scholarly journals A Petascale Automated Imaging Pipeline for Mapping Neuronal Circuits with High-throughput Transmission Electron Microscopy

2019 ◽  
Author(s):  
Wenjing Yin ◽  
Derrick Brittain ◽  
Jay Borseth ◽  
Marie E. Scott ◽  
Derric Williams ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Parallel Imaging ◽  
Large Scale ◽  
Network Connectivity ◽  
Image Capture ◽  
Microscopy Imaging ◽  
Transmission Electron ◽  
Section Electron ◽  
Electron Microscopes ◽  
Serial Section Electron Microscopy

ABSTRACTSerial-section electron microscopy is the method of choice for studying cellular structure and network connectivity in the brain. We have built a pipeline of parallel imaging using transmission electron automated microscopes (piTEAM) that scales this technology and enables the acquisition of petascale datasets containing local cortical microcircuits. The distributed platform is composed of multiple transmission electron microscopes that image, in parallel, different sections from the same block of tissue, all under control of a custom acquisition software (pyTEM) that implements 24/7 continuous autonomous imaging. The suitability of this architecture for large scale electron microscopy imaging was demonstrated by acquiring a volume of more than 1 mm3 of mouse neocortex spanning four different visual areas. Over 26,500 ultrathin tissue sections were imaged, yielding a dataset of more than 2 petabytes. Our current burst imaging rate is 500 Mpixel/s (image capture only) per microscope and net imaging rate is 100 Mpixel/s (including stage movement, image capture, quality control, and post processing). This brings the combined burst acquisition rate of the pipeline to 3 Gpixel/s and the net rate to 600 Mpixel/s with six microscopes running acquisition in parallel, which allowed imaging a cubic millimeter of mouse visual cortex at synaptic resolution in less than 6 months.

scholarly journals A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenjing Yin ◽  
Derrick Brittain ◽  
Jay Borseth ◽  
Marie E. Scott ◽  
Derric Williams ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Parallel Imaging ◽  
Large Scale ◽  
Network Connectivity ◽  
Brain Regions ◽  
Acquisition Rate ◽  
Tissue Sections ◽  
Transmission Electron ◽  
Electron Microscopes ◽  
The Brain

Abstract Electron microscopy (EM) is widely used for studying cellular structure and network connectivity in the brain. We have built a parallel imaging pipeline using transmission electron microscopes that scales this technology, implements 24/7 continuous autonomous imaging, and enables the acquisition of petascale datasets. The suitability of this architecture for large-scale imaging was demonstrated by acquiring a volume of more than 1 mm3 of mouse neocortex, spanning four different visual areas at synaptic resolution, in less than 6 months. Over 26,500 ultrathin tissue sections from the same block were imaged, yielding a dataset of more than 2 petabytes. The combined burst acquisition rate of the pipeline is 3 Gpixel per sec and the net rate is 600 Mpixel per sec with six microscopes running in parallel. This work demonstrates the feasibility of acquiring EM datasets at the scale of cortical microcircuits in multiple brain regions and species.

Two- or three-way observations of the identical cell elements within the same sections by LM, TEM and/or SEM

1978 ◽  
Vol 36 (2) ◽  
pp. 82-83 ◽  
Author(s):  
Nakazo Watari ◽  
Yasuaki Hotta ◽  
Yoshio Mabuchi
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Fine Structure ◽  
Light Microscopy ◽  
Thin Sections ◽  
Transmission Electron ◽  
Identical Cell ◽  
Electron Microscopes ◽  
Scanning Electron

It is very useful if we can observe the identical cell elements within the same sections by light microscopy (LM), transmission electron microscopy (TEM) and/or scanning electron microscopy (SEM) sequentially, because, the cell fine structure can not be indicated by LM, while the color is; on the other hand, the cell fine structure can be very easily observed by EM, although its color properties may not. However, there is one problem in that LM requires thick sections of over 1 μm, while EM needs very thin sections of under 100 nm. Recently, we have developed a new method to observe the same cell elements within the same plastic sections using both light and transmission (conventional or high-voltage) electron microscopes.In this paper, we have developed two new observation methods for the identical cell elements within the same sections, both plastic-embedded and paraffin-embedded, using light microscopy, transmission electron microscopy and/or scanning electron microscopy (Fig. 1).

