell electrodes after many start-stop cycles and discovered breakdown of the entire nanoporous structure leading to a significant reduction in the supply of reaction gases to the catalyst. In combination with other (X-ray based) tomography techniques and structural modeling, FIB tomography can also be used for correlative tomographic imaging⁹²⁴ to fill in missing information at the nanometer scale and to produce multiscale 3D data covering structural features over a broad length scale. For example, Zielke *et al.*⁹²⁵ have shown how FIB tomography can be used to supplement the information missing from synchrotron tomography data due to the limited spatial resolution. Here, high-resolution 3D data obtained using the FIB method was used to create a structural model at the nanometer scale, to enhance the synchrotron dataset with nanometer detail. In a recent study, Paulisch *et al.*⁹²⁶ used FIB tomography to analyze the complex 3D path network inside Ag-based gas diffusion electrodes (Fig. 21). 3D data acquired with FIB tomography has also been used for mathematical modeling of the 3D structure of energy materials,⁹²⁷ whereby the computer-generated 3D structures can later be used for the development of digital twins and for future virtual materials design.

FIB tomography is thus now well established for high-resolution 3D structural studies of materials for energy-technology research, including battery materials,⁹²⁸⁻⁹³⁸ fuel cell materials,⁹³⁹⁻⁹⁴² electrolyzers⁹⁴³⁻⁹⁴⁶ and catalytic materials.⁹⁴⁷⁻⁹⁵⁰ In the case of beam- and air-sensitive materials, cryogenic FIB-SEM implementations are becoming increasingly popular, since radiation damage can be significantly reduced at low temperature and cryotransfer workflows are by nature

<figure><img src="image_32.png" /><figcaption>**FIG. 21.** FIB-SEM tomography of Ag-based gas diffusion electrode. Gray: Ag grains, green: binder/PTFE within the pore system. Only the 3D image can reveal the complex pathways inside the pore system. For more information, see Ref. 926.</figcaption></figure>

air free. For example, cryo FIB-SEM techniques have enabled 3D nanoscale insight into Li dendrite formation and the so-called solid-electrolyte interface.⁹⁵¹⁻⁹⁵⁶

### 5. Data processing of FIB tomographies

With the growing volume of data, the analysis of large tensors containing mostly grayscale 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, artifacts that need to be detected and addressed. Here, ML approaches, especially easy-to-use mainly random forest based tools such as Ilastik⁹⁵⁷ or the trainable Weka segmentation,⁹⁵⁸ are becoming increasingly established for image annotation and classification.

One of the major issues in tomographic imaging of porous materials is the problem of separating the pore foreground from the background. In order to address this issue, infiltration of the pores with an appropriate resin may be carried out. Silicone-based resins are frequently used to infiltrate the pore system of energy materials due to the generally high carbon content of the latter.⁹⁵⁹ However, due to sample alteration upon this treatment, or inaccessibility of the pore system, pore infiltration is often either impossible or undesirable. Thus, when the FIB mills through a pore, the SEM image will also collect signal from the back of the pore. In such cases, the 3D reconstruction becomes much more complex, because only the foreground around the pore edges represents the actual material distribution corresponding to the exposed surface. To address this issue, various optimized segmentation algorithms have been developed,⁹⁶⁰⁻⁹⁶³ as well as some ML tools.⁹⁶⁴⁻⁹⁶⁶ Recently, Osenberg *et al.*⁹⁶⁷ demonstrated a technique combining two different SE signals (from an in-lens detector and from a detector sensitive to SEs from backscattering electrons) together with a ML algorithm to improve results for the separation of pore foreground and background in the case of a lithium battery
cathode material. However, despite much progress, the general porosity problem is still not completely solved for all material structures.

## 6. Outlook

Over the past 20 years, FIB-SEM has become a mainstream technique for investigating the 3D structure of a range of complex specimens, often with fully established cryo-workflows.

Further improvements involving optimized milling strategies to reduce local heating effects due to the FIB (in non-cryo implementations) would be beneficial for nanoscale milling to reveal the internal structure of biological samples and to reduce artifacts when milling energy materials, as these may also involve heat-sensitive components such as polymers.⁹⁶⁸

In parallel, the ever growing and complex data volumes demand many more automated analysis pipelines. To make this possible, standardized data and metadata formats are needed.⁹⁶⁹ The combination of standardized data sets and high quality individual image classifications generated based on, e.g., 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-Nets⁹⁷⁰ can be trained and applied to data that is very different from the original training set.⁸⁴⁷

On the instrument side, much progress has been made in increasing the sample volumes accessible to FIB based tomographies through the use of high-current PFIB sources for heavy noble gas ions, especially Xe. Due also to advances in automated data acquisition and analysis, FIB tomography of cubic millimeter volumes with a spatial resolution on the order of tens of nanometers is now possible. Complex data from different experimental sources with different lateral resolutions can be made available to the research community in large multiscale atlases. This is celebrated particularly in the life sciences, where Ga-FIB-SEM was used to map and reconstruct the connec-tome of the Drosophila fly brain.⁹¹⁸,⁹⁷¹ In terms of open data, life science offers prime examples: the virtual fly brain⁹⁷² and the fly brain atlas,⁹⁷³ a digital twin of Drosophila's brain combining huge amounts of data from different sources and methods in an easily accessible format. Creating and analyzing such massive data in an automated way has relied on the rapid development of ML, which will be one of the key factors for the future evolution of FIB technologies.

## D. Elemental analysis using FIB-SIMS

While many correlative FIB imaging and analysis approaches exist (mainly using FIB-SEM instruments), FIB-SIMS is by far the leading method for achieving ion beam based analysis of elemental distributions. Dedicated SIMS instruments often use one or two FIB columns in combination with a highly optimized mass spectrometer to provide high mass resolution and sensitivity,⁹⁷⁴,⁹⁷⁵ but a dedicated FIB instrument equipped with a SIMS add-on can provide greater versatility. So far, GFIS-based FIB instruments provide the highest spatial resolution for SIMS.¹²¹,⁹⁷⁶ Recently, LoTIS-based FIB-SIMS has also been introduced.⁹⁷⁷

## 1. Overview

SIMS is based on irradiating the sample with a 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). It is a powerful technique for analyzing surfaces owing in particular, to its ability to detect all elements from hydrogen (H) to uranium (U), its excellent sensitivity to low concentrations, 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 TEM based analysis techniques such as EDS or electron energy loss spectroscopy (EELS), or APT).

Therefore, equipping a FIB instrument with a SIMS system adds unique analytical capabilities for 3D chemical characterization. Furthermore, this add-on enables unique workflows for in situ multi-modal analytics by correlating the SIMS data with that obtained from other imaging/analytical techniques available using the same FIB platform (e.g., SE-imaging, EDS, EBSD, etc.).

## 2. FIB-SIMS 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, where 2D and 3D SIMS imaging provides analysis of elemental distributions with high lateral and depth resolution.⁹⁷⁸ Figure 22 shows an example of the 3D analysis of a fin field-effect transistor (FinFET) using FIB-SIMS.¹¹⁵ These data were obtained using a magnetic sector SIMS system installed on a HIM instrument, achieving a spatial resolution of better than 15 nm. 3D maps such as these can be used for end pointing and circuit edit applications.

<figure><img src="image_33.png" /><figcaption>FIG. 22. SE and SIMS images of a fin field-effect transistor (FinFET) device obtained using a HIM instrument equipped with a magnetic sector SIMS system: (a) SE image acquired using 25 keV He⁺ beam. (b)–(e) SIMS images for ²⁸Si and ⁶³Cu acquired using 20 keV Ne⁺ beam corresponding to a zoomed in region in the SE image. (c) Stack of eight successive SIMS images recorded for the same area [field of view (FOV) 3 × 3 µm²] allowing determination of the elemental composition in 3D. (d) and (e) Individual ²⁸Si and ⁶³Cu SIMS maps corresponding to the seventh slice. For more information, see Ref. 115.</figcaption></figure>
There are also a number of examples where FIB based SIMS has been a major asset in the development of photovoltaic 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. Their development requires a very comprehensive understanding of composition in order to correlate structure and chemical composition with performance and ageing. FIB based SIMS has allowed investigation of many questions related to the chemical heterogeneity of grains<sup>979</sup> and grain boundaries,<sup>122,980</sup> precipitation of secondary phases (e.g., PbI<sub>2</sub>), and chemical/structural modification at the interfaces with charge-collecting electrodes.<sup>981-983</sup> Optimizations based on these results have helped realize new photovoltaic cells with efficiencies approaching 25%.

In battery materials, SIMS technology allows the detection of Li (in addition to any other element of interest) with a very high sensitivity, which is not possible using, e.g., EDS. Therefore, with FIB-SIMS, the Li concentration gradient can be mapped over several orders of magnitude at high spatial resolution across different surfaces and interfaces.<sup>122,127,984-988</sup>

Further examples of the application of FIB-SIMS in materials science include studies of petroleum-based polyolefin plastics,<sup>114</sup> polyester and melamine resins,<sup>89</sup> the investigation of alloys and superalloys,<sup>990-992</sup> the study of nanoparticles,<sup>993-996</sup> the investigation of chemical inhomogeneities in grain sizes between 50 and 200 nm in Delafossite materials,<sup>997</sup> oxygen diffusion in grain boundaries<sup>998</sup> the distribution of rare earths in optical fibers,<sup>999,1000</sup> and the characterization of thin films.<sup>126,1001</sup>

### 3. FIB-SIMS in the life sciences

Ion beam analysis has been used for chemical micro-analytics of biological specimens since the 1970s when high-energy PIXE was found to be valuable for determining trace elements in bulk tissue sections.<sup>1002</sup> By the beginning of the 1990s accelerator-based proton beams could be focused down to 1 µm and could thus be employed for the spatial mapping of trace elements in biological samples.<sup>879</sup> The development of high-brightness LMIS in the second-half of the 1970s<sup>37</sup> also facilitated the introduction of medium-energy (<100 keV) ion beam microprobe techniques for bio-imaging and micro-analysis, in particular in the field of SIMS.<sup>1003,1004</sup> 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. Hence in the life sciences, numerous studies based on imaging with SIMS exist.<sup>1005</sup> For example, FIB-SIMS has been used to spatially resolve chemical signatures from the surface and interior of mammalian individual cells<sup>1006</sup> and bone tissue.<sup>1007</sup> In this area, the Cameca nanoSIMS (a sector-field mass spectrometer with about 50 nm lateral resolution) has become an important tool.<sup>1008</sup> It was designed to achieve a mass resolution high enough to resolve the stable isotopes of elements such as carbon and nitrogen (<sup>13</sup>C and <sup>15</sup>N), which are commonly used for isotope-labeling experiments.<sup>881</sup> In addition, TOF-SIMS approaches for 2D and 3D chemical imaging in the life sciences are becoming increasingly important.<sup>871,1005</sup> For example, metabolic imaging on a sub-cellular level with a mass resolution of 240 000 was recently achieved by combining TOF-SIMS with an orbitrap mass analyzer.<sup>856</sup>

FIB-SIMS at the highest spatial resolution has been enabled using the GFIS source, which can produce sub-nanometer spot sizes. Here, HIM instruments have been equipped with SIMS spectrometers and used for high-resolution chemical analysis of a range of life science samples including micro-organisms, viruses, cells, small animals, plants, etc.<sup>892</sup> Recent specific HIM-SIMS applications include the localization and identification of silver nanoparticles and nanowires in intestinal or alveolar cell cultures<sup>994,1009</sup> and the characterization of biogenic nanoparticles produced by bacteria.<sup>864</sup> Finally, correlative HIM based SE imaging, STIM<sup>138</sup> and SIMS (all in the same instrument) has been used in investigations of thin tissue sections of Daphnia magna exposed to TiO<sub>2</sub> nanoparticles (see Fig. 23).<sup>140</sup> In this correlative nano-toxicological test study, the nanoparticles were shown to accumulate in the gut without penetration of the epithelial barrier.

Beyond materials science and life science applications, FIB-SIMS is also proving valuable for high-resolution structural and chemical analysis in other fields, such as soil science,<sup>1010</sup> geology,<sup>113</sup> and cosmochemistry,<sup>1011,1012</sup> and even for the analysis of cultural heritage objects.<sup>1013-1015</sup>

### 4. Outlook

In order to further increase the spatial resolution of FIB-SIMS, we must now look beyond reducing the beam probe size. In HIM-SIMS,

<figure><img src="image_34.png" /><figcaption>**FIG. 23.** npSCOPE HIM-STIM-SIMS correlative high-resolution imaging and nano-analytics of keratinocyte cell cultures exposed to 30 nm Si–Al–TiO<sub>2</sub> nanoparticles: (a) He-FIB SE image. (b) He-FIB STIM bright field image. (c) Ne-FIB-SIMS false color image of CN (green) and Ti species (red). (d) Ne-FIB-SIMS spectra. He-FIB SE image: FOV 15 × 15 µm<sup>2</sup>, (1024 × 1024) pixel<sup>2</sup>, dwell time 1 µs; He-FIB STIM: FOV 8 × 8 µm<sup>2</sup>, beam current 2 pA, dwell time 400 µs, (512 × 512) pixel<sup>2</sup>. Ne-FIB-SIMS negative mode: FOV 8 × 8 µm<sup>2</sup>, magnetic field 300 mT, dwell time 9000 µs, (256 × 256) pixel<sup>2</sup>. Ne-FIB-SIMS positive mode: FOV 8 × 8 µm<sup>2</sup>, magnetic field 325 mT, dwell time 4000 µs, (256 × 256) pixel<sup>2</sup>.</figcaption></figure>
the lateral resolution is in fact mainly limited by the low signal yield and destructive nature of SIMS. In order to achieve the smallest possible detection limits, as much signal as possible must be extracted from the sputtered volume. One possibility here is to use other primary ions that produce a higher useful yield of sputtered ions. However, other primary ion species typically only achieve a higher yield of either positive or negative ions (not both). Higher yields of positive ions, which are particularly suitable for the detection of metal elements, are achieved using primary ions with high electronegativities, such as oxygen or halogen ions. Enhancement of positive ion yields could thus be achieved using smaller spot sizes from PFIBs or through the use of ILIS. Higher yields of negative ions are achieved by using primary ions that lower the work function of the sample surface, which is where developments using LoTIS can bring benefit by, e.g., providing Cs ions.⁹⁷ Alternatively, the use of precursor gases can also increase the ion yields (see Sec. II C).

