scholarly journals High-resolution limited-angle phase tomography of dense layered objects using deep neural networks

2019 ◽  
Vol 116 (40) ◽  
pp. 19848-19856 ◽  
Author(s):  
Alexandre Goy ◽  
Girish Rughoobur ◽  
Shuai Li ◽  
Kwabena Arthur ◽  
Akintunde I. Akinwande ◽  
...  
Keyword(s):  
Integrated Circuit ◽  
Deep Neural Networks ◽  
Tomographic Reconstruction ◽  
Synthetic Data ◽  
Single Step ◽  
Training Set ◽  
Step Method ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Optical Domain

We present a machine learning-based method for tomographic reconstruction of dense layered objects, with range of projection angles limited to ±10○. Whereas previous approaches to phase tomography generally require 2 steps, first to retrieve phase projections from intensity projections and then to perform tomographic reconstruction on the retrieved phase projections, in our work a physics-informed preprocessor followed by a deep neural network (DNN) conduct the 3-dimensional reconstruction directly from the intensity projections. We demonstrate this single-step method experimentally in the visible optical domain on a scaled-up integrated circuit phantom. We show that even under conditions of highly attenuated photon fluxes a DNN trained only on synthetic data can be used to successfully reconstruct physical samples disjoint from the synthetic training set. Thus, the need for producing a large number of physical examples for training is ameliorated. The method is generally applicable to tomography with electromagnetic or other types of radiation at all bands.

Three-Dimensional Reconstruction Using Stereo Pairs from Serial Thick Sections

1977 ◽  
Vol 35 ◽  
pp. 562-563
Author(s):  
Robert Glaeser ◽  
Thomas Bauer ◽  
David Grano
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Thin Sections ◽  
3 Dimensional ◽  
Transmission Electron ◽  
Freeze Dried ◽  
Dimensional Reconstruction ◽  
Stereo Imagery ◽  
Whole Mounts

In transmission electron microscopy, the 3-dimensional structure of an object is usually obtained in one of two ways. For objects which can be included in one specimen, as for example with elements included in freeze- dried whole mounts and examined with a high voltage microscope, stereo pairs can be obtained which exhibit the 3-D structure of the element. For objects which can not be included in one specimen, the 3-D shape is obtained by reconstruction from serial sections. However, without stereo imagery, only detail which remains constant within the thickness of the section can be used in the reconstruction; consequently, the choice is between a low resolution reconstruction using a few thick sections and a better resolution reconstruction using many thin sections, generally a tedious chore. This paper describes an approach to 3-D reconstruction which uses stereo images of serial thick sections to reconstruct an object including detail which changes within the depth of an individual thick section.

Structural preservation and absolute contrast of catalase crystal sections prepared with tannic acid

1983 ◽  
Vol 41 ◽  
pp. 448-449
Author(s):  
C.W. Akey ◽  
M. Szalay ◽  
S.J. Edelstein
Keyword(s):  
Tannic Acid ◽  
Beef Heart ◽  
X Rays ◽  
Screw Axis ◽  
General Applicability ◽  
Thin Sections ◽  
Beef Liver ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Structural Preservation

Three methods of obtaining 20 Å resolution in sectioned protein crystals have recently been described. They include tannic acid fixation, low temperature embedding and grid sectioning. To be useful for 3-dimensional reconstruction thin sections must possess suitable resolution, structural fidelity and a known contrast. Tannic acid fixation appears to satisfy the above criteria based on studies of crystals of Pseudomonas cytochrome oxidase, orthorhombic beef liver catalase and beef heart F1-ATPase. In order to develop methods with general applicability, we have concentrated our efforts on a trigonal modification of catalase which routinely demonstrated a resolution of 40 Å. The catalase system is particularly useful since a comparison with the structure recently solved with x-rays will permit evaluation of the accuracy of 3-D reconstructions of sectioned crystals.Initially, we re-evaluated the packing of trigonal catalase crystals studied by Longley. Images of the (001) plane are of particular interest since they give a projection down the 31-screw axis in space group P3121. Images obtained by the method of Longley or by tannic acid fixation are negatively contrasted since control experiments with orthorhombic catalase plates yield negatively stained specimens with conditions used for the larger trigonal crystals.

Design and calibration of an IVEM for general 3-dimensional imaging of non-diffracting materials

1992 ◽  
Vol 50 (2) ◽  
pp. 1040-1041
Author(s):  
Neil Rowlands ◽  
Jeff Price ◽  
Michael Kersker ◽  
Seichi Suzuki ◽  
Steve Young ◽  
...  
Keyword(s):  
3D Imaging ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
3 Dimensional ◽  
3D Microstructure ◽  
Image Translation ◽  
Digital Correlation ◽  
On Line ◽  
Mechanical Stage ◽  
Projection Angle

Three-dimensional (3D) microstructure visualization on the electron microscope requires that the sample be tilted to different positions to collect a series of projections. This tilting should be performed rapidly for on-line stereo viewing and precisely for off-line tomographic reconstruction. Usually a projection series is collected using mechanical stage tilt alone. The stereo pairs must be viewed off-line and the 60 to 120 tomographic projections must be aligned with fiduciary markers or digital correlation methods. The delay in viewing stereo pairs and the alignment problems in tomographic reconstruction could be eliminated or improved by tilting the beam if such tilt could be accomplished without image translation.A microscope capable of beam tilt with simultaneous image shift to eliminate tilt-induced translation has been investigated for 3D imaging of thick (1 μm) biologic specimens. By tilting the beam above and through the specimen and bringing it back below the specimen, a brightfield image with a projection angle corresponding to the beam tilt angle can be recorded (Fig. 1a).