Some early history of replica techniques for electron microscopy

1992 ◽  
Vol 50 (2) ◽  
pp. 1076-1077
Author(s):  
Robert M. Fisher
Keyword(s):  
Thin Film ◽  
Electron Microscopy ◽  
Optical Microscope ◽  
Early History ◽  
Bulk Materials ◽  
Thin Sections ◽  
Transmission Electron ◽  
Reflected Light ◽  
History Of ◽  
Electron Microscopes

By 1940, a half dozen or so commercial or home-built transmission electron microscopes were in use for studies of the ultrastructure of matter. These operated at 30-60 kV and most pioneering microscopists were preoccupied with their search for electron transparent substrates to support dispersions of particulates or bacteria for TEM examination and did not contemplate studies of bulk materials. Metallurgist H. Mahl and other physical scientists, accustomed to examining etched, deformed or machined specimens by reflected light in the optical microscope, were also highly motivated to capitalize on the superior resolution of the electron microscope. Mahl originated several methods of preparing thin oxide or lacquer impressions of surfaces that were transparent in his 50 kV TEM. The utility of replication was recognized immediately and many variations on the theme, including two-step negative-positive replicas, soon appeared. Intense development of replica techniques slowed after 1955 but important advances still occur. The availability of 100 kV instruments, advent of thin film methods for metals and ceramics and microtoming of thin sections for biological specimens largely eliminated any need to resort to replicas.

Remote On-Line Control of a High-Voltage in situ Transmission Electron Microscope with A Rational User Interface

1996 ◽  
Vol 54 ◽  
pp. 384-385
Author(s):  
M.A. O’Keefe ◽  
J. Taylor ◽  
D. Owen ◽  
B. Crowley ◽  
K.H. Westmacott ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
User Interface ◽  
Transmission Electron Microscope ◽  
High Voltage ◽  
Materials Science ◽  
Transmission Electron ◽  
On Line ◽  
Electron Microscopes

Remote on-line electron microscopy is rapidly becoming more available as improvements continue to be developed in the software and hardware of interfaces and networks. Scanning electron microscopes have been driven remotely across both wide and local area networks. Initial implementations with transmission electron microscopes have targeted unique facilities like an advanced analytical electron microscope, a biological 3-D IVEM and a HVEM capable of in situ materials science applications. As implementations of on-line transmission electron microscopy become more widespread, it is essential that suitable standards be developed and followed. Two such standards have been proposed for a high-level protocol language for on-line access, and we have proposed a rational graphical user interface. The user interface we present here is based on experience gained with a full-function materials science application providing users of the National Center for Electron Microscopy with remote on-line access to a 1.5MeV Kratos EM-1500 in situ high-voltage transmission electron microscope via existing wide area networks. We have developed and implemented, and are continuing to refine, a set of tools, protocols, and interfaces to run the Kratos EM-1500 on-line for collaborative research. Computer tools for capturing and manipulating real-time video signals are integrated into a standardized user interface that may be used for remote access to any transmission electron microscope equipped with a suitable control computer.

Methods to Monitor and Improve the Performance of Specimen Holders for Transmission Electron Cryomicroscopy

1996 ◽  
Vol 54 ◽  
pp. 454-455
Author(s):  
B. L. Armbruster ◽  
B. Kraus ◽  
M. Pan
Keyword(s):  
Electron Microscopy ◽  
Electron Beam ◽  
Electron Beam Irradiation ◽  
Beam Irradiation ◽  
Quality Of Data ◽  
Electron Cryomicroscopy ◽  
Thermal Equilibration ◽  
Transmission Electron ◽  
Electron Microscopes

One goal in electron microscopy of biological specimens is to improve the quality of data to equal the resolution capabilities of modem transmission electron microscopes. Radiation damage and beam- induced movement caused by charging of the sample, low image contrast at high resolution, and sensitivity to external vibration and drift in side entry specimen holders limit the effective resolution one can achieve. Several methods have been developed to address these limitations: cryomethods are widely employed to preserve and stabilize specimens against some of the adverse effects of the vacuum and electron beam irradiation, spot-scan imaging reduces charging and associated beam-induced movement, and energy-filtered imaging removes the “fog” caused by inelastic scattering of electrons which is particularly pronounced in thick specimens.Although most cryoholders can easily achieve a 3.4Å resolution specification, information perpendicular to the goniometer axis may be degraded due to vibration. Absolute drift after mechanical and thermal equilibration as well as drift after movement of a holder may cause loss of resolution in any direction.

scholarly journals Fabrication of a liquid cell for in situ transmission electron microscopy