Another approach that could be explored to increase yields and therefore also spatial resolution involves further development of SNMS schemes for FIBs, in which sputtered neutrals are analyzed. Through the use of lasers for post-ionization of these neutrals, the dependence of the ion yields on the surrounding material in the sample (the so-called matrix effect) is reduced. However, since high laser intensity is required, SNMS is only possible in pulsed operation, which inevitably requires pulsing of the primary ion beam. Here, the use of TOF spectrometers becomes an obvious choice. Post-ionization with focused electron beams is also conceivable, although preliminary experimental work in this area is scarce.

A further issue in FIB-SIMS that needs to be addressed is material intermixing induced by the primary ions. In order to achieve the smallest beam probe sizes, comparatively high beam energies in the range of 20–50 keV are typically used. However, the disadvantage is the resulting long range of the ions in the target (compared, e.g., to that of the low energy Ar ions commonly used for SIMS depth profiling). Long ion ranges can quickly lead to atom mixing of deeper layers and therefore to a decrease in depth resolution with increasing sputter depth.¹⁰¹ In the future, primary ions with high atomic number and/or small kinetic energy per nucleon could be used. For example, Cs ions from LoTIS or Xe ions from GFIS could provide both small beam sizes and good depth resolutions. Alternatively, the energy per nucleon can also be reduced by using cluster ions, e.g., Bi or Au clusters from LMAIS (see Table I).

Small cluster ions,¹⁰¹ reactive primary ions, e.g., Cs,³¹,⁴⁶ or laser post-ionization¹³⁰ can also reduce the fragmentation of molecules, which is another aim for future developments (see references in Table II). Molecule fragmentation needs to be understood both theoretically and experimentally in order to deduce the molecular composition of the sample from the measured spectra. In this regard, the creation of molecular fragmentation databases for typically used ion energies and types would enable fingerprinting in future work.

Continued spectrometer development is also needed to enable complete detection of all sputtered ions. Here, the TOF spectrometers and magnetic sector spectrometers with large area MCPs lead the way. Development efforts should also be invested into spectrometers that allow higher mass resolution in order to enable the separation of isobars. In this area, results obtained using Orbitraps are very promising.⁸⁵⁶

In the perfect FIB-SIMS instrument, all the key parameters (spatial resolution, mass resolution, detection limit, measurement time)

would be optimized simultaneously. In reality one has to compromise between different priorities. Furthermore, in situ combinations of FIB-SIMS with other analytical modes, e.g., SEM based analysis, are highly desirable. The integration of an electron flood gun for in situ charge neutralization (as is implemented in HIM) would be universally beneficial for the analysis of insulating sample surfaces, and cryo-FIB-SIMS would be of great interest for life science and other beam-sensitive samples. In situ AFM would allow correlation of the SIMS data with the actual sputtering depths enabling more accurate 3D reconstructions.

Finally, most elemental analysis methods, including SIMS, benefit from vacuum levels that are better than the usual high vacuum (HV) conditions of typical FIB chambers in order to avoid background signals originating from residual gas. FIB instruments with UHV or near UHV chambers have been built by researchers in the past¹⁴,⁰¹,¹⁰¹ and the benefits for normal imaging as well as analysis have been demonstrated.¹⁴⁹ Manufacturers should similarly consider the merits of UHV in future instrument development.

## E. Applications of gas-assisted FIB processing

Gas-assisted bottom-up prototyping of nanostructures using the FIB is known as focused ion beam induced deposition (FIBID). In this technique, the focused ion beam induces the partial decomposition of precursor molecules, dissociating them into volatile and nonvolatile 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. This direct writing of nanostructures using the FIB 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 (vapor pressure, sticking coefficient to the surface, residence time, dissociation cross section), 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 better theoretical understanding and empirical modeling tools that generate patterns based on few calibration routines, thus also enabling less experienced users to fabricate complex nanostructures. Table VIII provides an overview of the fields where FIBID processing has been employed so far.

## 1. Basics of ion induced chemistry

The ion-molecule reactions that have been studied in the context of FIBID involve 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 SEs produced
<table><caption>TABLE VIII. Overview of applications of gas-assisted FIB processing, in which gaseous precursor compounds are locally dissociated by the ion beam to grow nanostructures.</caption><thead><tr><th>Property</th><th>Target application</th><th>Ion</th><th>Deposit geometry and precursor</th></tr></thead><tbody><tr><td rowspan="10">Electrical and electronic</td><td rowspan="3">Electrical connections</td><td>He</td><td>Semiconducting nanowires from CpPtMe<sub>3</sub><sup>1019</sup> and metallic Co lines from Co<sub>2</sub>(CO)<sub>8</sub><sup>1020</sup></td></tr><tr><td>Ne</td><td>Metallic nanowires from CpPtMe<sub>3</sub><sup>1019</sup></td></tr><tr><td>Ga</td><td>Conducting nanowires from CpPtMe<sub>3</sub>,<sup>1021,1022</sup> MeCpPtMe<sub>3</sub>,<sup>1023-1025</sup> Au (hfac)Me<sub>2</sub>,<sup>1026,1027</sup> Co(CO)<sub>3</sub>NO,<sup>1028</sup> Cu(hfac)(VTMS),<sup>1029</sup> W(CO)<sub>6</sub> contacts to Co and Cu nanowires,<sup>1030-1032</sup> Pt-based sidewall contacts using MeCpPtMe<sub>3</sub> to MoSi layer stack<sup>1033</sup></td></tr><tr><td rowspan="2">Insulating barriers</td><td>Si</td><td>Thin layer from TMOS [Si(OCH<sub>3</sub>)<sub>4</sub>]<sup>1034</sup></td></tr><tr><td>Ga</td><td>Thin layer from TMOS<sup>1035,1036</sup> and PMCPS [(CH<sub>3</sub>SiHO)<sub>5</sub>]<sup>1037</sup></td></tr><tr><td rowspan="2">Superconductivity</td><td>He</td><td>Planar and 3D superconducting wires from W(CO)<sub>6</sub><sup>1038-1041</sup></td></tr><tr><td>Ga</td><td>Planar nanowires from W(CO)<sub>6</sub><sup>1042-1052</sup> and Nb(NMe<sub>2</sub>)<sub>3</sub>(N-t-Bu),<sup>1053,1054</sup> arrays of Josephson junctions from Nb(NMe<sub>2</sub>)<sub>3</sub>(N-t-Bu),<sup>1055</sup> 3D SQUID from W(CO)<sub>6</sub>,<sup>1056</sup> nanoSQUID from W(CO)<sub>6</sub><sup>1057</sup></td></tr><tr><td rowspan="3">Magnetic</td><td rowspan="2">Nanomagnets</td><td>He</td><td>Nanowires from Co<sub>2</sub>(CO)<sub>8</sub><sup>1020</sup></td></tr><tr><td>Ga</td><td>Nanoparticles from Co<sub>2</sub>(CO)<sub>8</sub>,<sup>1058</sup> nanowires from Co(CO)<sub>3</sub>NO<sup>1028</sup> and Co<sub>2</sub>(CO)<sub>8</sub><sup>1059</sup></td></tr><tr><td>Nanomagnetic probes</td><td>Ga</td><td>Filling FIB milled trenches with W,<sup>1060</sup> magnetic force microscopy (MFM) tips via deposition of thin layer by milling Co<sub>71</sub>Cr<sub>17</sub>Pt<sub>12</sub> target,<sup>1061</sup> Hall-probes from Co<sub>2</sub>(CO)<sub>8</sub><sup>1062</sup></td></tr><tr><td rowspan="3">Optical</td><td>Photonic components</td><td>Ga</td><td>Deposition of defects in etch mask for photonic crystal,<sup>1063</sup> deposition of the central Pt beamstop in Fresnel zone plates,<sup>566</sup> chiral nano-antennae, i.e., helices from MeCpPtMe<sub>3</sub><sup>1064-1066</sup> and from phenanthrene<sup>1067</sup></td></tr><tr><td>Plasmonic components</td><td>Ga</td><td>Chiral nano-antennae, i.e., helices from phenanthrene covered with Au<sup>1068-1070</sup></td></tr><tr><td>Chiral biosensing</td><td>Ga</td><td>Helix arrays from MeCpPtMe<sub>3</sub> coated with poly o-phenylediamine<sup>1071</sup></td></tr><tr><td rowspan="2">Mechanical</td><td>Atomic force microscopy (AFM) tips</td><td>He</td><td>Hammerhead probes from MeCpPtMe<sub>3</sub><sup>1072</sup></td></tr><tr><td>Tunable elastic moduli</td><td>Ga</td><td>DLC (diamond-like carbon) core-shell pillars and springs from phenanthrene,<sup>1073,1074</sup> metal containing pillars and springs from phenanthrene and ferrocene,<sup>1075</sup> MeCpPtMe<sub>3</sub>,<sup>1076</sup> W(CO)<sub>6</sub>,<sup>1077</sup> TMCTS [(HSiCH<sub>3</sub>O)<sub>4</sub>], and O<sub>2</sub><sup>1078</sup></td></tr></tbody></table>

by impact of ions with the substrate, and thermal processes driven by dissipation of the collision energy (see also Fig. 14).<sup>431,1079</sup> 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,<sup>451,1080</sup> 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<sup>1079,1081</sup> 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 UHV.<sup>1079,1081</sup> Although there are differences between FIBID and its UHV models (the UHV environment is cleaner than standard HV FIBID deposition conditions, 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.<sup>1082</sup>

As an example, a study of the reactions of Ru(CO)<sub>4</sub>I<sub>2</sub> with 860 eV Ar<sup>+</sup> ions on a surface in UHV demonstrated that the initial reaction was loss of all four CO ligands to form adsorbed RuI<sub>2</sub>.<sup>451</sup> 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 500 eV electrons results in loss of the CO ligands, but not the iodide, to afford RuI₂ as the final product.<sup>1083</sup> Rapid loss of all of the carbonyl ligands was also observed upon ion bombardment (860 eV) in a UHV model study of the heterobimetallic precursor (η<sup>5</sup>-C<sub>5</sub>H<sub>5</sub>)Fe(CO)<sub>2</sub>Re(CO)<sub>5</sub>.<sup>1080</sup> 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 Au from (Me)<sub>2</sub>Au(hfac) (hfac = hexafluoroacetylacetonate) with He<sup>+</sup>, Ne<sup>+</sup>, Ar<sup>+</sup>, Kr<sup>+</sup>, or Xe<sup>+</sup> at energies of 2–100 keV.<sup>452,1084</sup> The decomposition yield from the precursor increased with increasing ion mass and energy, consistent with a BCA 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 variation in ion mass impacts the deposition chemistry through differences in SE yields, sputter yields and ion implantation yields. Ar<sup>+</sup> and Ne<sup>+</sup> generate sufficient SEs at low beam energies (30 eV) but have a shallower beam penetration depth than He<sup>+</sup>, 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.<sup>56,1085</sup>

Gas phase studies of reactions of Fe(CO)<sub>5</sub> with He, Ne, Ar, and Kr
ions of varying charge and energy<sup>1082</sup> also demonstrated facile loss of
CO ligands upon ion-molecule collision. The distribution of fragment
ions from CO loss Fe(CO)<sub>5</sub>-x, where x = 1-5, was dependent on the
ion mass and the energy transfer in the collision. Under these condi-
tions, light ions such as He<sup>+</sup> resulted in electronic excitation with low
fragmentation efficiency. Heavier ions yielded more extensive CO disso-
ciation from energy transfer and nuclear stopping. The highest extent of
CO loss occurred upon collision with Ne<sup>+</sup>, 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,<sup>1079</sup> namely:

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 π-facial ligands such as cyclopenta-dienyl and allyl can be removed by sputtering, but this is also slow and competes with removal of metal.

## 2. FIBID nanostructures for electronics

The ease to directly write functional structures with different con-
ductivities renders FIBID a powerful tool in electronic applications,

with at least three different electrical conductivity regimes reported:
semiconducting, metallic, and superconducting at low temperature
(see Table IX).

Key parameters here are the carbon content of the deposit as well as its microstructure, which depend on the growth conditions (as well as on the precursor selected). Modulating the growth conditions thus offers an efficient way to tune electrical and electronic behavior. Examples include Pt<sup>1024</sup> and Au<sup>1026,1027</sup> deposition using Ga-FIBID, for which the conductivity increases with the thickness of the as-grown material. This dependence is the result of a gradient in metal content through the film thickness, with a higher carbon content in the first deposited layers vs at the bottom. Pt-based deposits below 50 nm in thickness behave as semiconductors, but display metallic behavior.<sup>1023</sup> for thicknesses above 150 nm.<sup>1024</sup> The metal content of these deposits is less than 33 at. %, consisting of fcc Pt nanocrystals with a diameter of 5–10 nm embedded in an amorphous carbon matrix.<sup>1025</sup> The observed conductivity regimes are expected to be strongly influenced by the disorder and doping introduced by Ga ion impact.<sup>1025</sup> In the case of Cu deposits (copper nanocrystals embedded in amorphous carbon), it has been found that the ion beam current also directly controls the metal content and thus the deposit conductivity.<sup>1029</sup> Furthermore, the ion species used for the deposition can have a great effect. For example, using Ne-FIBID, Pt deposits exhibit metallic behavior, whereas they behave as semiconductors using He-FIBID.<sup>1019</sup> In the case of Ga-FIBID of Au-based deposits, metallic behavior is easily obtained, with significant Au contents of 75 at. % and resistivities exceeding the bulk resistivity of Au by two orders of magnitude.<sup>1027</sup>

A number of works have investigated FIBID of Co deposits due to their magnetic properties, for example, as-grown<sup>1058,1086</sup> and annealed<sup>1028</sup> Ga-FIBID Co deposits (containing 50 at. % Co) exhibit ferromagnetic characteristics and resistivity values at room temperature that exceed the resistivity of bulk Co by several orders of magnitude. Using He-FIBID, nanostructures can be fabricated with higher lateral resolution, such as metallic Co lines of 10 nm in width displaying room temperature resistivities comparable to those grown using Ga-FIBID.<sup>1020</sup>

