Optimization of specimen preparation of thin cell section for AFM observation

High resolution imaging of intracellular structures of ultrathin cell section samples is critical to the performance of precise manipulation by atomic force microscopy (AFM). Here, we test the effect of multiple factors during section sample preparation on the quality of the AFM image. These factors include the embedding materials, the annealing process of the specimen block, section thickness, and section side. We found that neither the embedding materials nor the temperature and speed of the annealing process has any effect on AFM image resolution. However, the section thickness and section side significantly affect the surface topography and AFM image resolution. By systematically testing the image quality of both sides of cell sections over a wide range of thickness (40-1000 nm), we found that the best resolution was obtained with upper-side sections approximately 50-100 nm thick. With these samples, we could observe precise structure details of the cell, including its membrane, nucleoli, and other organelles. Similar results were obtained for other cell types, including Tca8113, C6, and ECV-304. In brief, by optimizing the condition of ultrathin cell section preparation, we were able to obtain high resolution intracellular AFM images, which provide an essential basis for further AFM manipulation.     

Micro‐CT scouting for transmission electron microscopy of human tissue specimens

Transmission electron microscopy (TEM) provides sub‐nanometre‐scale details in volumetric samples. Samples such as pathology tissue specimens are often stained with a metal element to enhance contrast, which makes them opaque to optical microscopes. As a result, it can be a lengthy procedure to find the region of interest inside a sample through sectioning. We describe micro‐CT scouting for TEM that allows noninvasive identification of regions of interest within a block sample to guide the sectioning step. In a tissue pathology study, a bench‐top micro‐CT scanner with 10 μm resolution was used to determine the location of patches of the mucous membrane in osmium‐stained human nasal scraping samples. Once the regions of interest were located, the sample block was sectioned to expose that location, followed by ultra‐thin sectioning and TEM to inspect the internal structure of the cilia of the membrane epithelial cells with nanometre resolution. This method substantially reduced the time and labour of the search process from typically 20 sections for light microscopy to three sections with no added sample preparation.     

A novel sample holder allowing atomic force microscopy on transmission electron microscopy specimen grids: repetitive, direct correlation between AFM and TEM images

A novel sample holder that allows atomic force microscopy (AFM) to be performed on transmission electron microscope (TEM) grids is described. Consequently, AFM and TEM images were repeatedly obtained on exactly the same sample area. For both techniques, a thin carbon film was used as the imaging substrate. Although these techniques have been previously used in conjunction, AFM and TEM images on exactly the same area have not been repeatedly obtained for any system. Correlation of AFM and TEM images is useful for work where the three‐dimensional topographical information provided by the AFM could be used to better interpret the two‐dimensional images provided by the TEM and vice versa. To demonstrate the applicability of such correlation, new results pertaining to a fibrillar collagen system are summarized.     

Alignment of AFM images using an iterative mathematical procedure

An iterative mathematical procedure for the alignment of sequentially recorded atomic force microscope images (AFM) is presented. The computer program is able to correct commonly observed drifts in vertical and lateral directions, rotations around a vertical or lateral axis and differences in scale. This method is applied on dissolution experiments of uranium dioxide (UO2) surfaces. Images recorded during in situ experiments, which are shifted probably due to thermal fluctuations, can be aligned with good accurancy. In a further approach the UO2 surface is marked by electron-beam-induced deposition (EBD or EBID) with microstructured reference points. The alignment can be distinctly improved using marked sample surfaces because of the characteristic shape of the markings, which do not change during the experiment. Furthermore, the markings can be used to find again a domain on a sample surface. Therefore, AFM images recorded before and after an ex situ experiment (e.g. treatment in corrosive medium for a longer period of time) can be aligned with a nanometer spatial resolution.     

Combined ultramicrotomy for AFM and TEM using a novel sample holder

A new sample holder that allows combined microtomy for atomic force microscopy (AFM) and transmission electron microscopy (TEM) is described. The main feature of this sample holder is a small central part holding the sample. This central part fits into the head of an atomic force microscope. AFM measurements can be performed with a sample mounted in this central part of the sample holder. This makes the alignment of a microtomed bulk sample unnecessary, and offers the opportunity of an easy and fast combined sample preparation for AFM and TEM.     

Thermal enhancement of AFM phase contrast for imaging diblock copolymer thin film morphology.

