Electron and ion imaging of gland cells using the FIB/SEM system

Morphomics via next-generation electron microscopy

The living body is composed of innumerable fine and complex structures. Although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.

Reconstructing 3D digital model without distortion for poorly conductive porous rock by nanoprobe-assisted FIB-SEM tomography

Oil and natural gas prospecting requires precise pore characterisation of insulating rock samples, which involves severe charging problems in the state-of-art FIB-SEM tomography, such as overexposure, drift and distortion. For weak cemented samples with very poor conductivity, the conventional ways such as decreasing accelerating voltage or current as well as coating a thin layer of carbon or gold fail to eliminate all the detrimental effect, leading to image distortion in the form of lateral shift and longitudinal stretching. A new nanoprobe-assisted method is explored in FIB-SEM tomography to address this problem and improve image quality. To be specific, a metallic nanoprobe is induced and attached on the sample surface to create an express path for the export of excess electrons near the region of interest, which effectively removes distortion and drift when imaging. Two adjacent areas were characterised and reconstructed into 3D digital models by FIB-SEM tomography with nanoprobe-assisted method applied to one region only. The lateral shift creates zigzag feature for distorted region and the longitudinal stretching of undistorted object can reach 14%. Average pore size of distorted region is larger than that of the undistorted region, however considering the longitudinal stretching, the average pore size of distorted region can be corrected to the same level as the undistorted region. The systematic error caused by distortion for poorly conductive porous rock is hazardous for digital rock physics analysis. Therefore, the nanoprobe-assisted FIB-SEM tomography should be regarded as a one of the optional and feasible procedures in case decreasing accelerating voltage or current as well as coating a thin layer of conductive material does not work.

Union operation image processing of data cubes separately processed by different objective filters and its application to void analysis in an all-solid-state lithium-ion battery

In this article, we propose a smart image-analysis method suitable for extracting target features with hierarchical dimension from original data. The method was applied to three-dimensional volume data of an all-solid lithium-ion battery obtained by the automated sequential sample milling and imaging process using a focused ion beam/scanning electron microscope to investigate the spatial configuration of voids inside the battery. To automatically fully extract the shape and location of the voids, three types of filters were consecutively applied: a median blur filter to extract relatively larger voids, a morphological opening operation filter for small dot-shaped voids and a morphological closing operation filter for small voids with concave contrasts. Three data cubes separately processed by the above-mentioned filters were integrated by a union operation to the final unified volume data, which confirmed the correct extraction of the voids over the entire dimension contained in the original data.

Developing 3D SEM in a broad biological context

When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.

FIB-SEM tomography in biology

Three-dimensional information is much easier to understand than a set of two-dimensional images. Therefore a layman is thrilled by the pseudo-3D image taken in a scanning electron microscope (SEM) while, when seeing a transmission electron micrograph, his imagination is challenged. First approaches to gain insight in the third dimension were to make serial microtome sections of a region of interest (ROI) and then building a model of the object. Serial microtome sectioning is a tedious and skill-demanding work and therefore seldom done. In the last two decades with the increase of computer power, sophisticated display options, and the development of new instruments, an SEM with a built-in microtome as well as a focused ion beam scanning electron microscope (FIB-SEM), serial sectioning, and 3D analysis has become far easier and faster.Due to the relief like topology of the microtome trimmed block face of resin-embedded tissue, the ROI can be searched in the secondary electron mode, and at the selected spot, the ROI is prepared with the ion beam for 3D analysis. For FIB-SEM tomography, a thin slice is removed with the ion beam and the newly exposed face is imaged with the electron beam, usually by recording the backscattered electrons. The process, also called "slice and view," is repeated until the desired volume is imaged.As FIB-SEM allows 3D imaging of biological fine structure at high resolution of only small volumes, it is crucial to perform slice and view at carefully selected spots. Finding the region of interest is therefore a prerequisite for meaningful imaging. Thin layer plastification of biofilms offers direct access to the original sample surface and allows the selection of an ROI for site-specific FIB-SEM tomography just by its pronounced topographic features.

Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution

Scanning Electron Microscopy (SEM) has long been the standard in imaging the sub-micrometer surface ultrastructure of both hard and soft materials. In the case of biological samples, it has provided great insights into their physical architecture. However, three of the fundamental challenges in the SEM imaging of soft materials are that of limited imaging resolution at high magnification, charging caused by the insulating properties of most biological samples and the loss of subtle surface features by heavy metal coating. These challenges have recently been overcome with the development of the Helium Ion Microscope (HIM), which boasts advances in charge reduction, minimized sample damage, high surface contrast without the need for metal coating, increased depth of field, and 5 angstrom imaging resolution. We demonstrate the advantages of HIM for imaging biological surfaces as well as compare and contrast the effects of sample preparation techniques and their consequences on sub-nanometer ultrastructure.