Intriguing FIBID-grown materials that exhibit metallic behavior at room temperature and transition into the superconducting state at low temperature include W and Nb based deposits, which become superconducting below 4.2–5.1 K (Refs. 1042, 1043, 1047, and 1050) and 5 K,<sup>1053</sup> respectively. In the case of freestanding 3D NbC nano-wires, a broadened superconducting transition between 4 and 11 K has been reported.<sup>1053</sup>

The WC nanostructures, in particular, exhibit remarkable super-
conducting properties, such as upper critical magnetic field values of
B<sub>c2</sub>(2K) = 7–8.5 T (Refs. 1048 and 1050) and critical current density
values of J<sub>c</sub>(2K) = 0.01–0.1 MA cm<sup>-2</sup>.<sup>1042,1044–1046,1050</sup> For very narrow
nanostructures (≤ 50 nm in width), finite size effects that are key to
their application in superconducting circuits have been studied. This
includes phenomena such as a magnetic field-driven re-entrance of the
superconductivity,<sup>1049</sup> the occurrence of non-local voltages,<sup>1051,1052</sup>
and electric field-induced control of superconductivity.<sup>1041</sup>

Furthermore, He-FIBID has facilitated the fabrication of sophisti-
cated 3D WC nanosuperconductors with additional outstanding char-
acteristics. These include a critical temperature ranging from
T<sub>c</sub> = 6.2-7.1 K and an upper critical magnetic field value extending
from B<sub>c2</sub>(0) = 12-15 T. Noteworthy among these structures are hollow
<table><caption>TABLE IX. Overview of various precursor ion combinations and the resulting electrical properties. Room temperature resistivity values $\rho_{RT}$ are given for the respective deposits and for the pure bulk metal from literature.</caption><thead><tr><th>Material</th><th>Precursor compound</th><th>Ion</th><th>Shape</th><th>Composition (at. %)</th><th>Microstructure</th><th>Electrical behavior</th><th>ρ<sub>RT</sub> (μΩ cm)</th><th>ρ<sub>RT</sub> bulk (μΩ cm)</th><th>References</th></tr></thead><tbody><tr><td rowspan="5">Platinum</td><td>MeCpPtMe<sub>3</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>Pt:C:Ga:O<br>46:24:28:2</td><td>Amorphous</td><td>Metal</td><td>70–700</td><td>10.4</td><td>1023</td></tr><tr><td>MeCpPtMe<sub>3</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>Pt:C:Ga:O<br>22:60:11:7</td><td>5–10 nm nanocrystals</td><td>Metal</td><td>700</td><td></td><td>1024</td></tr><tr><td>MeCpPtMe<sub>3</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>Pt:C:Ga<br>17:72:11</td><td>≈3 nm nanocrystals</td><td>Metal</td><td>800</td><td></td><td>1025</td></tr><tr><td>MeCpPtMe<sub>3</sub></td><td>Ne<sup>+</sup></td><td>Planar</td><td>Pt:C<br>17:83</td><td>≈4.5 nm nanocrystals</td><td>Metal</td><td>600</td><td></td><td>1019</td></tr><tr><td>MeCpPtMe<sub>3</sub></td><td>He<sup>+</sup></td><td>Planar</td><td>Pt:C<br>16:84</td><td>≈3 nm nanocrystals</td><td>Semiconductor</td><td>180000</td><td></td><td>1019</td></tr><tr><td rowspan="2">Gold</td><td>Au(hfac)Me<sub>2</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>Au:C:Ga<br>50:35:15</td><td>–</td><td>Metal</td><td>500–1500</td><td>2.4</td><td>1026</td></tr><tr><td>Au(hfac)Me<sub>2</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>Au:C:Ga:O<br>75:<5:20:<5</td><td>–</td><td>Metal</td><td>500–1300</td><td></td><td>1027</td></tr><tr><td rowspan="4">Cobalt</td><td>Co<sub>2</sub>(CO)<sub>8</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>–</td><td>–</td><td>Metal</td><td>189</td><td>6</td><td>1058</td></tr><tr><td>Co<sub>2</sub>(CO)<sub>8</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>–</td><td>Amorphous</td><td>Metal</td><td>19–38</td><td></td><td>1059</td></tr><tr><td>Co(CO)<sub>3</sub>NO</td><td>Ga<sup>+</sup></td><td>Planar</td><td>Co:C:Ga:N:O<br>54:7:9:13:17</td><td>>20 nm nanocrystals</td><td>Metal</td><td>189</td><td></td><td>1028</td></tr><tr><td>Co<sub>2</sub>(CO)<sub>8</sub></td><td>He<sup>+</sup></td><td>Planar</td><td>–</td><td>6 nm nanocrystals</td><td>Metal</td><td>64–116</td><td></td><td>1020</td></tr><tr><td rowspan="2">Copper</td><td>Cu(hfac)<br>(VTMS)</td><td>Ga<sup>+</sup></td><td>Planar</td><td>Cu:C<br>55:45</td><td>20 nm<br>Nanocrystals</td><td>Metal</td><td>50</td><td>1.7</td><td>1029</td></tr><tr><td>Tungsten</td><td>W(CO)<sub>6</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>W:C:Ga<br>40:40:20</td><td>Amorphous</td><td>Superconductor<br>below 5.2 K</td><td>200</td><td>5.6</td><td>1042,1043</td></tr><tr><td rowspan="4">Tungsten</td><td>W(CO)<sub>6</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>W:C:Ga:O<br>40:43:10:7</td><td>1–2 nm nanocrystals</td><td>Superconductor<br>below 4.2–5.1 K</td><td>275</td><td></td><td>1050</td></tr><tr><td>W(CO)<sub>6</sub></td><td>Ga<sup>+</sup></td><td>Planar</td><td>W:C:Ga:O<br>53:34:11:2</td><td>≈1 nm nanocrystals</td><td>Superconductor<br>below 5–5.5 K</td><td>100–350</td><td></td><td>1047</td></tr><tr><td>W(CO)<sub>6</sub></td><td>He<sup>+</sup></td><td>3D</td><td>W:C:O<br>72:20:8</td><td>20–30 nm nanocrystals</td><td>Superconductor<br>below 6.2–7.1 K</td><td>398</td><td></td><td>1038–1040</td></tr><tr><td>Niobium</td><td>Nb(NMe<sub>2</sub>)<sub>3</sub><br>(N-t-Bu)</td><td>Ga<sup>+</sup></td><td>Planar</td><td>Nb:C:Ga:N<br>29:43:15:13</td><td>15–20 nm nanocrystals</td><td>Superconductor<br>below 5.0 K</td><td>550</td><td>15</td><td>1053</td></tr><tr><td></td><td>Nb(NMe<sub>2</sub>)<sub>3</sub><br>(N-t-Bu)</td><td>Ga<sup>+</sup></td><td>3D</td><td>–</td><td>15–20 nm nanocrystals</td><td>Superconductor<br>below 8.1 K</td><td>380</td><td></td><td>1053</td></tr></tbody></table>

nanowires with an outer diameter of 32 nm and aspect ratios of about ≈ 200<sup>1038,1040</sup> as well as nano-helices with a diameter of 100 nm and an aspect ratio of about ≈ 65<sup>1039</sup> (see Fig. 24). These nanostructures exhibit a metallic content of 70 at. % W and consist of 20–30 nm-sized fcc WC<sub>1-x</sub> nanocrystals.

### 3. FIBID nanostructures for mechanics

One of the main advantages of FIBID over standard lithographic techniques is the capability to directly write high aspect ratio structures onto any substrate topography. When it comes to mechanical applications, this allows, e.g., placement of dedicated tips onto AFM cantilevers and spring structures into prefabricated mechanical devices. A recent review by Utke *et al.*<sup>1087</sup> summarizes the mechanical properties

of FIBID pillars and springs. All structures were deposited using Ga-FIBID (ion energies mainly 10–30 keV, beam currents 0.5–9 pA). An interesting finding was that the Ga-FIBID pillars tended to grow as core-shell structures. Using the precursor phenanthrene (C<sub>14</sub>H<sub>10</sub>), elastic moduli of the hydrogenated carbonaceous material in the core and shell were ≈ 300 GPa (stiff core with Ga implantation, low H content) and ≈ 30 GPa (soft shell, presumably high H content).<sup>1073,1074</sup> Depending on the inner diameter of the core and the thickness of the shell, the elastic modulus of the structure ranges between these boundary values. Metallic pillars with metal contents <40 at. % (i.e., below the percolation threshold) have mechanical properties dominated by the co-deposited carbonaceous matrix.<sup>1087</sup> Increasing metal contents yield elastic moduli as follows (metal at. %/elastic modulus normalized to that of pure metal): Fe (21 at. %/0.4),<sup>1075</sup> Pt (60 at. %/0.8),<sup>1076</sup> W
<figure><img src="image_35.png" /><figcaption>**FIG. 24.** 3D FIBID examples. (a) SEM image of a hollow crystalline WC superconducting nanopillar grown by He-FIBID.¹⁰³⁸ (b) Cross-sectional TEM view of the hollow nanowire. (c) Higher magnification SEM image of (a). Reproduced with permission from Córdoba et al., Nano Lett. 18, 1379-1386 (2018). Copyright 2018 American Chemical Society. (d) Superconducting WC nano-helix grown by He-FIBID.¹⁰³⁹ Inset shows its top view. (e) Superconducting transition of the nano-helix. Inset shows the nano-helix contacted for the electrical transport measurements. Reproduced with permission from Córdoba et al., Nano Lett. 19, 8597-8604 (2019). Copyright 2019 American Chemical Society.</figcaption></figure>

(80 at. %/0.4),¹⁰⁷⁷ and SiO₂ (95 at. %/0.8).¹⁰⁷⁸ The non-correlation between the metal content and elastic modulus of the pillars may be due to Ga implantation, which softens the metals. Furthermore, the carbonaceous matrix stiffens or softens the pillar depending on its sp² vs sp³ hybridization ratio and its hydrogen content.

So far, FIBID is typically not used to fabricate high aspect ratio scanning probe tips, in contrast to FEBID; see review by Plank et al.¹⁰⁸⁸ This can be attributed to the strong tendency of the Ga ions to mill the cantilever substrate rather than induce tip (pillar) growth. Implantation of Ga into the cantilever can also be a problem. Here, the enhancement of deposition yields using pulsed irradiation can bring benefit.¹³¹ Since the sputter yield of He ions is much lower, He-FIBID also shows promise in this area and has been used for the fabrication of 3D hammerhead AFM probes.¹⁰⁷² In the case of strain sensors

based on piezoresistive granular material, FEBID is also still the method of choice.¹⁰⁸⁹ However, here too changing to He or another light ion species for FIBID could prove fruitful.¹⁴³

### 4. FIBID nanostructures for photonics and plasmonics

FIBID is also a powerful nanofabrication tool for the exploration of novel optical properties thanks to its unique design flexibility.³⁰²,¹⁰⁹⁰,¹⁰⁹¹ The site specific and local nature of FIBID allows the growth of photonic structures on different material substrates,¹⁰⁹² providing a path to the fabrication of a number of optical elements, such as chiral optical antennae,¹⁰⁶⁴,¹⁰⁶⁹ Fresnel lenses,⁵⁶⁶ and nanosensors.¹⁰⁷¹ Combined with large area laser interference lithography to fabricate a large area photonic crystal, FIBID has been used to define defects to form a multimode waveguide.¹⁰⁶³

Under optimized parameter conditions, it is possible to evolve planar structures along the third dimension, thus manufacturing free-standing nanostructures with more exotic optical properties. For example, 3D chiral nano-helices, prototyped by FIBID, have shown tunable chiroptical response at optical frequencies¹⁰⁶⁵,¹⁰⁶⁶ [Fig. 25(a)], been used as subwavelength circular polarization optics [Fig. 25(b)]¹⁰⁶⁹ exploited in compact and miniaturized high-sensitivity biosensors,¹⁰⁷¹ and integrated onto the apex of background-free and broadband chiroptical probes.¹⁰⁶⁸

The wide range of available gas precursors enables the deposition of metal and dielectric materials that can be applied in the emerging field of photonic resonant nanostructures.⁴³¹ Pure and homogeneous compositions are, however, intrinsically hindered due to various aspects of the deposition process, such as incomplete dissociation of the precursor molecules and the residual contamination from hydrocarbons present in the vacuum chamber, both of which result in carbon content in the nanostructure, and the inevitability of implanted ions, which cause absorption losses, and in some cases, material damage. As a result, FIBID materials exhibit either a nanocrystalline composite structure¹⁰²³,¹⁰²⁵,¹⁰⁹³ or a core/shell architecture, depending on the precursor properties and on the FIB irradiation conditions.¹⁰⁹⁴ Apart from purification approaches, which have mostly been used for FEBID (and which might alter the nanostructure shape and dimensions),¹⁰⁹⁵⁻¹⁰⁹⁸ or reduced implantation effects due to enhanced deposition yields (which require the employment of cryo-FIBID²⁹⁴,²⁹⁵,¹⁰⁵¹) other promising strategies to control the final optical response are post-processing coating methods. In the case of complex 3D shapes, conformal coverage can be obtained by combining FIBID with glancing angle deposition of metals,¹⁰⁶⁸,¹⁰⁶⁹ cyclic voltammetry coating of polymers¹⁰⁷¹ and atomic layer deposition of oxides.¹⁰⁹⁹ Also, the core-shell architecture (resulting from the scattering of Ga into a lower molecular weight matrix) can be controlled to engineer specific optical effects.¹¹⁰⁰,¹¹⁰¹ Other approaches may emerge from the exploitation of other ion beam sources for FIBID, such as LMAIS.⁴⁷,¹¹⁰²

### 5. Outlook

Focused ion beams are a flexible and versatile tool for gas-assisted processing, but so far have been much less used than focused electron beams for this purpose. The reason for this may be the dominance of Ga-FIB, whereby Ga ions are not only implanted into the deposits but can also cause significant physical sputtering and trigger undesirable chemical and physical side effects. In addition, there is still no
<figure><img src="image_36.png" /><figcaption>FIG. 25. Examples of photonic nanostructures realized using FIBID and their related optical properties. (a) SEM image of an array of intertwined nano-helices and their transmission spectra T++, T−, T+, T−− for right and left circularly polarized incident light (RCP and LCP, respectively).$^{1066}$ The inset in the plot presents a scheme of the handedness of incident and transmitted circular polarization. Reproduced with permission from Esposito et al., Nat. Commun. 6, 6484 (2015). Copyright 2015 Springer Nature Limited. (b) SEM image of subwavelength optical device made of helices with opposite handedness (L and R) coupled to orthogonal apertures.$^{1069}$ This system enables conversion of an incoming light beam into four beams of tunable polarization and intensity. The plot shows helicity analysis of the device, recording the transmitted power after placing a rotating quarter-wave plate and a fixed polarizer in front of the detector. The insets show the far-field optical images of the device when the quarter-wave plate rotates by ±45°. Reproduced with permission from Wang et al., Light 8, 76 (2019). Copyright 2019, Authors, licensed under a Creative Commons Attribution (CC BY) license.</figcaption></figure>

precursor development specifically for FIBID. Deposition with ions
can in fact deliver purer and denser materials due to their much higher
mass compared to electrons. In this regard, ion beams from noble
gases, which are chemically inert, are of particular interest. While sev-
eral studies have already presented promising results for FIBID using
He and Ne ions (cf. Table VIII), FIBID using beams of Ar, Kr, or Xe
ions from PFIBs has not yet been reported and should be explored.