Methods for three-dimensional reconstruction of cellular components within a thick section

1986 ◽  
Vol 44 ◽  
pp. 18-21
Author(s):  
J. Frank ◽  
B. F. McEwen ◽  
M. Radermacher ◽  
C. L. Rieder
Keyword(s):  
Tilt Angle ◽  
Tomographic Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Thick Section ◽  
Three Dimensional Reconstruction ◽  
Axis Ratio ◽  
Dimensional Reconstruction ◽  
Cellular Components

The tomographic reconstruction from multiple projections of cellular components, within a thick section, offers a way of visualizing and quantifying their three-dimensional (3D) structure. However, asymmetric objects require as many views from the widest tilt range as possible; otherwise the reconstruction may be uninterpretable. Even if not for geometric obstructions, the increasing pathway of electrons, as the tilt angle is increased, poses the ultimate upper limitation to the projection range. With the maximum tilt angle being fixed, the only way to improve the faithfulness of the reconstruction is by changing the mode of the tilting from single-axis to conical; a point within the object projected with a tilt angle of 60° and a full 360° azimuthal range is then reconstructed as a slightly elliptic (axis ratio 1.2 : 1) sphere.

Spot-scan imaging of ice-embedded catalase crystal on a slow-scan CCD camera in a 400-kV electron cryomicroscope

1994 ◽  
Vol 52 ◽  
pp. 98-99
Author(s):  
Wah Chiu ◽  
Michael Sherman ◽  
Jaap Brink
Keyword(s):  
Electron Diffraction ◽  
Ccd Camera ◽  
Protein Crystal ◽  
Modulation Transfer ◽  
Measured Intensity ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Diffraction Patterns ◽  
Complex Crystal

In protein electron crystallography, both low dose electron diffraction patterns and images are needed to provide accurate amplitudes and phases respectively for a 3-dimensional reconstruction. We have demonstrated that the Gatan 1024x1024 model 679 slow-scan CCD camera is useful to record electron diffraction intensities of glucose-embedded crotoxin complex crystal to 3 Å resolution. The quality of the electron diffraction intensities is high on the basis of the measured intensity equivalence ofthe Friedel-related reflections. Moreover, the number of patterns recorded from a single crystal can be as high as 120 under the constraints of radiation damage and electron statistics for the reflections in each pattern.A limitation of the slow-scan CCD camera for recording electron images of protein crystal arises from the relatively large pixel size, i.e. 24 μm (provided by Gatan). The modulation transfer function of our camera with a P43 scintillator has been determined for 400 keV electrons and shows an amplitude fall-off to 0.25 at 1/60 μm−1.

Immunolocalization of nuclear antigens in cryofixed cells which have been prepared by molecular distillation drying or freeze-substitution

1990 ◽  
Vol 48 (3) ◽  
pp. 898-899
Author(s):  
David L. Spector ◽  
Robert J. Derby
Keyword(s):  
Cell Nucleus ◽  
Molecular Distillation ◽  
Functional Organization ◽  
Freeze Substitution ◽  
3 Dimensional ◽  
Small Nuclear Ribonucleoprotein ◽  
Nuclear Antigens ◽  
Dimensional Reconstruction ◽  
Nuclear Regions ◽  
Immunoperoxidase Labeling

Studies in our laboratory are involved in evaluating the structural and functional organization of the mammalian cell nucleus. Since several major classes (U1, U2, U4/U6, U5) of small nuclear ribonucleoprotein particles (snRNPs) play a crucial role in the processing of pre-mRNA molecules, we have been interested in the localization of these particles within the cell nucleus. Using pre-embedding immunoperoxidase labeling combined with 3-dimensional reconstruction, we have recently shown that nuclear regions enriched in snRNPs form a reticular network within the nucleoplasm which extends between the nucleolar surface and the nuclear envelope. In the present study we were inte rested in extending these nuclear localizations using cell preparation techniques which avoid slow penetration of fixatives, chemical crosslinking of potential antigens and solvent extraction. CHOC 400 cells were cryofixed using a CF 100 ultra rapid cooling device (LifeCell Corp.). After cryofixation cells were molecular distillation dried, vapor osmicated, in filtra ted in 100% Spurr resin in vacuo and polymerized in molds a t 60°C. Using this procedure we were able to evaluate the distribution of snRNPs in resin embedded cells which had not been chemically fixed, incubated in cryoprotectants or extracted with solvents.