3D imaging of cells and tissues by focused ion beam/scanning electron microscopy (FIB/SEM)

Integration of a scanning electron microscope (SEM) and focused ion beam (FIB) technology into a single FIB/SEM system permits use of the FIB as a nano-scalpel to reveal site-specific subsurface microstructures which can be examined in great detail by SEM. The FIB/SEM technology is widely used in the semiconductor industry and material sciences, and recently its use in the life sciences has been initiated. Samples for FIB/SEM investigation can be either embedded in a plastic matrix, the traditional means of preparation of transmission electron microscopy (TEM) specimens, or simply dried as in samples prepared for SEM imaging. Currently, FIB/SEM is used in the life sciences for (a) preparation by the lift-out technique of lamella for TEM analysis, (b) tomography of samples embedded in a matrix, and (c) in situ site-specific FIB milling and SEM imaging using a wide range of magnifications. Site-specific milling and imaging has attracted wide interest as a technique in structural research of single eukaryotic and prokaryotic cells, small animals, and different animal tissue, but it still remains to be explored more thoroughly. In the past, preparation of samples for site-specific milling and imaging by FIB/SEM has typically adopted the embedding techniques used for TEM samples, and which have been very well described in the literature. Sample preparation protocols for the use of dried samples in FIB/SEM have been less well investigated. The aim of this chapter is to encourage application of FIB/SEM on dried biological samples. A detailed description of conventional dried sample preparation and FIB/SEM investigation of dried biological samples is presented. The important steps are described and illustrated, and direct comparison between embedded and dried samples of same tissues is provided. The ability to discover links between gross morphology of the tissue or organ, surface characteristics of any selected region, and intracellular structural details on the nanometer scale is an appealing application of electron microscopy in the life sciences and merits further exploration.

Investigation of cell-substrate interactions by focused ion beam preparation and scanning electron microscopy

Cell-substrate interactions, which are an important issue in tissue engineering, have been studied using focused ion beam (FIB) milling and scanning electron microscopy (SEM). Sample cross-sections were generated at predefined positions (target preparation) to investigate the interdependency of growing cells and the substrate material. The experiments focus on two cell culturing systems, hepatocytes (HepG2) on nanoporous aluminum oxide (alumina) membranes and mouse fibroblasts (L929) and primary nerve cells on silicon chips comprised of microneedles. Cross-sections of these soft/hard hybrid systems cannot be prepared by conventional techniques like microtomy. Morphological investigations of hepatocytes growing on nanoporous alumina membranes demonstrate that there is in-growth of microvilli from the cell surface into porous membranes having pore diameters larger than 200 nm. Furthermore, for various cell cultures on microneedle arrays contact between the cells and the microneedles can be observed at high resolution. Based on FIB milled cross-sections and SEM micrographs cells which are only in contact with microneedles and cells which are penetrated by microneedles can be clearly distinguished. Target preparation of biological samples by the FIB technique especially offers the possibility of preparing not only soft materials but also hybrid samples (soft/hard materials). Followed by high resolution imaging by SEM, new insights into cell surface interactions can be obtained.

Ultrastructure of the asexual blood stages of Plasmodium falciparum

Plasmodium falciparum is the most deadly of the human malaria parasites. The particular virulence of this species derives from its ability to subvert the physiology of its host during the blood stages of its development. The parasite grows and divides within erythrocytes, feeding on the hemoglobin, and remodeling its host cells so they adhere to blood vessel walls. The advent of molecular transfection technology, coupled with optical microscopy of fluorescent protein reporters, has greatly improved our understanding of the ways in which the malaria parasite alters its host cell. However, a full interpretation of the information from these studies requires similar advances in our knowledge of the ultrastructure of the parasite. Here we give an overview of different electron microscopy techniques that have revealed the fine structure of the parasite at different stages of development. We present data on some of the unusual organelles of P. falciparum, in particular, the membrane structures that are elaborated in the erythrocyte cytoplasm and are thought to play an important role in trafficking of virulence proteins. We present and discuss some of the exciting whole cell imaging techniques that represent a new frontier in the studies of parasite ultrastructure.