F. Novel and unconventional approaches in FIB
processing

Apart from removing or depositing material, introducing dopants or creating defects, the interaction between ions and solids can be used to change materials chemically or morphologically. Such “nonstandard” approaches include FIB-induced cross-linking or dissociation in different types of organic and metal–organic surface layers and also the triggering of self-organization processes. Furthermore, “standard” FIB procedures can be combined with other nano- and microfabrication techniques to mitigate specific limitations and broaden applicability.

**1. Resist patterning by FIB**

In resist based lithography, the goal is to induce a chemical
change in the exposed resist layer to render it either soluble (positive
tone resist) or insoluble (negative tone resist) to the subsequent devel-
opment step. Resist based nanopatterning techniques using photons
/optical lithography) and electrons (EBL) are common in industry,
with the main properties being, respectively, high throughput and high
resolution.¹¹⁰³ With the aim of improving the throughput of EBL while
maintaining a high resolution, pioneering studies demonstrated the
use of Ga-FIB to expose resists.³⁹,¹¹⁰⁴⁻¹¹⁰⁶ Ions have the advantage
over electrons that due to their mass they do not induce backscattering
from the underlying substrate and, therefore, reduce unintended expo-
sure of neighboring pixels (known as the proximity effect). For exam-
ple, line widths of less than 100 nm and a sensitivity of 8 × 10¹¹ ions/
cm² were found using a commercial negative resist and 30 kV Ga-FIB

irradiation.¹¹⁰⁵ Line widths of less than 30 nm and a sensitivity of 1
× 10¹³ ions/cm² were achieved using the positive poly(methyl methac-
rylate) (PMMA) resist and 50 kV Ga-FIB irradiation.¹¹⁰⁴ Furthermore,
using 50 kV Ga-FIB irradiation of the negative poly(phenyl silses-
quioxane) (PPSQ) resist, sub-100 nm tunneling tip structures were fabric-
icated for a sensing device.¹¹⁰⁶ Yet the drawbacks of Ga-FIB include
sputtering of the resist and a relatively large beam spot size (several
nanometers) with significant beam tails. Compared to the significant
developments of EBL over the following years, these drawbacks ham-
pered further use of FIBs for resist exposure until the advent of the
HIM. Helium ion beam lithography (HIBL) combines a smaller probe
size with a low sputter yield, high resist sensitivity, and a reduced prox-
imity effect.¹¹⁰⁷

First studies published in 2009 already highlighted the potential
of HIBL for sub-10 nm patterning.<sup>1108,1109</sup> In both cases, hydrogen sil-
sesquioxane (HSQ) negative resist was used. An ion dose of only
31 µC cm<sup>-2</sup> was required for complete exposure<sup>1109</sup> [see Fig. 26(c)].
Compared to EBL using the same resist, the dose required for HIBL is
lower by a factor of four. HIBL can, therefore, simultaneously provide
a similar resolution to EBL with a better throughput. HIBL with HSQ
has also been employed to fabricate a hard mask for subsequent metal
etching<sup>1110</sup> [Fig. 26(a)] and as a mold for nanoimprint<sup>1111</sup> [Fig. 26(b)].

The 3D nanofabrication of complex crosslinked HSQ nanostruc-
tures, such as embedded nanochannels and suspended grids, was dem-
onstrated using different exposure configurations. ¹¹¹² Furthermore,
due to the large depth of field of HIBL, large-area dense patterns have
been achieved on HSQ as well as exposures on tilted surfaces. ¹¹¹³ The
use of the Ne-FIB for HSQ exposure has proven interesting, providing
a trade-off between high resolution and dose efficiency. ¹¹¹⁴

HIBL using other resists has also been investigated. For example,
sub-10 nm resolution has been obtained on a fullerene based resist
using a dose of 40 µC cm⁻², which is three orders of magnitude lower
than that of a similar process using EBL.¹¹¹⁵ Likewise, sub-10 nm reso-
lution was achieved on an alumina-based resist, and 10 nm lines (with
an aspect ratio of 1:10) were then transferred to Si by means of low-
bias reactive ion etching.¹¹¹⁶ HIBL using a new metalorganic negative
resist, Cr<sub>8</sub>F<sub>8</sub>(pivalate)<sub>16</sub>, has been shown to enable sub-10 nm
<figure><img src="image_37.png" /><figcaption>**FIG. 26.** (a) 8 nm-wide hydrogen silsesquioxane (HSQ) lines patterned by helium ion beam lithography (HIBL) and used as hard masks for subsequent etching of TiN gate.<sup>1110</sup> Reproduced with permission from J. Mater. Chem. C 9, 8285-8293 (2021). Copyright 2021 Royal Society of Chemistry. (b) High-resolution dense nano-patterns in HSQ written using HIBL. Reproduced with permission from Li *et al.*, J. Vac. Sci. Technol., B 30, 06F304 (2012). Copyright 2012 AIP Publishing. (c) Comparison of the charge dose required for HIBL vs electron beam lithography (EBL) using HSQ resist.<sup>1109</sup> Reproduced with permission from Sidorkin *et al.*, J. Vac. Sci. Technol., B 27, L18-L20 (2009). Copyright 2009 AIP Publishing.</figcaption></figure>

resolution patterning using a line irradiation dose of 20 pC/cm (three orders of magnitude lower compared to EBL), demonstrated for Si and W substrates with good resistance to subsequent dry etching.<sup>1117</sup> New hybrid organic-inorganic resists based on Ni have also been demonstrated to perform well in HIBL, requiring an irradiation dose of 22 µC/cm², producing sub-10 nm resolution with low line edge/width roughness.<sup>1118</sup> Notably, HIBL using a new resist composed of a radiation-sensitive monomer (MAPDST) with an organic functionality (TIPMA) only requires a very low exposure dose of 6 µC/cm².<sup>2,1119</sup> The exposure of PMMA to He and heavier ions has also been investigated.<sup>1120</sup>

Additionally, HIBL has shown good performance in combination with liftoff processes, in particular with Au, which has been used to fabricate plasmonic nanoantennae.<sup>1121</sup> A different approach consists of the direct He- and Ne-FIB milling of HSQ or PMMA resists that have been previously patterned using standard EBL.<sup>1122</sup> This can, for instance, be used for pattern repair. HIBL has also been proposed as a method for the (pre-) screening of EUV resists to help evaluate their performance.<sup>1123</sup>

In general, it can be stated that HIBL is very promising for high-resolution resist based nanopatterning due to the low proximity effect and the lower ion dose required in comparison with EBL. Thus, broader use of HIBL in the coming years can be anticipated. More detailed discussions on this topic can be found in previous review articles.<sup>471,1107,1124</sup>

## 2. Cryo-FIBID

In the past, it was found that electron or ion irradiation of Sn-based precursors condensed on a substrate at 120 K produced deposits with metallic behavior.<sup>1125</sup> The topic was recently revived through the use of Ga-FIB to dissociate condensed W(CO)₆ precursor at -100 °C, giving rise to WC nanodeposits that exhibit metallic resistivity.<sup>1051</sup> The particular advantage of the cryo method is the low ion dose required (600 times lower) compared to the standard Ga-FIBID process at room temperature. The new technique, coined cryo-FIBID, requires that the thickness of the condensed precursor layer is comparable to the ion penetration depth, so that the deposit does not lift off when heated back to room temperature.<sup>294,295</sup> Cryo-FIBID has also been carried out using the precursor MeCpPtMe₃,<sup>296</sup> although the resulting PtC deposits were less conductive than their WC counterparts.

So far, the best cryo-FIBID results have been achieved using the precursor Co₂(CO)₈.<sup>297</sup> In this case, the Ga ion dose required is only 15 µC cm⁻², and the obtained metallic resistivity is low (200 µΩ cm). Using cryo-FIBID it is thus possible to write electrical contacts with greater efficiency directly onto a micro-/nanostructure, as outlined in Figs. 27(a)–27(d), and applied to grow electrical contacts onto materials such as graphene, as shown in Fig. 27(e).

Conveniently, the need for a cryogenic module in order to decrease the substrate temperature for the cryo-FIBID experiment can be circumvented by means of a cheap, vibration-free and compact thermoelectric plate. Recent process optimization along these lines has enabled thermoelectric cooling to -60 °C for cryo-FIBID with W (CO)₆.<sup>1126</sup> The resistivity of the deposits (620 µΩ cm) is even lower than that obtained for cryo-FIBID performed at -100 °C. Cooling via the thermoelectric plate method thus provides a promising route for the widespread use of cryo-FIBID in any FIB chamber. Further cryo-FIBID studies will benefit from ongoing process optimization of the thermoelectric cooling method and from the use of alternative and novel precursors for metallic deposits in condensed form.<sup>1080,1127</sup> Future application of cryo-FIBID to directly and efficiently create electrical contacts onto 2D<sup>297</sup> and other ion-sensitive materials is to be expected.

## 3. FIB irradiation of metalorganic spin-coated layers

Although spin-coated layers such as resists are typically used as sacrificial material in a multi-step patterning process, it had also been proposed that metalorganic spin-coated layers could be directly patterned using ion irradiation, producing metallic structures based on Pd,<sup>514,1128</sup> Ir,<sup>1129</sup> and Au.<sup>1130</sup> However, post-annealing treatments were required to achieve the desired metallic resistivity values, which limited interest in this approach. Similarly, electron irradiation of Pd-based spin-coated layers has been used to create nanopatterned structures, but there too, a post-annealing step is required to achieve metallic resistivity.<sup>1131</sup> However, recent process optimization using Pd based spin-coated layers in combination with either focused electron<sup>1132</sup>
<figure><img src="image_38.png" /><figcaption>FIG. 27. Cryo-FIBID process used to grow electrical contacts on 2D materials (e.g., graphene).<sup>297</sup> (a) Graphene ribbons on Si/SiO<sub>2</sub> substrate loaded into chamber. (b) Substrate is cooled and precursor from gas injection system (GIS) delivered giving rise to a condensed precursor layer. (c) FIB irradiation of the condensed layer using prede- fined pattern. (d) Substrate heated up to 30 °C thus sublimating the non-irradiated condensed layer. (e) False color SEM image of a graphene ribbon with four electrical con- tacts grown by cryo-FIBID using Co precursor. Reproduced with permission from Salvador-Porroche et al., Nanoscale Adv. 3, 5656–5662 (2021). Copyright 2021, Authors, licensed under a Creative Commons Attribution (CC BY) license.</figcaption></figure>

or focused ion irradiation<sup>1133</sup> has led to the development of an efficient process that allows the direct patterning of metallic micro- and nano- structures at the wafer level without the need for annealing. Due to the simplicity of the process, together with its high resolution and scalabil- ity, it is tempting to foresee its wide application for the patterning of electrical contacts or other conductive structures in nanoelectronics.

### 4. FIB induced mass transport

Many effects known from broad beam irradiation studies are also observed during FIB processing. This includes the observation of ion hammering and the viscous flow of nanostructures under FIB irradia- tion.<sup>360,1134</sup> Spatially resolved ion beam mixing using FIB with subse- quent rapid thermal annealing has been used to create nanometer sized Si crystals at freely defined positions for single-electron transistor applications.<sup>410</sup> Furthermore, localized ion beam induced growth of nanostructures is often observed and can result in epitaxial over- growth<sup>406</sup> or the selective growth of nanopillars.<sup>1134</sup> An overview of these and other effects related to mass transport along surfaces or between layers, including variations such as atomic mixing, can be found in Ref. 471.

