scholarly journals MAUI (MBI Analysis User Interface)—An image processing pipeline for Multiplexed Mass Based Imaging

2021 ◽  
Vol 17 (4) ◽  
pp. e1008887
Author(s):  
Alex Baranski ◽  
Idan Milo ◽  
Shirley Greenbaum ◽  
John-Paul Oliveria ◽  
Dunja Mrdjen ◽  
...  
Keyword(s):  
User Interface ◽  
User Interfaces ◽  
Ion Beam ◽  
Parameter Tuning ◽  
Crosstalk Noise ◽  
Domain Experts ◽  
Imaging Artifacts ◽  
Cellular Phenotypes ◽  
Insight Into

Mass Based Imaging (MBI) technologies such as Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and Imaging Mass Cytometry (IMC) allow for the simultaneous measurement of the expression levels of 40 or more proteins in biological tissue, providing insight into cellular phenotypes and organization in situ. Imaging artifacts, resulting from the sample, assay or instrumentation complicate downstream analyses and require correction by domain experts. Here, we present MBI Analysis User Interface (MAUI), a series of graphical user interfaces that facilitate this data pre-processing, including the removal of channel crosstalk, noise and antibody aggregates. Our software streamlines these steps and accelerates processing by enabling real-time and interactive parameter tuning across multiple images.

Generating Interactive Prototypes from Query Annotated Discourse Models

i-com ◽  
2015 ◽  
Vol 14 (3) ◽  
Author(s):  
Filip Kis ◽  
Cristian Bogdan
Keyword(s):  
User Interface ◽  
User Interfaces ◽  
Transformation Process ◽  
Model Transformations ◽  
Interactive System ◽  
User Centered Design ◽  
Levels Of Abstraction ◽  
Domain Experts ◽  
Application Logic ◽  
High Level

AbstractModel Based User Interface Development offers the possibility to design User Interfaces without being concerned about the underlying implementation. This is achieved by devising models at a high level of abstraction, thus creating the potential for involving users or domain experts to achieve a user-centered design process. Obtaining a running interactive application from such models usually requires several model transformations. One of the current problems is that while a user interface is generated after these transformations, other parts of the interactive system such as the application logic need to pre-exist or they must be written manually before the interface can be tested in a realistic scenario. This leaves the domain experts dependent on programmers and increases the time between iterations. In this paper we work with Query Annotations, which were previously used only for modeling at low levels and for generating fully functional interfaces, and we aim to generalize them for the high-level modeling approach called Discourse Modeling. The direct expected benefit of this generalization is the possibility to generate complete, readily testable interactive prototypes, rather than just their user interfaces. In addition, Query Annotations can serve as the mapping between the various levels of abstraction and bring to the domain experts a better understanding of the transformation process, as well as the possibility to modify the interfaces and models directly.

scholarly journals Virus-Dependent Immune Conditioning of Tissue Microenvironments

2021 ◽  
Author(s):  
Sizun Jiang ◽  
Chi Ngai Chan ◽  
Xavier Rovira-Clave ◽  
Han Chen ◽  
Yunhao Bai ◽  
...  
Keyword(s):  
Ion Beam ◽  
Tumor Biology ◽  
Functional Markers ◽  
Lymphoid Tissues ◽  
Protein Levels ◽  
Preventative Measures ◽  
Immunodeficiency Virus ◽  
Cellular Phenotypes ◽  
Viral Dna Integration

A thorough understanding of complex spatial host-disease interactions in situ is necessary in order to develop effective preventative measures and therapeutic strategies. Here, we developed Protein And Nucleic acid IN situ Imaging (PANINI) and coupled it with Multiplexed Ion Beam Imaging (MIBI) to sensitively and simultaneously quantify DNA, RNA, and protein levels within the microenvironments of tissue compartments. The PANINI-MIBI approach was used to measure over 30 parameters simultaneously across large sections of archival lymphoid tissues from non-human primates that were healthy or infected with simian immunodeficiency virus (SIV), a model that accurately recapitulates human immunodeficiency virus infection (HIV). This enabled multiplexed dissection of cellular phenotypes, functional markers, viral DNA integration events, and viral RNA transcripts as resulting from viral infection. The results demonstrated immune coordination from an unexpected upregulation of IL10 in B cells in response to SIV infection that correlated with macrophage M2 polarization, thus conditioning a potential immunosuppressive environment that allows for viral production. This multiplexed imaging strategy also allowed characterization of the coordinated microenvironment around latently or actively infected cells to provide mechanistic insights into the process of viral latency. The spatial multi-modal framework presented here is applicable to deciphering tissue responses in other infectious diseases and tumor biology.

