scholarly journals In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

2020 ◽  
Author(s):  
Clarisse Uwizeye ◽  
Johan Decelle ◽  
Pierre-Henri Jouneau ◽  
Benoit Gallet ◽  
Jean-Baptiste Keck ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Cell Biology ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Phytoplankton Diversity ◽  
Cellular Energy ◽  
Unicellular Eukaryotes ◽  
3D Electron Microscopy ◽  
Abiotic And Biotic Factors ◽  
A Minor

AbstractPhytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.

scholarly journals Protocol for preparation of heterogeneous biological samples for 3D electron microscopy: a case study for insects

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alexey A. Polilov ◽  
Anastasia A. Makarova ◽  
Song Pang ◽  
C. Shan Xu ◽  
Harald Hess
Keyword(s):  
Electron Microscopy ◽  
Biological Samples ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Three Dimensional ◽  
Entire Volume ◽  
Simple Protocol ◽  
3D Electron Microscopy ◽  
3D Em

AbstractModern morphological and structural studies are coming to a new level by incorporating the latest methods of three-dimensional electron microscopy (3D-EM). One of the key problems for the wide usage of these methods is posed by difficulties with sample preparation, since the methods work poorly with heterogeneous (consisting of tissues different in structure and in chemical composition) samples and require expensive equipment and usually much time. We have developed a simple protocol allows preparing heterogeneous biological samples suitable for 3D-EM in a laboratory that has a standard supply of equipment and reagents for electron microscopy. This protocol, combined with focused ion-beam scanning electron microscopy, makes it possible to study 3D ultrastructure of complex biological samples, e.g., whole insect heads, over their entire volume at the cellular and subcellular levels. The protocol provides new opportunities for many areas of study, including connectomics.

scholarly journals Quantitative method for estimating stain density in electron microscopy of conventionally prepared biological specimens

2019 ◽  
Author(s):  
Andrea Fera ◽  
Qianping He ◽  
Guofeng Zhang ◽  
Richard D. Leapman
Keyword(s):  
Electron Microscopy ◽  
Focused Ion Beam ◽  
Electron Tomography ◽  
Blood Platelets ◽  
Ion Beam ◽  
Simple Expression ◽  
Heavy Atoms ◽  
3D Electron Microscopy ◽  
Block Face ◽  
Microscopy Techniques

SummaryStain density is an important parameter for optimizing the quality of ultrastructural data obtained from several types of 3D electron microscopy techniques, including serial block-face electron microscopy (SBEM), and focused ion beam scanning electron microscopy (FIB-SEM). Here, we show how some straightforward measurements in the TEM can be used to determine the stain density based on a simple expression that we derive. Numbers of stain atoms per unit volume are determined from the measured ratio of the bright-field intensities from regions of the specimen that contain both pure embedding material and the embedded biological structures of interest. The determination only requires knowledge of the section thickness, which can either be estimated from the microtome setting, or from low-dose electron tomography, and the elastic scattering cross section for the heavy atoms used to stain the specimen. The method is tested on specimens of embedded blood platelets, brain tissue, and liver tissue.

scholarly journals Multi-resolution correlative focused ion beam scanning electron microscopy: Applications to cell biology

2014 ◽  
Vol 185 (3) ◽  
pp. 278-284 ◽  
Author(s):  
Kedar Narayan ◽  
Cindy M. Danielson ◽  
Ken Lagarec ◽  
Bradley C. Lowekamp ◽  
Phil Coffman ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Cell Biology ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Beam Scanning ◽  
Scanning Electron

scholarly journals Correlation of organelle dynamics between light microscopic live imaging and electron microscopic 3D architecture using FIB-SEM

Microscopy ◽  
2020 ◽  
Author(s):  
Keisuke Ohta ◽  
Shingo Hirashima ◽  
Yoshihiro Miyazono ◽  
Akinobu Togo ◽  
Kei-ichiro Nakamura
Keyword(s):  
Electron Microscopy ◽  
Cell Biology ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Optical Microscope ◽  
Live Imaging ◽  
Reconstruction Technique ◽  
Electron Microscopic