A further example of such irradiation effects is the formation of self-organized patterns (such as “ripples”) on the surface of semicon- ductors, depending on the angle of incidence and the energy of the ions. The broad beam process using noble gas ions is qualitatively understood with mass redistribution playing an important role.<sup>1135–1137</sup> FIB induced self-organized pattern formation has mostly been studied for other (mostly metallic) ion species.<sup>1138–1145</sup> Here, the underlying physics is more complex due to the unavoidable change in stoichiometry of the sample as a result of the high fluence of primary ions. The situation could be simplified by using inert gas ions from GFIS or PFIB. In combination with spatially resolved surface structur- ing, these mass transport effects have the potential for interesting applications, e.g., controlling the wettability of FIB milled trenches for

microfluidic applications. Here, understanding and control of the wavelength of the surface ripples will be key.<sup>1146,1147</sup>

### 5. Hybrid fabrication and heterogeneous integration

Despite the flexibility of FIB based processing, the intrinsically low throughput of the serial technique means that large-scale pattern- ing remains elusive. A way to overcome this limitation is to combine the FIB step with other lithography methods, using the so-called ‘mix and match’ approach. For example, in a method combining FIB pat- terning with nanoimprint lithography (NIL), HSQ resist was patterned by He-FIB and used as a nanoimprint template after development.<sup>1111</sup> Remarkably, this allowed the transfer of lines with a half-pitch of 4 nm into the UV-curable nanoimprint resist. Similarly, miniaturized fluidic channels for single molecule analysis consisting of complex, multilevel, multiscale fluidic circuits have been patterned using FIB and photoli- thography to make a silicon master stamp followed by UV-NIL to fab- ricate a negative replica that was used as the working stamp to imprint the fluidic devices quickly and with high fidelity.<sup>1148</sup> The fabrication of arrays of complex plasmonic nanostructures has been achieved by combining EBL and Au-FIB, demonstrating both planar and 3D nano- structures with high patterning accuracy over large areas.<sup>1102</sup> In further examples, optical lithography has been combined with FIB milling to allow the fabrication of nanochannels in Si-glass microfluidic chips for studies of ion and molecule transport<sup>1149,1150</sup> and for the separation of nanoparticles by size exclusion.<sup>1151</sup> FIB techniques have also been combined with other processing methods, offering improved versatility in terms of the material to be processed and reducing total processing times. For example, FIB patterning of molds into Si was applied for subsequent hot-filament CVD growth of diamond nanocone arrays on a free-standing diamond membrane formed after silicon removal.<sup>1152</sup> Similarly, direct patterning of inorganic hardmask layers has been demonstrated using FIB milling and FIBID combined with reactive ion etching, comparing favorably with the much more complex and
material-limited resist based lithography techniques that are conventionally used in this area.¹¹⁵³ Instead of using the hard mask for later etching steps, it can also serve as a sacrificial layer that enables the use of high ion beam currents. For example, milling through a chromium oxide mask about 63 nm thick provided the same spatial resolution with 100-fold increase in ion beam current (2.6 nA instead of 26 pA). This approach has been used to fabricate Fresnel lenses from silicon dioxide, increasing throughput by a factor of 75 for functionally identical structures.⁵⁶⁷

A further promising application is the use of the FIB as a post-processing tool in CMOS chip manufacture. This extends the semiconductor industry's conventional use of the FIB as a debugging and inspection tool, to the top-down FIB based integration of novel semiconductor circuitry, such as nanometer-scale mechanical devices.¹¹⁵⁴,¹¹⁵⁵ In connection with new (nano)-electronic materials, such as single walled CNTs, it has also been shown that there is low, amendable damage to electrical circuits when a FIB patterning process is implemented after fabrication of the basic structure.¹¹⁵⁶,¹¹⁵⁷

## 6. Outlook

In terms of applications, machining using FIBs goes far beyond a purely top-down approach, since it can also be used to trigger various chemical and physical processes, and combined with various other micro-/nanofabrication techniques. Device fabrication based on unconventional processing steps, as well as unique combinations or alternative advanced sequences, may further gain in importance since these methods can mitigate typical limitations in either FIB processing or the other fabrication techniques. It is hard to foresee in which way such unconventional processing techniques will develop, but they will certainly benefit from progress made in many other areas, e.g., new insights into ion induced chemical processes, novel precursor materials, as well as novel ion species and newly accessible energy ranges.

## V. ROADMAP

Focused ion beams can be employed as an all-in-one tool for studying and modifying matter down to the nanoscale. A showcase example of these diverse applications is given by the He-FIB, which enables imaging of corona virus particles and the fabrication of Josephson tunnel junctions (and much in between), all using the same instrument.

Building on Secs. II-IV of this article describing the current state of the art of FIB instrumentation, theory, and applications, we can now ask where to go next with FIB technology. There are many avenues to pursue, so the answer to this question is multifaceted and complex. This section is devoted to trying to answer this question in some detail.

Figure 28 provides an overview of the fields that drive various FIB techniques and the resulting challenges and demands for the further development of instrumentation, hardware/software interfaces, accessories, process modeling, and fundamental understanding. As the figure outlines, all of these required developments are driven by established or newly emerging research fields that use the FIB as a tool for any or all of the following: localized and comprehensive analytics, material modification, and advanced device fabrication.

To account for the complexity of the situation without getting buried in detail, this section is organized around the important future developments that we have identified as necessary in order to meet the

needs of the drivers. Each driver requires different FIB techniques, brings its own challenges, and demands different actions to move forward. In the following, a short description of these drivers is given and an evaluation of the needs of the user community is then presented. The latter is based on the results of a survey completed by over 50 scientists from across all FIB research fields. The developments necessary for future progress are then derived and described in terms of their challenges and overall potential.

## A. Drivers for future applications

The drivers for FIB technologies span a wide range of fields in science and technology. Currently, the semiconductor industry is the largest driver, demanding process automation, modeling, and the analysis of big data.

In general, the drivers can be separated into two interrelated areas. In the first, the FIB is mainly used for analytical purpose, providing access to a wealth of structural information and physical properties. In the second, the FIB enables rapid, flexible device prototyping and stimulates novel device development. In both of these areas, material modification using the FIB is key, be it to enable a particular form or analysis, or to fabricate novel structures and devices.

A leading example of FIB based analysis is in the life sciences, where it often involves large-volume 3D tomographic analysis of cells and tissues under cryogenic conditions (see Sec. IV C 3). This drives the need for increased processing speed, advanced cryo capabilities and automation. One potential way to increase throughput is through cryo plasma-FIB milling, which enables faster removal of bulk material, as discussed in Sec. IV D. However, cryogenic processing is not straightforward and is further complicated by insufficient vacuum levels in the sample chamber of current dual beam instruments. A better vacuum, as has been demonstrated in the past, can reduce contamination, and in the case of cryo-FIB, can also lead to less water condensation on the target structure.

In both the life sciences and materials science, as well as in environmental research, FIB techniques such as cross sectioning, tomography, and sample fabrication (e.g., for TEM and APT studies, or ex situ characterization of physical properties) have become established standards that would now benefit from powerful process automation. Materials science in particular, can benefit from other ion types, such as ions from noble gas elements that (a) may not accumulate in the material, since they can either pass right through if the sample is thin enough or leave by out-diffusion, and (b) will not undergo chemical reactions. This also applies to radiation hardness testing of materials, where FIB is used as a means to locally mimic the effects of a plasma or solar radiation. Increasingly, cryo-FIB techniques are also being applied to beam-sensitive samples, such as novel battery materials that are relevant for energy-technology applications, which also calls for the cryo-related developments mentioned above. In the case of multi-modal imaging approaches and the identification of target areas for, e.g., TEM lamella preparation, workflows are currently hindered by the very different contrast mechanisms in, e.g., the fluorescence light microscope vs SEM. Addressing this will require improved correlative techniques as well as more advanced data management and analysis (cf. Sec. II F).

In a broader context, FIB research into quantum and 2D materials, as well as other novel materials, can largely be subsumed under materials science, but should be recognized as drivers of “non-
<figure><img src="image_39.png" /><figcaption>FIG. 28. Sankey diagram showing an overview of the interrelated drivers, techniques, challenges and to-do items for future development of FIB science and technology.</figcaption></figure>
conventional” FIB techniques in their own right. For example, the growing interest in quantum materials is driving the need for rapid and high-precision patterning of large 3D structures from novel materials. This could be achieved by combining process modeling with an easy-to-use interface for 3D shape definition and calculation of the required beam and patterning parameters. In addition, chemical functionalities can be integrated into patterning through the development of novel ion sources; oxygen, in particular, is an important tuning parameter for the electronic structure of many quantum materials.

At a more fundamental level, the maskless approach of FIB processing renders it an ideal technique for the precise creation of defects at the exact location where they are needed. This is driven by applications in quantum technology, where defects in an otherwise perfect crystal can act as quantum emitters or, if they carry spin information, as qubits.

On the theoretical side, the creation of specific defects and especially single ion implantation (SII) require a deeper understanding of the mechanisms of defect formation and the evolution of the defect's local environment, which in turn determines the physical properties. Such challenges can be addressed by modeling at different levels of sophistication, as described in Sec. III.

In terms of instrumentation, a key technological challenge for quantum applications is to be able to place individual ions in a (quasi-) deterministic manner and detect them with very high efficiency. Certain defect types may require the implantation of a specific ion for which stable ion sources still need to be developed. The implantation depth is controlled by the mass and kinetic energy of the incident ion, and in order to reduce dephasing, quantum emitters in photonic chip architectures are usually desired to have a depth of 10–100 nm beneath the surface. As such, the ion energy ranges of tens of keV that are currently available are mostly well suited. However, in the case of spatially resolved heavy element implantation, a higher primary beam energy would be required, which poses challenges for the power supplies and for electrical isolation in the ion optical column. If instead non-native atoms are to be implanted into 2D materials, e.g., for high resolution flexible area doping, lower energies are needed. In this context, low energy means less than 100 eV to ensure a significant number of replacement collisions in which the ion exchanges position with a target atom and the latter is removed from the 2D material.<sup>376</sup> Methods to reduce the primary energy of the beam include using deceleration lenses in the final stage of the beam focusing or implementing reverse sample biasing (see also Sec. V C). For the detection of the transiting

primary ion itself or the resulting interaction with the substrate, various approaches are under development (see the Outlook of Sec. IV B).

Another strong driver for FIB technologies are micro-electro-mechanical systems (MEMS)/nano-electro-mechanical systems (NEMS) and microfluidic devices, which are ubiquitous in our modern world, be it in sensors, displays, printers, transducers or microphones. Such devices often combine various active and passive components consisting of electronic and moving parts, and therefore typically rely on a whole chain of thin film lithographic, deposition, and etching techniques. However, these fabrication techniques require that the devices are built up layer by layer. As such, true 3D geometries are difficult to achieve.

FIB processing by milling and deposition, on the other hand, enables the flexible fabrication of complex multi-level geometric structures and smooth 3D shapes, as it permits direct top-down and bottom-up structuring in the same instrument. What has limited the default implementation of FIB technologies in device manufacturing thus far is the slow processing speed of the inherently serial process. Here, the availability of a multibeam system comprising thousands of individually addressable focused beams would represent a major leap forward (see also Sec. II B).

## B. The generic needs of the community

FIB systems have become a standard in scientific research and industrial processing, but the market is still heavily dominated by the Ga-FIB. While Ga represents a good compromise between spatial resolution and sputtering yield for many material systems, other applications require different beam parameters and/or suffer from Ga contamination. In our survey, the participants were therefore asked in which areas they conduct research and upon which material systems and/or devices they focus. The corresponding results and percentages, thus, reflect the perspectives of this particular group of users. Figure 29 shows that materials science, physics, and engineering are the most prominent research areas in the FIB community surveyed. Fields such as biology, medicine, and earth science may be underrepresented in these statistics, since fewer scientists from those areas participated in the survey. It would be interesting to repeat the survey with a larger number of participants from a wider range of fields in order to be more statistically representative. The material systems most commonly studied by the respondents are 2D materials and semiconductors, followed by various other systems including biological samples, ceramics,

<figure><img src="image_40.png" /><figcaption>FIG. 29. Results of a survey of the fields of research (left) and the target materials systems or devices (right) being investigated or addressed.</figcaption></figure>
polymers and environmental samples. This reflects current research trends, but also underscores the universality of the FIB as a tool for modifying matter at the nanoscale.

The typical problems encountered by the FIB users participating in our survey (see Fig. 30) show a clear trend, with surface damage, unwanted implantation/doping and contamination being the most dominant problems. This last point on contamination is mostly related to the typical vacuum operating range of around $10^{-6}$ – $10^{-7}$ mbar and the associated residual gases in the vacuum chamber. In this pressure range, a monolayer of molecules still forms on the sample roughly every second, and with a typical water content of around 60% in the residual gas, most surfaces will also be covered with a double layer of water molecules. The hydrocarbons from the residual gas are also decomposed by the ion beam and, depending on the ratio of the sputtering to deposition yield, can form a carbonaceous layer on the sample. Especially in the case of FIB processing with light ions, even a small amount of contamination can result in greatly reduced net sputtering rates or in the extreme, net contamination deposition. Generally, both water and hydrocarbons can add various, mostly unwanted, chemical reaction channels (cf. Sec. IV E 1). Here, a significant improvement of the vacuum level toward UHV would be an important development. Since some of the contamination is introduced with the sample itself, a dedicated load lock for plasma cleaning of samples prior to FIB processing would be an ideal complement. Other unwanted chemical side-effects may occur when the ion interacts inside the sample and can be mitigated using inert Ion species. However, unwanted physical side-effects such as interlayer mixing or

dealloying are difficult to avoid as this would require a significant reduction in primary ion energies; in the shorter term these effects can be better addressed through process modeling (cf. Secs. III A and III B).

Problems with long patterning times are either due to beam currents not being high enough or to stability issues of the system. PFIB columns address the first issue by proving higher beam currents, but at the expense of a larger probe size. One especially intriguing way of increasing processing speed and thereby reducing patterning times would be the implementation of a multibeam system. Thousands of parallel beams could in principle be available while maintaining small probe sizes (cf. Sec. II B). System stability is mainly limited by the use of mechanical stages, which suffer from drift over time and from inaccuracies in positioning. In principle, laser interferometric stages solve this problem. However, since most FIB systems use a tilted column, the sample must also be tilted in order to allow FIB processing under normal incidence. Thus, novel system designs with a vertical FIB column are of great value. Finally, instabilities in the beam current itself (more of a problem for some of the novel ion sources) can also limit patterning performance, so the development of novel and stable emitters is needed (cf. Sec. II A).

Interestingly, the survey answers to questions about desired spatial resolution, milling depths, deposition thicknesses, and beam energy ranges more or less correspond to what is currently technologically possible. This makes sense, in that users often aim for what is feasible with their instruments. Only a few users were interested in depositing

<figure><img src="image_41.png" /><figcaption>**FIG. 30.** Results of a survey of the typical problems and limiting factors in FIB processing (top left), the target spatial resolution (top right), the target milling depth and deposition thickness (bottom left), and the target ion beam energy range (bottom right).</figcaption></figure>
single molecules or removing/implanting single atoms. Currently, such approaches are beyond the technological capabilities of commercial systems and would require substantial developments. However, with these developments the impact on areas such as quantum technology research would be substantial.

### C. Important future developments

Having discussed the needs and wants of the FIB research community in terms of future applications and user experiences, we now turn to specific technologies that need to be developed. For this purpose, Fig. 28 has been divided into subplots based on different groups of to-do items. This allows us to trace the impact that certain developments will have on specific challenges, to explore the techniques that are then enabled, and ultimately link back to the drivers.