A simple and effective means of increasing the morphological detail in AFM phase micrographs of microphase separated block copolymer films is presented. Effective AFM phase imaging of microphase separated systems hinges upon the existence of appropriate contrast mechanisms such as differences in elasticity between the microphase separated domains. For some systems, AFM phase imaging at room temperature results in low contrast images due to a paucity of differential mechanical behavior between the microphase domains, e.g. at room temperature both species are glassy. Through the use of a heating apparatus custom-designed for AFM, an elastic contrast mechanism can be created in some systems by raising the specimen to a temperature between the glass transitions of the constituent polymer species. This serves to preferentially soften one species with respect to the other, thus enhancing the phase contrast mechanism, which results in micrographs with superior detail. This simple technique is demonstrated using films of a series of polystyrene-b-poly(n-alkyl methacrylate) diblock copolymers and both commercial and custom-built heating stages. By choosing appropriate measurement temperatures, AFM phase contrast could be greatly enhanced, or indeed created, when compared to room temperature images of these specimens. For these materials, contrast enhancement required that the sample be heated roughly 20 degrees C above the glass transition of the lower-Tg species.     

NanoSIMS imaging of Bacillus spores sectioned by focused ion beam

Preparation and sectioning of bacterial spores by focused ion beam and subsequent high resolution secondary ion mass spectrometry analytical imaging is demonstrated. Scanning transmission electron microscopy mode imaging in a scanning electron microscope is used to show that the internal structure of the bacterial spore can be preserved during focused ion beam sectioning and can be imaged without contrast staining. Ion images of the sections show that the internal elemental distributions of the sectioned spores are preserved. A rapid focused ion beam top‐sectioning method is demonstrated to yield comparable ion images without the need for sample trenching and section lift‐out. The lift‐out and thinning method enable correlated transmission electron microscopy and high resolution secondary ion mass spectrometry analyses. The top‐cutting method is preferable if only secondary ion mass spectrometry analyses are performed because this method is faster and yields more sample material for analysis; depth of useful sample material is ～300 nm for top‐cut sections versus ～100 nm for electron‐transparent sections.     

Atomic force microscopy of freeze-fracture replicas of rat atrial tissue

Atomic force microscopy (AFM) has provided three-dimensional (3-D) surface images of many biological specimens at molecular resolution. In the absence of spectroscopic capability for AFM, it is often difficult to distinguish individual components if the specimen contains a population of mixed structures such as in a cellular membrane. In an effort to understand the AFM images better, a correlative study between AFM and the well-established technique of transmission electron microscopy (TEM) was performed. Freeze-fractured replicas of adult rat atrial tissue were examined by both TEM and AFM. The same replicas were analysed and the same details were identified, which allowed a critical comparison of surface topography by both techniques. AFM images of large-scale subcellular structures (nuclei, mitochondria, granules) correlated well with TEM images. AFM images of smaller features and surface textures appeared somewhat different from the TEM images. This presumably reflects the difference in the surface sensitivity of AFM versus TEM, as well as the nature of images in AFM (3-D surface contour) and TEM (2-D projection). AFM images also provided new information about the replica itself. Unlike TEM, it was possible to examine both sides of the replica with AFM; the resolution on one side was significantly greater compared with the other side. It was also possible to obtain quantitative height information which is not readily available with TEM.     

Design and performance of a combined secondary ion mass spectrometry-scanning probe microscopy instrument for high sensitivity and high-resolution elemental three-dimensional analysis

State-of-the-art secondary ion mass spectrometry (SIMS) instruments allow producing 3D chemical mappings with excellent sensitivity and spatial resolution. Several important artifacts however arise from the fact that SIMS 3D mapping does not take into account the surface topography of the sample. In order to correct these artifacts, we have integrated a specially developed scanning probe microscopy (SPM) system into a commercial Cameca NanoSIMS 50 instrument. This new SPM module, which was designed as a DN200CF flange-mounted bolt-on accessory, includes a new high-precision sample stage, a scanner with a range of 100 μm in x and y direction, and a dedicated SPM head which can be operated in the atomic force microscopy (AFM) and Kelvin probe force microscopy modes. Topographical information gained from AFM measurements taken before, during, and after SIMS analysis as well as the SIMS data are automatically compiled into an accurate 3D reconstruction using the software program "SARINA," which was developed for this first combined SIMS-SPM instrument. The achievable lateral resolutions are 6 nm in the SPM mode and 45 nm in the SIMS mode. Elemental 3D images obtained with our integrated SIMS-SPM instrument on Al/Cu and polystyrene/poly(methyl methacrylate) samples demonstrate the advantages of the combined SIMS-SPM approach.     