Purification of Urokinase from Complex Mixtures Using Immobilized Monoclonal Antibody Against Urokinase Light Chain

1983 ◽  
Vol 49 (01) ◽  
pp. 024-027 ◽  
Author(s):  
David Vetterlein ◽  
Gary J Calton
Keyword(s):  
Monoclonal Antibody ◽  
Light Chain ◽  
Culture Media ◽  
Biological Fluids ◽  
Single Step ◽  
High Yield ◽  
Step Method ◽  
Commercial Preparation ◽  
E Coli ◽  
Tissue Culture Media

SummaryThe preparation of a monoclonal antibody (MAB) against high molecular weight (HMW) urokinase light chain (20,000 Mr) is described. This MAB was immobilized and the resulting immunosorbent was used to isolate urokinase starting with an impure commercial preparation, fresh urine, spent tissue culture media, or E. coli broth without preliminary dialysis or concentration steps. Monospecific antibodies appear to provide a rapid single step method of purifying urokinase, in high yield, from a variety of biological fluids.

scholarly journals Quantized electronic transitions in electrodeposited copper indium selenide nanocrystalline homojunctions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shalini Menezes ◽  
Anura P. Samantilleke ◽  
Bryon W. Larson
Keyword(s):  
Scale Up ◽  
Indium Selenide ◽  
State Density ◽  
Single Step ◽  
Copper Indium Selenide ◽  
Ambient Atmosphere ◽  
Inorganic Semiconductors ◽  
3 Dimensional ◽  
Roll To Roll ◽  
Copper Indium

AbstractPairing semiconductors with electrochemical processing offers an untapped opportunity to create novel nanostructures for practical devices. Here we report the results of one such pairing: the in-situ formation of highly-doped, interface-matched, sharp nanocrystalline homojunctions (NHJs) with single step electrodeposition of two copper-indium-selenide (CISe) compounds on flexible foil. It produces a homogenous film, comprising inherently ordered, 3-dimensional interconnected network of pn-CISe NHJs. These CISe NHJs exhibit surprising non-linear emissions, quantized transitions, large carrier mobility, low trap-state-density, long carrier lifetime and possible up-conversion. They facilitate efficient separation of minority carriers, reduce recombination and essentially function like quantum materials. This approach mitigates the material issues and complex fabrication of incumbent nanoscale heterojunctions; it also overcomes the flexibility and scale-up challenges of conventional planar pn junctions. The self-stabilized CISe NHJ film can be roll-to-roll processed in ambient atmosphere, thus providing a promising platform for a range of optoelectronic technologies. This concept exemplified by CISe compounds can be adapted to create nano-scale pn junctions with other inorganic semiconductors.

Computational Analysis of Olfactory Airspace in Patients With Unilateral Cleft Lip Nasal Deformity

2020 ◽  
pp. 105566562098275
Author(s):  
Reanna Shah ◽  
Jeffrey R. Marcus ◽  
Dennis O. Frank-Ito
Keyword(s):  
Cleft Lip ◽  
Computational Analysis ◽  
Normal Subjects ◽  
Nasal Deformity ◽  
Normal Anatomy ◽  
3 Dimensional ◽  
Computed Tomography Images ◽  
High Prevalence ◽  
Dimensional Reconstruction ◽  
The Impact

Objectives: To evaluate the magnitude of olfactory recess opacity in patients with unilateral cleft lip nasal deformity (uCLND). Design: Subject-specific 3-dimensional reconstruction of the nasal airway anatomy was created from computed tomography images in 11 (4 males and 7 females) subjects with uCLND and 7 (3 males, and 4 females) normal subjects. The volume and surface area of each subject’s unilateral and bilateral olfactory airspace was quantified to assess the impact of opacification. Qualitatively speaking, patients with 75% to 100% olfactory recess opacification were classified as extreme, 50% to 75% as severe, 25% to 50% as moderate, and 0% to 25% as mild. Results: Of the 11 subjects with uCLND, 5 (45%) were classified as having extreme olfactory recess opacification, 3 (27%) subjects had severe opacification, and 3 (27%) subjects had moderate opacification. Mean (±SD) bilateral olfactory recess volume was significantly greater in normal subjects than in subjects with uCLND (0.9668 cm3 ± 0.4061 cm3 vs 0.3426 cm3 ± 0.1316 cm3; P < .001). Furthermore, unilateral olfactory airspace volumes for the cleft and non-cleft sides in subjects with uCLND were considerably less than unilateral olfactory volume in subjects with normal anatomy (uCLND cleft side = 0.1623 cm3 ± 0.0933 cm3; uCLND non-cleft side = 0.1803 cm3 ± 0.0938 cm3; normal = 0.4834 cm3 ± 0.2328 cm3; P < .001). Conclusions: Our findings indicate a high prevalence of olfactory recess opacification among subjects with uCLND when compared to subjects with normal anatomy. The majority of subjects with uCLND had extreme olfactory recess opacity, which will likely influence their sense of smell.

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