Abstract Correlative light and electron microscopy (CLEM) methods combined with live imaging can be applied to understand the dynamics of organelles. Although recent advances in cell biology and light microscopy have helped in visualizing the details of organelle activities, observing their ultrastructure or organization of surrounding microenvironments is a challenging task. Therefore, CLEM, which allows us to observe the same area as an optical microscope with an electron microscope, has become a key technique in cell biology. Unfortunately, most CLEM methods have technical drawbacks, and many researchers face difficulties in applying CLEM methods. Here, we propose a live three-dimensional CLEM method, combined with a three-dimensional reconstruction technique using focused ion beam scanning electron microscopy tomography, as a solution to such technical barriers. We review our method, the associated technical limitations and the options considered to perform live CLEM.

scholarly journals Fluorescence-based 3D targeting of FIB-SEM acquisition of small volumes in large samples

2021 ◽  
Author(s):  
Paolo Ronchi ◽  
Pedro Machado ◽  
Edoardo D’Imprima ◽  
Giulia Mizzon ◽  
Benedikt T. Best ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Focused Ion Beam ◽  
Single Cells ◽  
Ion Beam ◽  
Three Dimensional ◽  
3D Culture ◽  
Fluorescence Signal ◽  
Three Dimensional Objects ◽  
3D Electron Microscopy ◽  
3D Electron

AbstractCells are three dimensional objects. Therefore, 3D electron microscopy is often crucial for correct interpretation of ultrastructural data. Today samples are frequently imaged in 3D at ultrastructural resolution using volume Scanning Electron Microscopy (SEM) methods such as Focused Ion Beam (FIB) SEM and Serial Block face SEM. While these imaging modalities allow for automated data acquisition, precise targeting of (small) volumes of interest within a large sample remains challenging. Here, we provide an easy and reliable approach to target FIB-SEM acquisition of fluorescently labelled cells or subcellular structures with micrometer precision. The strategy relies on fluorescence preservation during sample preparation and targeting based on confocal acquisition of the fluorescence signal in the resin block. Targeted trimming of the block exposes the cell of interest and laser branding of the surface after trimming creates landmarks to precisely position the FIB-SEM acquisition. Using this method, we acquired volumes of specific single cells within large tissues such as a 3D culture of mouse primary mammary gland organoids, tracheal terminal cells in Drosophila melanogaster larvae and ovarian follicular cells in adult Drosophila, discovering ultrastructural details that could not be appreciated before.SummaryRonchi et al. present a workflow to facilitate the precise targeting of three-dimensional (3D) Electron Microscopy acquisitions, guided by fluorescence. This method allows ultrastructural visualization of single cells within a millimeter-range large specimen, based on molecular identity characterized by fluorescence.

TEM Sample Preparation Tricks for Advanced DRAMs

2015 ◽  
Author(s):  
Ching Shan Sung ◽  
Hsiu Ting Lee ◽  
Jian Shing Luo
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Sample Preparation ◽  
Integrated Circuit ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Tem Analysis ◽  
Cross Sectional ◽  
Transmission Electron ◽  
Characterization Of Materials

Abstract Transmission electron microscopy (TEM) plays an important role in the structural analysis and characterization of materials for process evaluation and failure analysis in the integrated circuit (IC) industry as device shrinkage continues. It is well known that a high quality TEM sample is one of the keys which enables to facilitate successful TEM analysis. This paper demonstrates a few examples to show the tricks on positioning, protection deposition, sample dicing, and focused ion beam milling of the TEM sample preparation for advanced DRAMs. The micro-structures of the devices and samples architectures were observed by using cross sectional transmission electron microscopy, scanning electron microscopy, and optical microscopy. Following these tricks can help readers to prepare TEM samples with higher quality and efficiency.