#### 1. Ion beam generation and transport

Figure 31 displays the required developments (i.e., to-do items) and the associated challenges, techniques and drivers in the area of next-generation FIB sources and ion beam transport. Specific needs for novel ion sources, ion optics for both low and high energy beams, and fast beam control/blanking have been identified.

a. *Novel source types including single isotope sources.* A key area requiring development concerns novel ion sources, in particular, high brightness and light element sources, which are crucial for high-resolution imaging and nanostructuring applications. Here, further development of GFIS based sources to operate with gases other than He, Ne, and $N_2$ is desired. The first steps in this direction have already been taken by various researchers testing GFIS based emission of $H^{1158}$ $Xe^{60}$ and Kr.$^{61}$ However, the heavier noble gas elements have

numerous isotopes, sometimes in nearly equal proportions; if the ion optical column is not well shielded from magnetic fields, this can affect spatial resolution, since magnetic fields present in the column can split the ion beam according to the mass of the isotopes. Solutions to this problem, other than shielding, include the addition of a Wien filter. Again, these developments will require new ion optical columns that can reduce or correct the aberration induced by the Wien filter. Alternatively, isotopically pure source gases can be used, similar to the already successful implementation of isotopically pure source materials by manufacturers of Ga-LMIS and AuGeSi-LMAIS. Further LMAIS single isotope sources might also be of interest in the context of SII,$^{194,293,829,835}$ local isotope enrichment$^{76}$ and for a wide range of other applications, e.g., SIMS, also in combination with reactive gas flooding.$^{123,125,992,1001}$ The GaBiLi-source,$^{46,1159}$ for example, provides heavy Bi atoms and small Bi clusters for milling, and a reactive Li ion beam for analysis by SIMS. With the LMAIS, switching between ion beams for these different species is fast (only takes a few seconds) and can be automated. For the future, new alloy concepts that include heavier reactive species are desired; to date only Au-Si, Au-Ge, Au-Ge-Si, and Ga-Bi-Li LMAIS are commercially available.

Ion sources for heavy ions are desirable for applications such as SIMS in order to increase sputter yields and also for device debugging in the semiconductor industry, where the shorter penetration depth of the heavier ion is an advantage. Furthermore, ions from group 1 and group 17 in the periodic table are of interest due to their chemical reactivity, which enhances sputter yields. While successful attempts have been made in the past with group 1 elements,$^{29,31,46,1160}$ efforts for the development of sources based on group 17 elements such as fluorine or iodine are more limited. A possible approach for reactive ion sources using group 17 elements could be the ILIS if implementing the appropriate salts.$^{54}$ Such ILIS prototypes have been developed, but

<figure><img src="image_42.png" /><figcaption>FIG. 31. Developments that are required with respect to the generation and transport of focused ion beams.</figcaption></figure>
they did not yet enter the market. One of the intrinsic issues when operating an ILIS is the need to switch the polarity of the extracted ion beam in order to keep the source composition in balance. While this is usually considered a nuisance it can become an advantage, since by using clever chemistry, ion beams suitable for performing SIMS with both polarities could be extracted. However, collateral damage by the reactive ions to the ion optical elements needs to be considered and avoided as much as possible. We note that the first commercial FIB systems combining reactive ion species with SIMS are currently entering the market.<sup>977,1161</sup>

With regard to source brightness, the recently developed MOTIS/ LoTIS have been shown to achieve high brightness for a number of ion types.<sup>29,31,1160</sup> Furthermore, fundamentally new concepts based on, e.g., insulator-on-conductor ion sources<sup>1162</sup> and other ideas that currently have a very low technology readiness level (TRL) may also have potential for application as high brightness sources, since they partially exploit similar concepts to the GFIS technology.

An aspect that is becoming more and more important for users is instrument uptime, which can be increased by minimizing source maintenance needs. For example, LMIS and LMAIS lifetimes could be increased by increasing the reservoir size of the liquid metal/alloy. The lifetimes of the apertures could be increased by adjusting the material and thickness of the aperture strip, as well as the number of apertures incorporated.

**b. Ion optics for low and high energy ion beams.** Access to low energy ion beams (<1 keV) is becoming increasingly important for a range of FIB applications in which the penetration depth and ion straggle in the material must be minimized. However, the transport of a low-energy beam without sacrificing on resolution is a challenge. This is mainly due to chromatic aberrations (see also Sec. II B). To address this issue, specialized beam optics such as energy filters and chromatic aberration correctors are needed, which are, in general, complicated to produce, align, and tune,<sup>1163</sup> thus posing extra challenges for system automation. Low-energy beams also pose challenges in terms of the stability and precision of the associated electronics.

Key areas where low-energy high-resolution FIBs will bring benefit are in FIB based debugging and mask repair in the semiconductor industry,<sup>507</sup> where minimized ion penetration and thus minimal damage to underlying layers and structures is required. If these low-energy FIBs employ heavy ions, the beam-sample interactions can be confined even more closely to the surface. A further application that requires ultra-low energy beams (down to a few tens of eV) is the controlled and spatially resolved doping of 2D materials or the ion-beam induced modification of surfaces (see Sec. III A). For the latter, the energy spread of the ions emitted from the source must be exceptionally small to begin with, smaller even than the LoTIS and GFIS can deliver. Indeed, in order to reduce chromatic aberrations for all of the above, it makes sense to start with new types of ion sources that have a reduced energy spread and then employ subsequent beam elements for chromatic aberration correction accordingly.

For other applications, higher energy beams are required, such as for the deep placement of (heavy) atoms for quantum technology applications, and for applications requiring even higher spatial resolution. Since the ion collision cascade expands the FIB beam in the material and most damage occurs at the end (cf. again Sec. III A), it may be useful to use high energies for devices based on (potentially suspended)

thin films. The target defects are then generated close to the surface with high spatial precision, but low yield, and the beam damage occurs spatially separated from this in the substrate (or not at all in the case of suspended membranes). While the technological challenges for increasing the beam energy are moderate, the increased size of the required electrical isolation and power supplies will actually limit the achievable resolution, since they may act as additional noise sources.

**c. Fast beam control and blanking.** Standard beam blankers installed on FIB instruments typically achieve blanking times (known as rise times) on the order of 20–100 ns. However, for a number of applications, rise times below 10 ns are desirable and have been demonstrated in isolated cases.<sup>120</sup> Applications requiring faster blanking times include resist patterning, high-end FIBID and SII, in all cases to avoid unintentional exposure.

Another need for specialized beam blanking arises from the fact that ion beam sources typically also create a certain fraction of neutrals in the beam, which is generally unwanted. These neutrals result from charge exchange collisions between energetic ions and neutral gas atoms. The latter are generally present due to insufficient vacuum at the source and in the ion optical column, and in the case of the GFIS, as a direct result of the gas based source technology. In the case of the GFIS, 0.29% He⁰ have been reported under conditions used for medium resolution imaging and for TOF-SIMS (6.3 × 10⁻⁶ mbar He pressure, 20 µm aperture).<sup>1164</sup> However, these numbers depend heavily on the gas pressure and aperture used. Since neutral species are not influenced by electric or magnetic fields and thus cannot be deflected away using ion optical elements or the standard electrostatic blankers, they can result in broad background exposure, especially in the case of long FIB processing times. This is detrimental in applications concerned with few or single-ion impacts at specific target locations, which often also involve high-dose irradiation (and hence even more unwanted neutrals reaching the sample) to make fiducial markers for subsequent correlative analysis. In order to eliminate the neutral beam, a physical obstacle can be introduced into the central portion of the column, which only the ions can bypass by means of a series of electrostatic deflectors. This is known as a chicane blanker. Similar solutions, such as a curved column, could also be explored but come with their own challenges.

## 2. Accessories and complementary instrumentation

In Fig. 32, the required developments related to new accessories (add-ons) for FIBs and complementary instrumentation are outlined. These to-do items can be broken down into categories focused on ion induced chemistry, adaptable sample environments, and analytical add-ons.

**a. Ion induced chemistry.** Applications using FIBID, gas-assisted etching, and resist-based lithography could all be greatly enhanced by the development of more advanced modeling tools, new gaseous precursors and new resists.

In the case of FIBID, new precursor chemistries that enable higher deposit purity (e.g., for plasmonic applications) and superior resistivity (e.g., for circuit edit applications) are needed. The prerequisite for the development of these precursors is a deeper understanding of the ion-molecule reactions that occur during the deposition process.<sup>431</sup> For high-purity metallic deposits, the precursor molecule will ideally be fully decomposed so that only the desired metal component
<figure><img src="image_43.png" /><figcaption>FIG. 32. Developments that are required with respect to accessories and complementary instrumentation.</figcaption></figure>

is deposited and the ligand fragments are pumped away. Similarly, in the case of gas-assisted etching, the precursor molecules should undergo ligand loss to generate empty coordination sites that bind with the substrate to enhance the rate of removal of substrate atoms without forming a residue of nonvolatile reaction products. Once the fundamentals of beam induced chemical reactions are better understood (including aspects such as the effect of beam induced heating), researchers will be better poised to develop simulation tools to enable the prediction and design of more complex deposition and etching scenarios. The development of these simulation tools will also rely on input from systematic parameter optimization, where automated beam control and data analysis will play a key role.

A common but generally undesired effect from ion induced chemistry is the deposition of a thin carbon film over ion-irradiated regions, arising due to residual hydrocarbon species present on the sample surface and in the microscope chamber.⁸⁹⁰ This effect can be minimized by, e.g., plasma cleaning samples before loading into the microscope or working in UHV. Other unwanted beam induced effects that can occur during intentional deposition processes include implantation of the ions themselves into the deposit during the growth process, or concurrent milling of the deposit. To minimize these effects, it is desirable to increase the deposition rate, so that a lower total ion dose is needed for the process. Recently, it has been shown that cryogenic cooling of the substrate is one way to increase deposition rates, which could be investigated further.¹⁰⁵¹ However, it is worth mentioning at least one application where a balance between deposition and concurrent milling by the primary ion beam is actually desired, namely, the formation of high-aspect-ratio hollow nanopillar deposits with unique electronic properties using He-FIBID.¹⁰³⁸ Overall, fine control over the rate of deposition should prove highly beneficial for future applications.

For resist based lithography, further development of resists specifically for lithography using ion beams is needed. It has already been shown that resists tend to be much more sensitive to ions compared to electrons, but so far most resist development has still been for EBL. In order to optimize resists for lithography using different ion species, a deeper understanding of the ion-resist interaction process is required.¹¹²⁰ Consequently, the full potential of FIB resist lithography has yet to be realized, even though HIBL has already demonstrated high resolution patterning with dramatically reduced proximity effects compared with EBL.¹¹⁰⁸,¹¹⁰⁹

b. *Adapted sample environments.* In electron microscopy, sample environments are now routinely adapted through the use of liquid cells that separate, e.g., chemical reagents, from the surrounding vacuum in the chamber. This principle does not readily translate to the FIB, since the typically used Ga ions can easily damage the cell membrane by sputtering and also suffer from limited penetration depths. Accordingly, only He-FIB has been used in a prototype liquid cell,¹¹⁶⁵ because He ions combine negligible sputtering of the cell membrane with a sufficient penetration depth to reach the reaction volume. In contrast, heating of samples during FIB processing has been used for decades, including more recently for the reduction of ion beam induced amorphization and blistering during He- and Ne-FIB processing. Quasi-local heating with an infrared laser¹¹⁶⁶ and homogeneous heating using a heating stage³⁶⁰ have both been tested. However, the latter approach, in particular, suffers from sample drift induced by the high thermal mass of the sample heater. Low drift implementations are thus needed that also have lower power requirements in order to protect the rest of the system (e.g., the piezo motors in the stage and ion optical components in the pole piece) from overheating and to allow faster heating ramps.¹¹⁶⁷ FIBID-related applications could also
benefit from new simple heating stages for exploring *in situ* annealing of the deposited structures.

Sample cooling can also be of interest to reduce beam damage, de-alloying, and surface microstructure formation, and for applications using FIBID or HIBL. For example, often temperatures slightly below 0 °C are sufficient to prevent the formation of eutectic phases or phase separation. In the same manner, molecular desorption rates may be tuned by either decreasing (or increasing) the temperature by only a few tens of Kelvin. Hence, for many experiments with a relatively small temperature range to bridge, Peltier based solutions become possible.¹¹²⁶

A pressing requirement for substantial cooling comes from bio-
logical applications, where cryo-stages and cryo-transfer units have
been developed to enable complete cryo workflows (see Sec. IV C for
examples). However, due to the stage cooling mechanism and shield-
ing, these systems can suffer from reduced imaging performance as
well as limitations regarding sample geometry and compatibility with
certain accessories in the FIB chamber. Further development of spe-
cialized FIB instruments dedicated to the handling of biological and
other sensitive samples is expected. These systems require special load
locks for vacuum and/or cryo transfer, and better vacuum conditions,
in general, will result in less condensation on the specimens.

By adding fluorescence light microscopy to a FIB-SEM system, a dedicated and time-efficient platform for the correlative preparation of TEM lamellae for biology, medicine, and related fields becomes possible, since well-established fluorescence light microscopy protocols can be used to locate regions of interest for FIB milling *in situ*. Indeed, a system including fluorescence light microscopy has recently been demonstrated in a cryo triple-beam configuration.²⁰⁶ Other implementations for fluorescent light detection either employ an ellipsoidal mirror in conventional Ga and plasma FIB-SEM systems for fluorescence spectroscopy of the atoms sputtered by the ion beam,⁸³⁴ or a full confocal microscope setup integrated into the vacuum chamber of a 100 kV LMAIS-FIB with a high-precision stage to move between working positions.⁸³⁵

The latter system demonstrated the *in situ* detection of fluorescent light from arrays of optically active defects created by the FIB, thus representing an important step toward realizing the deterministic creation of quantum emitters (cf. Outlook of Sec. IV B). For this application, it is of utmost importance to reduce all kinds of residual contamination (fluorescent and chemically active), both on the sample and in the vacuum chamber using UHV chambers and ideally inert sample transfer. Dedicated UHV FIB systems for quantum technology do not yet belong to the commercial standard, but have recently been demonstrated.⁹¹,⁸¹⁴

c. *Novel detectors and analytical add-ons.* Quantum technology and therewith the deterministic implantation of ions is one of the main drivers in science and technology today, and correspondingly, there is an urgent need for single ion detection. As outlined in the Outlook of Sec. IV B, specialized detectors¹⁹³,¹⁹⁴ or specific types of ion sources like a Paul trap,⁸²⁷,⁸²⁸ can either count the ions that impinge on the sample or measure the ion impact event. The latter can be realized using an on-chip IBIC measurement,¹⁹⁹,⁸²⁹ which can be implemented for many CMOS compatible quantum devices that are not affected if there is an amplifier nearby. For all other quantum devices, truly agnostic SII detectors that detect, e.g., SEs will constitute an

especially important development. In addition to very high detection efficiencies approaching 100%,⁷⁷⁷,⁸³³ appropriate theory support is needed to calculate the expected SE yields. If such detectors are combined with a complementary system that detects device function, e.g., fluorescence⁸³⁵ associated with single-photon emission from the defects generated, truly deterministic implantation can be realized for an industry-ready commercial platform.