Direct Observations of the Epitaxial Growth of Sputtered Ag on Si

1973 ◽  
Vol 31 ◽  
pp. 122-123
Author(s):  
J. S. Maa ◽  
Thos. E. Hutchinson
Keyword(s):  
Epitaxial Growth ◽  
Film Growth ◽  
Ion Beam ◽  
Ion Beam Sputtering ◽  
Microscopy Technique ◽  
Direct Observations ◽  
In Situ Electron Microscopy ◽  
Beam Sputtering ◽  
The Subject

The growth of Ag films deposited on various substrate materials such as MoS2, mica, graphite, and MgO has been investigated extensively using the in situ electron microscopy technique. The three stages of film growth, namely, the nucleation, growth of islands followed by liquid-like coalescence have been observed in both the vacuum vapor deposited and ion beam sputtered thin films. The mechanisms of nucleation and growth of silver films formed by ion beam sputtering on the (111) plane of silicon comprise the subject of this paper. A novel mode of epitaxial growth is observed to that seen previously.The experimental arrangement for the present study is the same as previous experiments, and the preparation procedure for obtaining thin silicon substrate is presented in a separate paper.

Nucleation and Early Growth of Sputtered thin Films

1970 ◽  
Vol 28 ◽  
pp. 516-517
Author(s):  
Dudley M. Sherman ◽  
Thos. E. Hutchinson
Keyword(s):  
Thin Films ◽  
Electron Beam ◽  
Ion Beam ◽  
Ion Source ◽  
Water Cooling ◽  
Stages Of Growth ◽  
Lens Assembly ◽  
Microscope Technique ◽  
Ion Beam Sputter Deposition

The in situ electron microscope technique has been shown to be a powerful method for investigating the nucleation and growth of thin films formed by vacuum vapor deposition. The nucleation and early stages of growth of metal deposits formed by ion beam sputter-deposition are now being studied by the in situ technique.A duoplasmatron ion source and lens assembly has been attached to one side of the universal chamber of an RCA EMU-4 microscope and a sputtering target inserted into the chamber from the opposite side. The material to be deposited, in disc form, is bonded to the end of an electrically isolated copper rod that has provisions for target water cooling. The ion beam is normal to the microscope electron beam and the target is placed adjacent to the electron beam above the specimen hot stage, as shown in Figure 1.

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.

Electron and ion irradiation-induced dissolution of mechanical twins in the intermetalic U3Si: An in situ HVEM study

1989 ◽  
Vol 47 ◽  
pp. 652-653
Author(s):  
Charles W. Allen ◽  
Robert C. Birtcher
Keyword(s):  
Elevated Temperatures ◽  
Ion Irradiation ◽  
Ion Beam ◽  
National Laboratory ◽  
Argonne National Laboratory ◽  
Heavy Ion ◽  
High Energy ◽  
Mechanical Twinning ◽  
In Situ Experiments

The uranium silicides, including U3Si, are under study as candidate low enrichment nuclear fuels. Ion beam simulations of the in-reactor behavior of such materials are performed because a similar damage structure can be produced in hours by energetic heavy ions which requires years in actual reactor tests. This contribution treats one aspect of the microstructural behavior of U3Si under high energy electron irradiation and low dose energetic heavy ion irradiation and is based on in situ experiments, performed at the HVEM-Tandem User Facility at Argonne National Laboratory. This Facility interfaces a 2 MV Tandem ion accelerator and a 0.6 MV ion implanter to a 1.2 MeV AEI high voltage electron microscope, which allows a wide variety of in situ ion beam experiments to be performed with simultaneous irradiation and electron microscopy or diffraction.At elevated temperatures, U3Si exhibits the ordered AuCu3 structure. On cooling below 1058 K, the intermetallic transforms, evidently martensitically, to a body-centered tetragonal structure (alternatively, the structure may be described as face-centered tetragonal, which would be fcc except for a 1 pet tetragonal distortion). Mechanical twinning accompanies the transformation; however, diferences between electron diffraction patterns from twinned and non-twinned martensite plates could not be distinguished.