Comparison of different preparation methods of biological samples for FIB milling and SEM investigation

When a new approach in microscopy is introduced, broad interest is attracted only when the sample preparation procedure is elaborated and the results compared with the outcome of the existing methods. In the work presented here we tested different preparation procedures for focused ion beam (FIB) milling and scanning electron microscopy (SEM) of biological samples. The digestive gland epithelium of a terrestrial crustacean was prepared in a parallel for FIB/SEM and transmission electron microscope (TEM). All samples were aldehyde-fixed but followed by different further preparation steps. The results demonstrate that the FIB/SEM samples prepared for conventional scanning electron microscopy (dried) is suited for characterization of those intracellular morphological features, which have membranous/lamellar appearance and structures with composition of different density as the rest of the cell. The FIB/SEM of dried samples did not allow unambiguous recognition of cellular organelles. However, cellular organelles can be recognized by FIB/SEM when samples are embedded in plastic as for TEM and imaged by backscattered electrons. The best results in terms of topographical contrast on FIB milled dried samples were obtained when samples were aldehyde-fixed and conductively stained with the OTOTO method (osmium tetroxide/thiocarbohydrazide/osmium tetroxide/thiocarbohydrazide/osmium tetroxide). In the work presented here we provide evidence that FIB/SEM enables both, detailed recognition of cell ultrastructure, when samples are plastic embedded as for TEM or investigation of sample surface morphology and subcellular composition, when samples are dried as for conventional SEM.

A technique for improved focused ion beam milling of cryo-prepared life science specimens

The combination of focused ion beam and scanning electron microscopy with a cryo-preparation/transfer system allows specimens to be milled at low temperatures. However, for biological specimens in particular, the quality of results is strongly dependent on correct preparation of the specimen surface. We demonstrate a method for deposition of a protective, planarizing surface layer onto a cryo-sample, enabling high-quality cross-sectioning using the ion beam and investigation of structures at the nanoscale.

Focused ion beam/scanning electron microscopy characterization of cell behavior on polymer micro-/nanopatterned substrates: A study of cell–substrate interactions

Topographic micro and nanostructures can play an interesting role in cell behaviour when cells are cultured on these kinds of patterned substrates. It is especially relevant to investigate the influence of the nanometric dimensions topographic features on cell morphology, proliferation, migration and differentiation. To this end, some of the most recent fabrication technologies, developed for the microelectronics industry, can be used to produce well-defined micro and nanopatterns on biocompatible polymer substrates. In this work, osteoblast-like cells are grown on poly(methyl methacrylate) substrates patterned by nanoimprint lithography techniques. Examination of the cell-substrate interface can reveal important details about the cell morphology and the distribution of the focal contacts on the substrate surface. For this purpose, a combination of focused ion beam milling and scanning electron microscopy techniques has been used to image the cell-substrate interface. This technique, if applied to samples prepared by freeze-drying methods, allows high-resolution imaging of cross-sections through the cell and the substrate, where the interactions between the nanopatterned substrate, the cell and the extracellular matrix, which are normally hidden by the bulk of the cell, can be studied.

Molecular design and characterization of the neuron-microelectrode array interface

Electrophysiological activities of neuronal networks can be recorded on microelectrode arrays (MEAs). This technique requires tight coupling between MEA-surfaces and cells. Therefore, this study investigated the interface between DRG neurons and MEA-surface materials after adsorption of neurite promoting proteins: laminin-111, fibronectin, L1Ig6 and poly-l-lysine. Moreover, substrate-induced effects on neuronal networks with time were analyzed. The thickness of adsorbed protein layers was found between approximately 1 nm for poly-l-lysine and approximately 80 nm for laminin-111 on platinum, gold and silicon nitride. The neuron-to-substrate interface was characterized by Scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and SEM after in situ focused-ion-beam milling demonstrating that the ventral cell membrane adhered inhomogeneously to laminin-111 or L1Ig6 surfaces. Tight areas of 20-30 nm and distant areas <1 microm alternated and even tightest areas did not correlate with the physical thickness of the protein layers. This study illustrates the difficulties to predict cell-to-material interfaces that contribute substantially to the success of in vitro or in vivo systems. Moreover, focused ion beam (FIB)/SEM is explored as a new technique to analyze such interfaces.

FIB/SEM characterization of carbon-based fibers

The aim of this paper is to show how a focused ion beam combined with a scanning electron microscope (FIB/SEM machine) can be adopted to characterize composite fibers with different electrical behavior and to gain information about their production and modification. This comparative morphology investigation is carried out on polyacrylonitrile (PAN) carbon fibers and their chemical precursor (the oxidized PAN or oxypan) which has different electrical properties. Fibers are imaged by electron and ion beams and sectioned by the focused ion beam (FIB). A sample of oxypan fibers processed by a radio frequency (RF) plasma is also investigated and the role of the conductive carbon layer around their unmodified, insulating bulk is discussed. A suitable developed edge detection technique (EDT) on electron, ion images, and after the FIB sectioning, provides quantitative information about the thickness of the created layer.