Several types of detection systems exist, which can often be com-
bined to enable the acquisition of unique multimodal data sets. The
general trend is toward better spatial resolution in 3D, higher sensitiv-
ity (and hence lower detection limits), and better quantification of
results. A promising approach in this area is FIB-SIMS. Resolution and
sensitivity are directly linked, which must be considered in efforts to
improve performance. For example, in the case of GFIS and LoTIS
based SIMS, simultaneous improvement in both resolution and sensi-
tivity is not possible, since further reducing the sampling volume ren-
ders the number of target species in that volume statistically
insignificant. Another analytical approach that is complementary to
SIMS uses fluorescence spectroscopy to detect and identify atoms sput-
tered by the FIB and has been shown to be feasible for certain
applications.⁸³⁴

Various other “classic” ion beam analytical methods have been implemented in FIB instruments or are interesting candidates for future implementations. These include IL<sup>175</sup> and RBS,<sup>143</sup> which have been explored by a number of researchers but are not available as commercial solutions. In IL, the luminescence of excited target atoms, defects or recoiled ions is detected using parabolic mirrors and a combination of gratings and lenses to obtain spectral information that allows identification of the emission source. IL was recently demonstrated for semiconductor heterostructures and Li-ion batteries<sup>834</sup> and also has potential for various insulating samples in fields such as geology, mineralogy, biology, and medicine, including nanoparticle research such as nanotoxicology. In contrast, RBS measures the energy and scattering angle of backscattered ions and allows standard-free and depth-resolved elemental analysis. However, RBS in FIB systems has largely been abandoned due to fundamental problems related to the high number of multiple scattering events. Implementing a low energy ion scattering (LEIS) configuration may be a good alternative, as it only measures the energy of the charged particles that are primarily scattered at or close to the sample surface. Nevertheless, due to the low yield of charged scattered particles, high fluences are required to obtain good statistics.

There has been some debate around the potential to use X-rays as
a signal for ion induced processes. Some reports indicate that this could
indeed be possible.¹⁶⁹ However, in that particular case, the observed
X-rays were not generated by the interaction of the primary ion beam
with the sample. Instead, non-conductive samples became positively
charged under ion impact and backscattered ions caused the emission
of SEs from components in the chamber. These SEs were then acceler-
ated toward the positively charged sample surface and generated X-ray
peaks due to random interactions with the chamber components. It
turns out that because the inelastic interactions that are responsible for
X-ray generation depend on velocity and not on energy, typical primary
beam energies in FIB systems are not sufficient for X-ray production.
As stated by Joy et al.,¹¹⁶⁸ a beam energy of about 53 MeV for He ions,
for example, would be required in order to excite the same X-ray lines
as can be obtained using a 6 keV electron beam. Such high beam
<figure><img src="image_44.png" /><figcaption>FIG. 33. Developments that are required with respect to automation and data management.</figcaption></figure>

energies are out of reach for conventional FIB systems and thus the high-energy PIXE technique remains elusive to FIB.

In contrast to X-ray spectroscopy, the generation and detection of Auger electrons is indeed possible using the beam energies of current FIB systems. Auger electrons are generated due to the creation of core-holes in both the projectile ions and the substrate atoms, thus Auger signals emanate from both colliding particles, resulting in spectra with rich features that can be quantitatively evaluated.¹⁶⁶

Another analytical approach is based on *in situ* monitoring of ion beam-induced property changes, such as *in situ* electrical measurements to test nanostructured samples or to probe, e.g., magnetization via the measurement of a Hall voltage. Various other analytical techniques can also be incorporated into the FIB chamber, including AFM for *in situ* surface characterization or a nanoindenter for *in situ* mechanical testing. The benefit of performing these techniques *in situ* is not only control of the sample environment (e.g., no exposure to air), but also the possibility of real-time imaging (usually with the SEM) enabling immediate quality control of the measurement. For improved implementation of all these approaches, open hard- and software APIs are required.

Further developments that will facilitate work with analytical add-ons are related to the continued integration of sample cleaning options based on UV light or remote plasma, as well as the combination of FIB processing with direct laser milling.¹¹⁶⁹ Systems integrating femtosecond laser milling with FIB have recently become available and the associated workflows and possibilities are currently being explored.

### 3. Automation and data management

Figure 33 shows the technological developments required in terms of automation and data management. Both of these areas are

rapidly growing in importance due to the sheer volume of samples and data. There is enormous potential to facilitate the daily work of technologists and researchers using recent developments in ML and artificial intelligence. However, the black-box nature of such routines requires awareness and regular cross-checking of both the training data used and the results obtained. In the following, open interfaces for hardware and software, and then needs related to data access and management, are discussed in more detail.

a. *Open hardware and software interfaces.* In recent decades, science has increasingly moved toward openness and transparency. Today, this is generally a prerequisite for receiving taxpayer money for scientific research.¹¹⁷⁰ The idea of sharing not only raw data (as discussed in Subsection VC3b) but also task-specific developments in terms of machine operation and data analysis holds great potential. Instead of developing isolated solutions specific to particular research groups, which often become obsolete or are lost when the original developers move on, a larger community can maintain and further develop methods much more efficiently. In addition, the overall speed of development is significantly increased, as existing data and tools can be reviewed much more easily before “reinventing the wheel.”

Open access to nonproprietary development is already standard in many scientific fields, but the more technologically sophisticated and commercially valuable scientific work becomes, the more conflicts over intellectual property, licenses and potential patents can arise. Nevertheless, the major FIB instrument manufacturers have recognized the benefits of opening up their machines for modification by the users. Everyday users seek the ultimate in machine performance. Therefore, a key resource for driving future developments comes from enabling those users to make the most efficient use of instrument time and gain the most insight from the data generated. The larger the
active user community is, the more far-reaching the benefit, which in turn translates to increased sales for the manufacturers even if new technological developments do not have immediate impact on a patent or a price tag. What users need are open hardware interfaces to give them real-time access to detector signals and to enable them to add their own custom components. Even more important is a full-fledged API that allows control of all system parameters accessible in the GUI and ideally all others in developer mode. In this respect, software development on the manufacturer side must be a compromise between the needs of those who require easy-to-use software yet with more limited access, and those who require full access.

For process automation, certain tools are already included in some FIB systems. For example, routines that have already been executed can be stored and modified in a quasi-graphical approach, removing the hurdle of programming in a text-based interface. A key area needing a high degree of automation is in the efficient acquisition of tomographic data sets with imaging based on SE detection, as well as EDS and EBSD. FIB based tomography is particularly used in the life sciences and in environmental research, and increasingly in all branches of materials science, including for battery research and energy conversion. In all cases, high precision and repeatability are required.

In the future, automation tools should be complemented by ML algorithms that help with experimental control and real-time data analysis. Integration of an active learning user interface (human in the loop)<sup>1171</sup> for *in operando* improvement of the supporting ML algorithms would then allow easy continuous training and thus automatic control and/or optimization of processing based on predefined quality parameters or figures of merit. Such feedback control would also be beneficial for advanced patterning tasks, where modeling-informed pattern generation and optimization could be coupled with FIB-processing in a fully automatic way.

Open software interfaces are also required for data analysis, which varies greatly depending on the application typically requiring a tailored approach. ML-based solutions are similarly very diverse, with application to problems including simple data noise reduction, the broad field of feature recognition and data reduction, super-resolution imaging, and full quantification. The integration or linking of different methods and data streams thus needs open interfaces. Therefore, in place of closed all-in-one tools for data analysis and automation, manufacturers should instead provide the infrastructures needed for users to efficiently develop solutions for the broader community.

### b. Data access and management.
Likewise, all data generated should be open and ideally FAIR. The acronym FAIR, coined by Wilkinson *et al.*<sup>1172</sup> in 2016, stands for Findable, Accessible, Interoperable, and Reusable. The FAIR principles have led to global initiatives in all scientific disciplines.<sup>1173–1176</sup> In particular, research areas that generate large amounts of data, such as the life sciences and materials science, are driving the development of data harmonization including a comprehensive set of metadata, ontologies, and workflows that are accessible along with the data.<sup>969</sup> For experimentally derived data, this includes sample tagging, e.g., with QR codes linked to each resulting dataset, along with the corresponding experimental workflows documented in electronic lab journals. One of the biggest challenges with open and FAIR data are the diversity of data sets from different sources. The Novel Materials Discovery (NOMAD)

laboratory<sup>1177,1178</sup> can serve as a blueprint here, as it maintains a collection of data repositories (called oases) for data from virtually all codes in computational materials science.

Several factors are crucial for the successful implementation of such data repositories:

* The data must be easy to upload and integrate into the repository.

* The data must be presented in a common format that allows easy access and efficient searching.

* Ideally, additional toolkits such as metadata crawlers or ML tools for data analysis or prediction should be offered.

* There should be an embargo period option to restrict access to collaborators and/or industry partners before publication or patent.

* The data sets themselves, as well as scripts used for data processing and analysis, should be given DOIs to make them citable.

With respect to data from (FIB-related) microscopy and spectroscopy, proprietary file formats are used by various manufacturers. While this can be useful when providing additional functionality or easier access to certain data analysis routines, it poses a major problem if there is no way to access the raw unprocessed data to analyze it and make it available. In order to integrate such data into a FAIR infrastructure, a standardized and multidimensional open file format specifically for correlative image and spectroscopy data are highly desirable. HDF5 would be such an option (where HDF stands for hierarchical data format), allowing raw data to be stored in image or spectroscopy file formats (such as tiff or binary files) together with metadata and all other types of information in a structured way.<sup>1179</sup> However, this would require that instrument manufacturers agree on such a uniform standard, possibly following the lead of the neutron, x-ray and muon research communities where the HDF5-based data format nexus is used.<sup>1180</sup>

In general, open and FAIR data enables platform- and tool-independent analysis as well as correlation with data from other sources. Furthermore, image processing tools originally developed for other purpose (which may be based on completely different data generation platforms) can be applied and further developed for FIB-specific analysis. A prime example is the open source and platform-independent image processing software ImageJ and its derivatives,<sup>239,1181,1182</sup> which has already been extended through a variety of community-developed plug-ins as well as further adapted and integrated into other programs via its API. Here again, ML can be leveraged as an extremely powerful tool for automated data evaluation, especially for large and complex data sets from correlative measurements or tomography. For example, external programming libraries for ML-based image classification and analysis such as scikit-learn,<sup>1183</sup> Tensorflow,<sup>1184</sup> PyTorch,<sup>1185</sup> dragonfly,<sup>1186</sup> and Ilastik<sup>257</sup> are already available, actively developed and are becoming easier to use.

Ultimately, protocols will need to be established for the preprocessing of raw data into data packages for storage while others parts are to be discarded. In this regard, bottom-up harmonization of FAIR data including hierarchical and structured data repositories with full metadata can help with data management and sorting in order to provide “useful” raw data for further processing both internally and externally, while avoiding or at least minimizing the typical data graveyards.
4. Process modeling

The required developments concerning process modeling are outlined in Fig. 34. Process modeling plays a key role in technology development for integrated circuits (ICs)¹¹⁸⁷,¹¹⁸⁸ and together with other types of simulation, is considered one of the drivers of Moore’s law. It is also heavily used beyond traditional device scaling (“Beyond CMOS” and “More than Moore”¹¹⁸⁹) However, in spite of FIB processes sharing much physics and chemistry with IC processes, process modeling is much less used in the FIB community. This is due to the hefty price tag for commercial simulation tools from the IC business and the much smaller industry behind FIB activities. Nevertheless, the success of process modeling for IC development demonstrates its potential for the further development of related FIB processes.

In the following, process modeling needs for FIB applications are discussed in terms of new BCA simulation tools, continuum modeling and approaches for modeling FIBID, as well as further areas where more advanced computational techniques are critical for progress.

a. BCA simulations beyond TRIM. The simulation program most widely used by the FIB community is TRIM,²⁵³ which allows the calculation of range and damage statistics, in addition to rough estimates of sputtering yields in 1D amorphous targets (see Sec. III A 2). Its success is based on the fact that it provides reasonable estimates for any ion-target combination, and the fact that it incorporates a convenient user interface. Other BCA simulation tools that in addition allow consideration of dynamic changes to the target and other target types (2D and 3D, and crystalline targets) would certainly benefit from more intuitive user interfaces. Work toward this goal has recently been reported for one particular code¹¹⁹⁰ and could probably be translated to other codes

with moderate effort. This would promote adoption of a wider range of BCA simulation codes by the community.

A further desired feature is the implementation of SE generation in BCA codes. This will allow more accurate interpretation of FIB images, will foster model development for precursor dissociation in FIBID processes, and may also aid SII when detecting single ion impacts using an SE detector.

b. Continuum modeling and approaches toward FIBID modeling. Continuum simulations of surface evolution are hampered by the need for various input parameters and the fact that they neglect processes taking place beneath the surface (see Secs. III D 1 and III D 3). However, these simulations are still useful for qualitative investigations. Wider applicability is expected from coupling BCA with continuum simulations, which could enable modeling of surface diffusion and reactions, heat transport and/or relaxation of density changes. This could pave the way for accurate and general process simulation of FIB processes, although taking into account physical and chemical parameters will still be an issue. Here, input from more fundamental methods, or strategies for experimental parameter determination, will be required. The former is already standard in IC process simulation, while an example of the latter in the context of FEBID can be found in the use of tilted nanowires on a pedestal for model calibration.⁴⁶⁹

As an alternative to physico-chemical modeling, ML has opened up new possibilities in many fields of research. In FIB technology, an example of this is a neural network that has been trained on a set of binary design patterns, the corresponding SEM images, and the ion beam parameters used in their production.¹¹⁹¹ The trained network was then able to accurately predict the patterning outcome for previously unseen designs in nearly real time. Such a neural network

<figure><img src="image_45.png" /><figcaption>FIG. 34. Developments that are required with respect to process modeling.</figcaption></figure>
approach holds promise for process control and, in a more general setup, for reducing the number of trial and error iterations in the fabrication of nanostructures.

c. *Addressing the gap in understanding.* The most important fundamental issues which cannot be addressed at the BCA or continuum level are:

* Accurate description of the energy loss of energetic ions and recoils accounting for their charge state and the electronic structure of the target.