Out‐of‐focus background subtraction for fast structured illumination super‐resolution microscopy of optically thick samples

We propose a structured illumination microscopy method to combine super resolution and optical sectioning in three‐dimensional (3D) samples that allows the use of two‐dimensional (2D) data processing. Indeed, obtaining super‐resolution images of thick samples is a difficult task if low spatial frequencies are present in the in‐focus section of the sample, as these frequencies have to be distinguished from the out‐of‐focus background. A rigorous treatment would require a 3D reconstruction of the whole sample using a 3D point spread function and a 3D stack of structured illumination data. The number of raw images required, 15 per optical section in this case, limits the rate at which high‐resolution images can be obtained. We show that by a succession of two different treatments of structured illumination data we can estimate the contrast of the illumination pattern and remove the out‐of‐focus content from the raw images. After this cleaning step, we can obtain super‐resolution images of optical sections in thick samples using a two‐beam harmonic illumination pattern and a limited number of raw images. This two‐step processing makes it possible to obtain super resolved optical sections in thick samples as fast as if the sample was two‐dimensional.     

Surface modification of AFM silicon probes for adhesion and wear reduction

Tip wear of silicon probes used for an atomic force microscope (AFM) is a critical issue. Wear can result in an increase of tip radius and adhesion between tip and sample, thus reducing the image resolution and introducing artifacts. In order to reduce adhesion, friction, and wear so as to reduce tip related artifacts, liquid lubricant (Z-TETRAOL), self-assembled monolayers (pentafluorophenyltriethoxysilane (PFPTES)), and fluorocarbon polymer (Fluorinert™) were applied on the silicon probe. A comprehensive investigation of adhesion, friction, and wear of the uncoated/coated tips in both ambient air and various humidity levels as well as the influence of the coatings on the image resolution was performed. Experiments showed that the coatings reduced the adhesion, friction, and wear of the silicon tip, improved the initial image resolution, and exhibited less deterioration as compared to that of uncoated tip in the long-term test.     

Atomic force microscopy applied to study macromolecular content of embedded biological material

We demonstrate that atomic force microscopy represents a powerful tool for the estimation of structural preservation of biological samples embedded in epoxy resin, in terms of their macromolecular distribution and architecture. The comparison of atomic force microscopy (AFM) and transmission electron microscopy (TEM) images of a biosample (Caenorhabditis elegans) prepared following to different types of freeze-substitution protocols (conventional OsO4 fixation, epoxy fixation) led to the conclusion that high TEM stainability of the sample results from a low macromolecular density of the cellular matrix. We propose a novel procedure aimed to obtain AFM and TEM images of the same particular organelle, which strongly facilitates AFM image interpretation and reveals new ultrastructural aspects (mainly protein arrangement) of a biosample in addition to TEM data.     

运用碳纳米管原子力显微镜针尖减小长程力作用的研究

减小探针和样品表面之间的长程宏观力是原子力显微镜获得高分辨率成像的关键。首先通过理论分析得出影响长程力的主要因素是探针的几何形状和尺寸。然后分别运用几何形状和尺寸不同的原子力显微镜的传统Si针尖和碳纳米管针尖对样品进行扫描试验研究,结果显示碳纳米管针尖较传统针尖获得了高分辨率的图像。这一结果表明,碳纳米管针尖减小了成像中宏观长程作用力的影响,是理想的原子力显微镜针尖。     

Design of a scanning probe microscope with advanced sample treatment capabilities: An atomic force microscope combined with a miniaturized inductively coupled plasma source

We describe the design and performance of an atomic force microscope (AFM) combined with a miniaturized inductively coupled plasma source working at a radio frequency of 27.12 MHz. State-of-the-art scanning probe microscopes (SPMs) have limited in situ sample treatment capabilities. Aggressive treatments such as plasma etching or harsh treatments such as etching in aggressive liquids typically require the removal of the sample from the microscope. Consequently, time consuming procedures are required if the same sample spot has to be imaged after successive processing steps. We have developed a first prototype of a SPM which features a quasi in situ sample treatment using a modified commercial atomic force microscope. A sample holder is positioned in a special reactor chamber; the AFM tip can be retracted by several millimeters so that the chamber can be closed for a treatment procedure. Most importantly, after the treatment, the tip is moved back to the sample with a lateral drift per process step in the 20 nm regime. The performance of the prototype is characterized by consecutive plasma etching of a nanostructured polymer film.     