Microscopy ◽  
2020 ◽  
Author(s):  
Xiaoguang Li ◽  
Kazutaka Mitsuishi ◽  
Masaki Takeguchi
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Cost Effective ◽  
Production Method ◽  
Microscopy Imaging ◽  
Transmission Electron ◽  
In Situ Electron Microscopy ◽  
Liquid Cell ◽  
Si Wafer

Abstract Liquid cell transmission electron microscopy (LCTEM) enables imaging of dynamic processes in liquid with high spatial and temporal resolution. The widely used liquid cell (LC) consists of two stacking microchips with a thin wet sample sandwiched between them. The vertically overlapped electron-transparent membrane windows on the microchips provide passage for the electron beam. However, microchips with imprecise dimensions usually cause poor alignment of the windows and difficulty in acquiring high-quality images. In this study, we developed a new and efficient microchip fabrication process for LCTEM with a large viewing area (180 µm × 40 µm) and evaluated the resultant LC. The new positioning reference marks on the surface of the Si wafer dramatically improve the precision of dicing the wafer, making it possible to accurately align the windows on two stacking microchips. The precise alignment led to a liquid thickness of 125.6 nm close to the edge of the viewing area. The performance of our LC was demonstrated by in situ transmission electron microscopy imaging of the dynamic motions of 2-nm Pt particles. This versatile and cost-effective microchip production method can be used to fabricate other types of microchips for in situ electron microscopy.

Normal Synaptonemal Complex and Abnormal Recombination Nodules in Two Alleles of the Drosophila Meiotic Mutant mei-W68

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1337-1356 ◽  
Author(s):  
Adelaide T C Carpenter
Keyword(s):  
Electron Microscopy ◽  
Synaptonemal Complex ◽  
High Frequency ◽  
Serial Section ◽  
The Other ◽  
Wild Type ◽  
Recombination Nodules ◽  
Section Electron ◽  
Serial Section Electron Microscopy ◽  
Section Electron Microscopy

Abstract The meiotic phenotypes of two mutant alleles of the mei-W68 gene, 1 and L1, were studied by genetics and by serial-section electron microscopy. Despite no or reduced exchange, both mutant alleles have normal synaptonemal complex. However, neither has any early recombination nodules; instead, both exhibit high numbers of very long (up to 2 μm) structures here named “noodles.” These are hypothesized to be formed by the unchecked extension of identical but much shorter structures ephemerally seen in wild type, which may be precursors of early recombination nodules. Although the mei-W68L1 allele is identical to the mei-W681 allele in both the absence of early recombination nodules and a high frequency of noodles (i.e., it is amorphic for the noodle phene), it is hypomorphic in its effects on exchange and late recombination nodules. The differential effects of this allele on early and late recombination nodules are consistent with the hypothesis that Drosophila females have two separate recombination pathways—one for simple gene conversion, the other for exchange.

Low Temperature Large Scale CVD Synthesis of Nano Onion-Like Fullerenes

2012 ◽  
Vol 490-495 ◽  
pp. 3211-3214 ◽  
Author(s):  
Lei Shan Chen ◽  
Cun Jing Wang
Keyword(s):  
Electron Microscopy ◽  
Low Temperature ◽  
Aluminum Hydroxide ◽  
Large Scale ◽  
Iron Catalyst ◽  
Chemical Vapor ◽  
X Ray Diffraction ◽  
Transmission Electron ◽  
Naoh Solution ◽  
Synthesis Reactions

Synthesis reactions were carried out by chemical vapor deposition using iron catalyst supported on aluminum hydroxide at 400 °C and 420 °C, in the presence of argon as carrier gas and acetylene as carbon source. The aluminum hydroxide support was separated by refluxing the samples in 40% NaOH solution for 2 h and 36% HCl solution for 24 h, respectively. The samples were characterized by field-emission scanning electron microscopy, energy dispersive spectroscopy, high-resolution transmission electron microscopy and X-ray diffraction. The results show that carbon nanotubes were the main products at 420 °C, while large scale high purity nano onion-like fullerenes encapsulating Fe3C, with almost uniform sizes ranging from 10-50 nm, were obtained at the low temperature of 400 °C.

scholarly journals Annular Bright Field Scanning Transmission Electron Microscopy Imaging Dynamics

2010 ◽  
Vol 16 (S2) ◽  
pp. 80-81 ◽  
Author(s):  
SD Findlay ◽  
N Shibata ◽  
H Sawada ◽  
E Okunishi ◽  
Y Kondo ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Scanning Transmission Electron Microscopy ◽  
Bright Field ◽  
Microscopy Imaging ◽  
Scanning Transmission Electron ◽  
Transmission Electron ◽  
Scanning Transmission

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.

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