* Production of defects in the irradiated material accounting for electronic excitations.

* Evolution of the atomic structure of the target over macroscopic time scales at room or elevated temperatures during annealing.

* Effects of defects and impurities on the mechanical, electronic, optical and magnetic properties of the irradiated system.

The simulations needed here can be divided into three groups: modeling of the collision, evolution of the system after the ion impact, and assessment of the influence of defects on materials properties.

Future progress in these fields is expected simply due to increasingly powerful computers, which allow for the simulation of larger systems and longer times. These advances will lead to more widespread use of MD and kMC simulations for specific FIB applications and to explore the physics of ion-target interaction in general. Currently these research areas are only accessible using BCA-type simulations. In addition, new developments in computational techniques widen the range of applicability of these advanced methods. For example, MD simulations with ML-derived interatomic potentials trained by DFT calculations (see Sec. III B 2) raise the accuracy and reliability of MD predictions to DFT level while being applicable to much larger systems.

Combinations of various techniques in a single run (e.g., first-principles approaches combined with ML-potential MD, or analytical-potential MD combined with BCA methods) can also help elucidate irradiation effects in various situations, such as in strongly non-uniform systems when the main focus is on the description of damage production in one of the subsystems, or over longer time scales. Examples are the response of 2D materials on substrates to ion bombardment³⁷⁰,¹¹⁹² or the evolution of the target under high-dose FIB irradiation.

Computers with massively parallel architectures and recent development of Ehrenfest dynamics allow prediction of the energy transfer from the ion to the target through ballistic collisions and electronic excitations, and of the energy dissipation in the target involving defect formation without any empirical parameters. In particular, the direct juxtaposition of experimental data and corresponding simulation results concerning ion transit through atomically thin targets (e.g., graphene and other 2D materials) should shed light on the mechanisms of ion neutralization and energy transfer. Indeed, if the initial/final charge states of the ion and its kinetic energy are known, along with the scattering angle, this information can be correlated with impact parameter-dependent results of atomistic simulations carried out using TDDFT-based Ehrenfest dynamics with the assumption that the nuclei behave as classical particles. TDDFT-based Ehrenfest dynamics can also improve parameterization of two-temperature models, bridging the gap between different approaches in multiscale atomistic

simulations. Though very useful, their application will remain limited to small systems for quite some time.

While significant progress in process modeling has been made, there are still challenges for the development of more advanced methods and their application to irradiation simulations. One of the challenges is simulation of more complex scenarios of ions passing through 2D materials (touched on above), and interpretation of the theoretical results. After passing through the target, the ion may be in a mixed charge state because the nuclei move in an average potential created by the electron subsystem, which can be in an excited state. For example, in the experiment, a hydrogen atom (proton) which has passed through the target can be in charge state zero or plus one, while non-integral charge localized around the atom can be found in the simulations. This problem is related to the fundamental question of the connection between quantum-mechanical averages and observable quantities, and requires careful analysis in the context of ion-target interaction.

There are also challenges in the methodology to be overcome. As an example, the common computational schemes of DFT codes fail at small separations between the nuclei, when atom cores overlap. Even for full-electron codes, numerical instabilities in the eigenvalue solvers are expected at small interatomic distances. There are also other challenges related to spin-polarization energies of atoms, as recent calculations have indicated.³⁷⁶

As for the long-term evolution of the system after irradiation (e.g., during post-treatments such as annealing at temperatures of several hundred Kelvin over hours), techniques other than MD with DFT or ML/analytical potentials are required. The bottleneck is the large number of computational steps to be performed. Parallelization can resolve the issue of system size (ultimately each processor calculates the forces acting on one specific atom) and thus reduce the cost of the time step down to a certain minimum. However, the time step in MD simulations should still be at the atomic scale (normally a few femtoseconds), which indicates that ~10¹⁵ steps must still be performed in order to simulate one second of the physical time. Even if performing each time step takes ~10⁻⁴ seconds (a typical value for a system comprised of less than 100 atoms), the total CPU time will be several years. In some cases (e.g., migration of point defects and their annealing in crystalline solids), kMC simulations may provide insights into the evolution of the system on a macroscopic timescale (see Sec. III C). However, kMC can hardly be applied to systems with a high degree of amorphization or when the atomic structure of the system changes substantially during annealing.

Assessment of the effects of defects on the properties of materials is in a much better situation. DFT-based approaches make it possible to calculate the electronic and magnetic properties of the defective system and directly juxtapose the results of calculations with the experimental data. In particular, insights into the optical properties and exciton binding energies of defective materials have recently been obtained,¹¹⁹³ and photoluminescence spectra of materials with defects such as single-photon emitters have been calculated.⁸¹⁸,¹¹⁹⁴⁻¹¹⁹⁷

## VI. EXECUTIVE SUMMARY AND PERSPECTIVE

A focused ion beam (FIB) instrument employs a finely focused beam of ions with an energy of typically 2–30 keV that is scanned across a sample to effect modifications down to the nanometer scale. The technique relies on the transfer of energy from the energetic primary ion to target atoms, resulting in the displacement of the substrate atoms and potentially their removal from the sample. As such the FIB instrument
is a universal tool for all areas of research enabling comprehensive anal-
yses, maskless local material changes and rapid prototyping of devices.

The aim of this document is to provide an overview of the current
state of the art of FIB technology, its applications and important tool
developments, all of which require attention by researchers and tech-
nologists developing new FIB based workflows and instrumentation.
This document can thus serve as an important reference work for stu-
dents, FIB users, academic and commercial developers of related tech-
nologies, and funding agencies. It includes overview tables, providing a
bird's eye view of the relevant works in this field. New developments in
the various driving fields of research pose new challenges for FIB tech-
niques, for which we propose targeted solutions and provide a list of
technical developments that will be required.

From an instrumentation point of view, the ubiquitous gallium
FIB is an excellent tool for the preparation of both transmission elec-
tron microscopy (TEM) samples and functional nanostructures.
However, FIB sources producing ions of other elements are becoming
increasingly common and provide additional degrees of freedom for
the fabrication of new functional materials. In fact, liquid metal alloy
ion sources (LMAISs) and gas field-ionization sources (GFISs) were
used even before the gallium liquid metal ion source (LMIS) started to
control the market. Newer developments include the plasma focused
ion beam (PFIB), which has quickly gained relevance due to its ability
to remove large volumes of material while maintaining a lateral resolu-
tion sufficient for many applications. Combined with the very recent
addition of the magneto-optical trap ion source (MOTIS), about two
thirds of the elements of the periodic table can now be accessed for FIB
applications (see Fig. 1 and Table I).

New applications related to, e.g., life and environmental science, quantum technology, energy conversion and storage, present new challenges for existing techniques that will require innovations in ion sources, beam transport and detectors. Low energy FIBs (<1 keV), for example, are particularly relevant for the semiconductor industry, quantum technology, and applications based on low dimensional materials. New developments related to heavy and unconventional ion beams are important for single ion implantation (SII) and analytical applications such as secondary ion mass spectrometry (SIMS).

The theory of ion-solid interactions and all related processes that
may occur in FIB processing must bridge many orders of magnitude
in terms of time and length scales (see Fig. 5). Therefore, a trade-off
must always be found between accuracy and the size of the modeled
system. The binary collision approximation (BCA) provides insight
into a range of FIB-relevant quantities that are mainly driven by the
ballistic phase of the collision cascade, such as sputtering yield, ion
penetration depth, and degree of amorphization (see Table III for an
overview of available BCA codes). Other techniques such as molecular
dynamics (MD), kinetic Monte Carlo (kMC), density functional theory
(DFT), and continuum modeling can address further important
aspects. These include short-term defect evolution (MD), long-term
system evolution at elevated temperatures (kMC), charge state of
defects and charge transfer (DFT), and ion induced chemistry as well
as surface processes (continuum modeling).

An important FIB application that needs support from theory
and simulation in this respect is gas-assisted processing, usually
referred to as focused ion beam induced deposition (FIBID). This is
the nanometer-scale counterpart to industrial and consumer-based 3D
printing. The variety of precursor gases (see Table IX) and the

patterning flexibility of the FIB enable the fabrication of nanoscale
devices with unique properties and geometries for emerging applica-
tions (see Table VIII). Here, an in-depth understanding of the complex
processes related to the non-uniform gas flow, the surface kinetics of
all involved molecular species, and the secondary particle generation,
together with the related energy-dependent dissociation cross sections
of molecular bonds, is needed for accurate process simulation.

Process modeling is also relevant for other FIB applications, such
as subtractive processing (see Table V) and defect engineering (see
Table VI). Applicability, however, will also require an extension of the
existing knowledge on ion-solid interactions into the energy range rel-
evant for FIB applications. This knowledge transfer would be particu-
larly helpful for calculations of the production rate of charged
secondary particles, especially secondary electrons (SEs). The yield of
SEs is relevant for several applications, including SII and also general
imaging and analysis. For analysis applications, robust models for the
prediction of secondary ion (SI) yields are needed. In addition to
addressing these fundamental questions, efforts are required in the
areas of empirical process modeling and shape prediction for additive
and subtractive patterning. Here, open application programming inter-
faces (APIs) and open source software in combination with machine
learning (ML) will enable better control over the focused ion beams,
which will in turn allow higher precision, resulting in faster and more
reproducible device fabrication.

New software and computing technologies enable the collection
and evaluation of large data sets, e.g., for the FIB based analytical
methods of FIB-SIMS and serial sectioning (see Table VII). ML algo-
rithms can assist with the acquisition, alignment, and segmentation of
these typically multidimensional data sets, which should ideally be
made available in a FAIR data infrastructure. Currently, biological
applications are driving this field by using data sets from various ana-
lytical modalities, including FIB based tomography, to generate nano-
scale 3D representations of biological specimens that provide new
insight into microscopic structures and how they function. Other driv-
ers are energy storage and conversion, meta- and functional materials,
and the semiconductor industry.

As the applications of FIB processing are extremely diverse, it will
not be a single technological development that brings a breakthrough.
Instead, numerous advances will be needed in order to address the chal-
lenges that have been identified. The resulting developments will often
impact several scientific fields, as can be seen from the overview graph
in Fig. 28. Therefore, we look to an exciting future where FIB processing
will grow in importance and open new avenues in many areas of sci-
ence and technology, spanning quantum technology to the life sciences.

ACKNOWLEDGMENTS

This publication is based on the work from the COST Action
FIT4NANO CA19140, supported by COST (European Cooperation
in Science and Technology) https://www cost.eu/ and http://www.
fit4nano.eu/. The authors would like to thank the FIT4NANO
members for participating in the survey that forms part of Sec. V B,
as well as for input provided during in-person meetings and online
discussions. Specifically, we would like to thank (in alphabetical
order) Richard J. Curry, Damjana Drobne, Ádám Gali, Hans
Hofsäss, Peter Hosemann, Karen L. Kavanagh, Daniel Kiener,
Wolfgang Lang, Elisabeth A. Müller Gubler, Pablo A. Postigo, Paul
Räcke, Joakim Reuteler, Samuel M. Stavis, Iwona B. Szymańska,
Edgar J.D. Vredenbregt, and Robert Winkler for their valuable feedback on the manuscript. The writing of this document and the implementation of FIT4NANO also benefitted greatly from the guidance and support of worldwide FIB manufacturers and add-on producers, including (in alphabetical order) Carl Zeiss, Ionoptika, Kleindiek Nanotechnik, Nanores, NenoVision, Orsay Physics, PlasmaSolve, Quantum Design Microscopy, RAITH, Tescan, ThermoFisher Scientific, TOFWERK, and X-Spektrum.

## AUTHOR DECLARATIONS

### Conflict of Interest

The authors have no conflicts to disclose.

### Author Contributions

**Katja Höflich:** Conceptualization (equal); Data curation (equal); Visualization (lead); Writing – original draft (lead); Writing – review & editing (equal). **Gerhard Hobler:** Conceptualization (equal); Writing – original draft (lead); Writing – review & editing (equal). **Frances Allen:** Writing – original draft (lead), Writing – review & editing (lead). **Tom Wirtz:** Conceptualization (equal) Writing – original draft (lead). **Gemma Rius:** Conceptualization (equal); Data curation (lead); Visualization (equal); Writing – original draft (equal). **Lisa McElwee-White:** Writing – original draft (equal); Writing – review & editing (lead). **Arkady V. Krasheninnikov:** Writing – original draft (equal). **Matthias Schmidt:** Writing – original draft (equal). **Ivo Utke:** Writing – original draft (equal). **Nico Klingner:** Writing – original draft (equal). **Markus Osenberg:** Writing – original draft (equal). **Rosa Córdoba:** Writing – original draft (equal). **Flyura Djurabekova:** Writing – original draft (equal). **Ingo Manke:** Writing – original draft (equal). **Philip Moll:** Writing – original draft (equal). **Mariachiara Manoccio:** Writing – original draft (equal). **José María De Teresa:** Writing – original draft (equal). **Lothar Bischoff:** Writing – original draft (equal). **Johann Michler:** Writing – original draft (equal). **Olivier De Castro:** Writing – original draft (equal). **Anne Delobbe:** Writing – original draft (equal). **Peter Dunne:** Writing – original draft (equal). **Oleksandr V. Dobrovolskiy:** Writing – original draft (equal). **Natalie Frese:** Writing – original draft (equal). **Armin Gölzhäuser:** Writing – original draft (equal). **Paul Mazarov:** Writing – original draft (equal). **Dieter Koelle:** Writing – original draft (equal). **Wolfhard Möller:** Writing – original draft (equal). **Francesc Pérez-Murano:** Writing – original draft (equal). **Patrick Philipp:** Writing – original draft (equal). **Florian Vollnhals:** Writing – original draft (equal). **Gregor Hlawacek:** Conceptualization (lead); Funding acquisition (lead); Visualization (equal); Writing – original draft (equal); Writing – review & editing (equal).

## DATA AVAILABILITY

Data sharing is not applicable to this article as no new data were created or analyzed in this study.

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