Examination of enamel-adhesive interface with focused ion beam and scanning electron microscopy

INTRODUCTION

The purpose of this study was to observe, with a scanning electron microscope, the interface between enamel and orthodontic adhesive after focused ion-beam milling. In addition, enamel etched with phosphoric acid was compared with enamel conditioned with self-etching primer.

METHODS

Four freshly extracted human premolars were collected and pumiced by using rubber cups with fluoride-free paste, washed, and dried. The enamel of 2 teeth was etched with 37% phosphoric acid for 30 seconds, washed, and dried; the enamel of the other 2 teeth was conditioned with self-etching primer for 5 seconds. Stainless steel brackets were bonded with Transbond XT adhesive (3M Unitek, Monrovia, Calif) according to the manufacturer's instructions. The specimens were milled by focused ion beam and observed under the scanning electron microscope.

RESULTS

The scanning electron micrographs showed that 37% phosphoric acid seemed to produce more enamel loss than the self-etching primer. Moreover, the enamel-adhesive interface was more irregular when the enamel was etched with 37% phosphoric acid. Finally, a gentler etch pattern of the self-etching primer on the enamel surface was observed, and this conditioner could be used clinically for minimal intervention in the orthodontic bonding procedure.

CONCLUSIONS

Focused ion-beam milling to prepare samples allowed clear observation of the enamel-adhesive interface without artificial damage.

Focused-ion-beam Milling: A Novel Approach to Probing the Interior of Particles Used for Inhalation Aerosols

PURPOSE

The current study aimed to examine the pharmaceutical applications of the focused-ion-beam (FIB) in the inhalation aerosol field, particularly to particle porosity determination (i.e. percentage of particles having a porous interior).

MATERIALS AND METHODS

The interior of various spray dried particles (bovine serum albumin (BSA) with different degrees of surface corrugation, mannitol, disodium cromoglycate and sodium chloride) was investigated via FIB milling at customized conditions, followed by viewing under a high resolution field-emission scanning electron microscope. Two sets of ten particles for each sample were examined.

RESULTS

For the spray-dried BSA particles, a decrease in particle porosity (from 50 to 0%) was observed with increasing particle surface corrugation. Spray-dried mannitol, disodium cromoglycate and sodium chloride particles were determined to be 90-100%, 0-10% and 0% porous, respectively. The porosity in the BSA and mannitol particles thus should be considered for the aerodynamic behaviour of these particles.

CONCLUSIONS

The FIB technology represents a novel approach useful for probing the interior of particles linking to the aerosol properties of the powder. Suitable milling protocols have been developed which can be adapted to study other similar particles.

Surface damage induced by FIB milling and imaging of biological samples is controllable

Focused ion beam (FIB) techniques are among the most important tools for the nanostructuring of surfaces. We used the FIB/SEM (scanning electron microscope) for milling and imaging of digestive gland cells. The aim of our study was to document the interactions of FIB with the surface of the biological sample during FIB investigation, to identify the classes of artifacts, and to test procedures that could induce the quality of FIB milled sections by reducing the artifacts. The digestive gland cells were prepared for conventional SEM. During FIB/SEM operation we induced and enhanced artifacts. The results show that FIB operation on biological tissue affected the area of the sample where ion beam was rastering. We describe the FIB-induced surface major artifacts as a melting-like effect, sweating-like effect, morphological deformations, and gallium (Ga(+)) implantation. The FIB induced surface artifacts caused by incident Ga(+) ions were reduced by the application of a protective platinum strip on the surface exposed to the beam and by a suitable selection of operation protocol. We recommend the same sample preparation methods, FIB protocol for milling and imaging to be used also for other biological samples.

Focused ion beam manipulation and ultramicroscopy of unprepared cells

The focused ion beam (FIB) technique of nanomachining combined with simultaneous scanning electron microscopy (SEM) was used for submicron manipulation and imaging of unprepared (fresh) cells to demonstrate the potentiality of the FIB/SEM technique for ultramicroscopic studies. Sectioning at the nanoscale level was successfully performed by means of ion beam-driven milling operations that reveal the ultrastructure of fresh yeast cells. The FIB/SEM has many advantages over other ultramicroscopy techniques already applied for unprepared/fresh biological samples.