To Eliminate Curtain Effect of FIB TEM Samples by a Combination of Sample Dicing and Backside Milling

2014 ◽  
Author(s):  
Jian-Shing Luo ◽  
Hsiu Ting Lee
Keyword(s):  
Sample Preparation ◽  
Focused Ion Beam ◽  
Preparation Method ◽  
Low Cost ◽  
Ion Beam ◽  
Sample Preparation Method ◽  
Site Specific ◽  
Dual Beam ◽  
Transmission Electron

Abstract Several methods are used to invert samples 180 deg in a dual beam focused ion beam (FIB) system for backside milling by a specific in-situ lift out system or stages. However, most of those methods occupied too much time on FIB systems or requires a specific in-situ lift out system. This paper provides a novel transmission electron microscopy (TEM) sample preparation method to eliminate the curtain effect completely by a combination of backside milling and sample dicing with low cost and less FIB time. The procedures of the TEM pre-thinned sample preparation method using a combination of sample dicing and backside milling are described step by step. From the analysis results, the method has applied successfully to eliminate the curtain effect of dual beam FIB TEM samples for both random and site specific addresses.

Investigations of Leakage Paths in Sub-0.35μm DRAM Products Using Advanced Focused Ion Beam Techniques

1998 ◽  
Author(s):  
H. Lorenz ◽  
C. Engel
Keyword(s):  
Focused Ion Beam ◽  
Cell Function ◽  
Dielectric Breakdown ◽  
Ion Beam ◽  
Electrical Characterization ◽  
Floating Gate ◽  
Leakage Path ◽  
Contrast Technique ◽  
Voltage Contrast

Abstract Due to the continuously decreasing cell size of DRAMs and concomitantly diminishing thickness of some insulating layers new failure mechanisms appear which until now had no significance for the cell function. For example high resistance leakage paths between closely spaced conductors can lead to retention problems. These are hard to detect by electrical characterization in a memory tester because the involved currents are in the range of pA. To analyze these failures we exploit the very sensitive passive voltage contrast of the Focused Ion Beam Microscope (FIB). The voltage contrast can further be enhanced by in-situ FIB preparations to obtain detailed information about the failure mechanism. The first part of this paper describes a method to detect a leakage path between a borderless contact on n-diffusion and an adjacent floating gate by passive voltage contrast achieved after FIB circuit modification. In the second part we will demonstrate the localization of a DRAM trench dielectric breakdown. In this case the FIB passive voltage contrast technique is not limited to the localization of the failing trench. We can also obtain the depth of the leakage path by selective insitu etching with XeF2 stopped immediately after a voltage contrast change.

In-Situ Dual Beam (FIBSEM) Techniques for Probe Pad Deposition and Dielectric Integrity Inspection in 0.2 μm Technology DRAM Single Cells

1999 ◽  
Author(s):  
Gunnar Zimmermann ◽  
Richard Chapman
Keyword(s):  
Electron Beam ◽  
Single Cell ◽  
Single Cells ◽  
Ion Beam ◽  
Gate Oxide ◽  
Ion Milling ◽  
Dual Beam ◽  
Sem Imaging ◽  
Innovative Techniques

Abstract Dual beam FIBSEM systems invite the use of innovative techniques to localize IC fails both electrically and physically. For electrical localization, we present a quick and reliable in-situ FIBSEM technique to deposit probe pads with very low parasitic leakage (Ipara < 4E-11A at 3V). The probe pads were Pt, deposited with ion beam assistance, on top of highly insulating SiOx, deposited with electron beam assistance. The buried plate (n-Band), p-well, wordline and bitline of a failing and a good 0.2 μm technology DRAM single cell were contacted. Both cells shared the same wordline for direct comparison of cell characteristics. Through this technique we electrically isolated the fail to a single cell by detecting leakage between the polysilicon wordline gate and the cell diffusion. For physical localization, we present a completely in-situ FIBSEM technique that combines ion milling, XeF2 staining and SEM imaging. With this technique, the electrically isolated fail was found to be a hole in the gate oxide at the bad cell.

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