Fin Level Defect Isolation Inside a FinFET Using Electron Beam Alteration of Current Flow

2017 ◽  
Author(s):  
H.J. Ryu ◽  
A.B. Shah ◽  
Y. Wang ◽  
W.-H. Chuang ◽  
T. Tong
Keyword(s):  
Electron Microscopy ◽  
Electron Beam ◽  
Focused Ion Beam ◽  
Current Flow ◽  
Ion Beam ◽  
The Body ◽  
Complete Understanding ◽  
Root Cause ◽  
Transmission Electron ◽  
Defect Isolation

Abstract When failure analysis is performed on a circuit composed of FinFETs, the degree of defect isolation, in some cases, requires isolation to the fin level inside the problematic FinFET for complete understanding of root cause. This work shows successful application of electron beam alteration of current flow combined with nanoprobing for precise isolation of a defect down to fin level. To understand the mechanism of the leakage, transmission electron microscopy (TEM) slice was made along the leaky drain contact (perpendicular to fin direction) by focused ion beam thinning and lift-out. TEM image shows contact and fin. Stacking fault was found in the body of the silicon fin highlighted by the technique described in this paper.

Transmission Electron Microscopy (TEM) Specimen Preparation Technique using Focused Ion Beam (FIB): Application to Material Characterization of Chemical Vapor Deposition of Tungsten (W) and Tungsten Silicides (WSix)

1997 ◽  
Author(s):  
K. Doong ◽  
J.-M. Fu ◽  
Y.-C. Huang
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Chemical Vapor Deposition ◽  
Vapor Deposition ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Chemical Vapor ◽  
Specimen Preparation ◽  
Preparation Technique ◽  
Transmission Electron

Abstract The specimen preparation technique using focused ion beam (FIB) to generate cross-sectional transmission electron microscopy (XTEM) samples of chemical vapor deposition (CVD) of Tungsten-plug (W-plug) and Tungsten Silicides (WSix) was studied. Using the combination method including two axes tilting[l], gas enhanced focused ion beam milling[2] and sacrificial metal coating on both sides of electron transmission membrane[3], it was possible to prepare a sample with minimal thickness (less than 1000 A) to get high spatial resolution in TEM observation. Based on this novel thinning technique, some applications such as XTEM observation of W-plug with different aspect ratio (I - 6), and the grain structure of CVD W-plug and CVD WSix were done. Also the problems and artifacts of XTEM sample preparation of high Z-factor material such as CVD W-plug and CVD WSix were given and the ways to avoid or minimize them were suggested.

A Methodology to Reduce Ion Beam Induced Damage in TEM Specimens Prepared by FIB

2002 ◽  
Author(s):  
Chin Kai Liu ◽  
Chi Jen. Chen ◽  
Jeh Yan.Chiou ◽  
David Su
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Sample Preparation ◽  
Integrated Circuit ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Specimen Preparation ◽  
Tem Analysis ◽  
Sensitive Issue ◽  
Transmission Electron

Abstract Focused ion beam (FIB) has become a useful tool in the Integrated Circuit (IC) industry, It is playing an important role in Failure Analysis (FA), circuit repair and Transmission Electron Microscopy (TEM) specimen preparation. In particular, preparation of TEM samples using FIB has become popular within the last ten years [1]; the progress in this field is well documented. Given the usefulness of FIB, “Artifact” however is a very sensitive issue in TEM inspections. The ability to identify those artifacts in TEM analysis is an important as to understanding the significance of pictures In this paper, we will describe how to measure the damages introduced by FIB sample preparation and introduce a better way to prevent such kind of artifacts.

BiCMOS Die Sort Yield Improvement from Isolation of a Localized Defect Mechanism and Precision TEM Cross Section

1997 ◽  
Author(s):  
J. Douglass ◽  
T. D. Myers ◽  
F. Tsai ◽  
R. Ketcheson ◽  
J. Errett
Keyword(s):  
Electron Microscopy ◽  
Cross Section ◽  
Focused Ion Beam ◽  
Yield Loss ◽  
Process Analysis ◽  
Ion Beam ◽  
Yield Improvement ◽  
Transmission Electron ◽  
Defect Mechanism ◽  
Water Residue

Abstract This paper describes how the authors used a combination of focused ion beam (FIB) microprobing, transmission electron microscopy (TEM), and data and process analysis to determine that localized water residue was causing a 6% yield loss at die sort.

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