Combining AFM and FRET for high resolution fluorescence microscopy

Here we demonstrate a new microscopic method that combines atomic force microscopy (AFM) with fluorescence resonance energy transfer (FRET). This method takes advantage of the strong distance dependence in Förster energy transfer between dyes with the appropriate donor/acceptor properties to couple an optical dimension with conventional AFM. This is achieved by attaching an acceptor dye to the end of an AFM tip and exciting a sample bound donor dye through far-field illumination. Energy transfer from the excited donor to the tip immobilized acceptor dye leads to emission in the red whenever there is sufficient overlap between the two dyes. Because of the highly exponential distance dependence in this process, only those dyes located at the apex of the AFM tip, nearest the sample, interact strongly. This limited and highly specific interaction provides a mechanism for obtaining fluorescence contrast with high spatial resolution. Initial results in which 400 nm resolution is obtained through this AFM/FRET imaging technique are reported. Future modifications in the probe design are discussed to further improve both the fluorescence resolution and imaging capabilities of this new technique.     

Atomic force microscopy of histological sections using a chemical etching method

Physiology and pathology have a big deal on tissue morphology, and the intrinsic spatial resolution of an atomic force microscope (AFM) is able to observe ultrastructural details. In order to investigate cellular and subcellular structures in histological sections with the AFM, we used a new simple method for sample preparation, i.e. chemical etching of semithin sections from epoxy resin-embedded specimens: such treatment appears to melt the upper layers of the embedding resin; thus, removing the superficial roughness caused by the edge of the microtome knife and bringing into high relief the biological structures hidden in the bulk. Consecutive ultrathin sections embedded in epoxy resin were observed with a transmission electron microscope (TEM) to compare the different imaging properties on the same specimen sample. In this paper we report, as an example, our AFM and TEM images of two different tissue specimens, rat pancreas and skeletal muscle fibres, showing that most of the inner details are visible with the AFM. These results suggest that chemical etching of histological sections may be a simple, fast and cost-effective method for AFM imaging with ultrastructural resolution.     

配置程控样品台的原子力显微镜重定位成像方法

原子力显微镜(Atomic Force Microscopy)已成为在纳米尺度对样品进行观察和操纵的重要工具。基于原子力显微镜观测的重定位技术提供一种微观区域内对样品处理前后原位对比观测的方法。本文利用坐标实时显示的程控高精度样品台系统,联合使用表面双标记定位法,建立一种新的重定位方法,方便、高效地实现样品重定位AFM成像。     

The analysis of morphological distortion during AFM study of cells

Atomic force microscopy (AFM) has been widely applied in cellular morphology study. However, morphological information including volume and roughness obtained by AFM are usually affected by different kinds of factors, which include the microscopic system itself, imaging mode, or external factors such as AFM probe or tip condition. In this study, based on red blood cell model, the dependence of cellular morphology, volume, and roughness on several parameters of the imaging was evaluated and, furthermore, a general rule and resolution for trustful analysis had been suggested. In addition, the potential effects that resulted from sample itself had also been analyzed based on adhesive force analysis. The results indicated that the scanning range and the imaging mode affect cellular volume and roughness, and the distorted images should be ascribed to blunt tip, contaminated tip, and the shape of tip. The analysis of morphological distortion during AFM investigation of cells provides a reference for researchers using AFM.     

High‐performance serial block‐face SEM of nonconductive biological samples enabled by focal gas injection‐based charge compensation

A longstanding limitation of imaging with serial block‐face scanning electron microscopy is specimen surface charging. This charging is largely due to the difficulties in making biological specimens and the resins in which they are embedded sufficiently conductive. Local accumulation of charge on the specimen surface can result in poor image quality and distortions. Even minor charging can lead to misalignments between sequential images of the block‐face due to image jitter. Typically, variable‐pressure SEM is used to reduce specimen charging, but this results in a significant reduction to spatial resolution, signal‐to‐noise ratio and overall image quality. Here we show the development and application of a simple system that effectively mitigates specimen charging by using focal gas injection of nitrogen over the sample block‐face during imaging. A standard gas injection valve is paired with a precisely positioned but retractable application nozzle, which is mechanically coupled to the reciprocating action of the serial block‐face ultramicrotome. This system enables the application of nitrogen gas precisely over the block‐face during imaging while allowing the specimen chamber to be maintained under high vacuum to maximise achievable SEM image resolution. The action of the ultramicrotome drives the nozzle retraction, automatically moving it away from the specimen area during the cutting cycle of the knife. The device described was added to a Gatan 3View system with minimal modifications, allowing high‐resolution block‐face imaging of even the most charge prone of epoxy‐embedded biological samples.