EDS and WDS Automation: Past Development and Future Technology

1999 ◽  
Vol 5 (S2) ◽  
pp. 556-557
Author(s):  
J. J. McCarthy ◽  
J. J. Frief
Keyword(s):  
Data Collection ◽  
Programming Languages ◽  
Electron Probe ◽  
Light Element ◽  
Automated Analysis ◽  
Spectral Processing ◽  
Electron Probe Analysis ◽  
Beam Position ◽  
Data Collection And Analysis ◽  
Automation Systems

Early Development Automation of electron probe analysis began to flourish in the early 1970s spurred on by advances in computer technology and the availability of operating systems and programming languages that the individual researcher could afford to dedicate to a single instrument. By the end of the decade, most researchers and vendors in the microanalysis field had adopted the PDP-11 minicomputer, and languages such as FOCAL, FORTRAN and BASIC that ran on these computers. A good summary of these early efforts was given by Hatfield. The first use of the energy dispersive detector on the electron probe in 1968 added the need to control the acquisition, display and processing of EDS spectra. As a result, the 70’s were also a time when much attention was focussed on development of software for on-line data reduction and analysis. These efforts produced a suite of programs to provide matrix corrections and spectral processing, and automation of WDS data collection. The culmination of these development efforts was first reported in 1977 with the analysis of a lunar whitlockite mineral by simultaneous EDS/WDS measurement. This analysis determined the concentration of 23 elements, 8 by EDS and took a total of 37 minutes for data collection and analysis. In this paper, the authors noted the complementary use of the EDS and WDS (WDS for trace elements and severe peak overlaps, EDS for other elements and rapid qualitative analysis) in their automated instrument, a convention that remains common on the electron probe even today. Toward the end of the decade the analytical accuracy and precision achieved by automated analysis of bulk samples approached the limits of the instrumentation, with the exception of analysis of light element concentrations.Two Decades of Improvements The explosive growth in digital electronics and microprocessors for data processing and control functions during the 80’s was rapidly applied to electron probe automation. Second and third generation automation systems included direct control of many microscope functions, beam position and imaging conditions. Motor positioning was more precise and far faster. As a result, the data collection and analysis of 23 elements reported in 1977 could be accomplished at least three times faster on a modern instrument.

scholarly journals ImageJ and 3D Slicer: open source 2/3D morphometric software

2019 ◽  
Author(s):  
Fiona Pye ◽  
Nussaȉbah B Raja ◽  
Bryan Shirley ◽  
Ádám T Kocsis ◽  
Niklas Hohmann ◽  
...  
Keyword(s):  
Data Collection ◽  
Open Source ◽  
Programming Languages ◽  
Quality Data ◽  
Software Projects ◽  
High Quality Data ◽  
3D Slicer ◽  
Data Collection And Analysis ◽  
Digital Methods ◽  
Imagej Plugin

In a world where an increasing number of resources are hidden behind paywalls and monthly subscriptions, it is becoming crucial for the scientific community to invest energy into freely available, community-maintained systems. Open-source software projects offer a solution, with freely available code which users can utilise and modify, under an open source licence. In addition to software accessibility and methodological repeatability, this also enables and encourages the development of new tools. As palaeontology moves towards data driven methodologies, it is becoming more important to acquire and provide high quality data through reproducible systematic procedures. Within the field of morphometrics, it is vital to adopt digital methods that help mitigate human bias from data collection. In addition,m mathematically founded approaches can reduce subjective decisions which plague classical data. This can be further developed through automation, which increases the efficiency of data collection and analysis. With these concepts in mind, we introduce two open-source shape analysis software, that arose from projects within the medical imaging field. These are ImageJ, an image processing program with batch processing features, and 3DSlicer which focuses on 3D informatics and visualisation. They are easily extensible using common programming languages, with 3DSlicer containing an internal python interactor, and ImageJ allowing the incorporation of several programming languages within its interface alongside its own simplified macro language. Additional features created by other users are readily available, on GitHub or through the software itself. In the examples presented, an ImageJ plugin “FossilJ” has been developed which provides semi-automated morphometric bivalve data collection. 3DSlicer is used with the extension SPHARM-PDM, applied to synchrotron scans of coniform conodonts for comparative morphometrics, for which small assistant tools have been created.

scholarly journals ImageJ and 3D Slicer: open source 2/3D morphometric software

2019 ◽  
Author(s):  
Fiona Pye ◽  
Nussaȉbah B Raja ◽  
Bryan Shirley ◽  
Ádám T Kocsis ◽  
Niklas Hohmann ◽  
...  
Keyword(s):  
Data Collection ◽  
Open Source ◽  
Programming Languages ◽  
Quality Data ◽  
Software Projects ◽  
High Quality Data ◽  
3D Slicer ◽  
Data Collection And Analysis ◽  
Digital Methods ◽  
Imagej Plugin

In a world where an increasing number of resources are hidden behind paywalls and monthly subscriptions, it is becoming crucial for the scientific community to invest energy into freely available, community-maintained systems. Open-source software projects offer a solution, with freely available code which users can utilise and modify, under an open source licence. In addition to software accessibility and methodological repeatability, this also enables and encourages the development of new tools. As palaeontology moves towards data driven methodologies, it is becoming more important to acquire and provide high quality data through reproducible systematic procedures. Within the field of morphometrics, it is vital to adopt digital methods that help mitigate human bias from data collection. In addition, mathematically founded approaches can reduce subjective decisions which plague classical data. This can be further developed through automation, which increases the efficiency of data collection and analysis. With these concepts in mind, we introduce two open-source shape analysis software, that arose from projects within the medical imaging field. These are ImageJ, an image processing program with batch processing features, and 3D Slicer which focuses on 3D informatics and visualisation. They are easily extensible using common programming languages, with 3D Slicer containing an internal python interactor, and ImageJ allowing the incorporation of several programming languages within its interface alongside its own simplified macro language. Additional features created by other users are readily available, on GitHub or through the software itself. In the examples presented, an ImageJ plugin “FossilJ” has been developed which provides semi-automated morphometric bivalve data collection. 3D Slicer is used with the extension SPHARM-PDM, applied to synchrotron scans of coniform conodonts for comparative morphometrics, for which small assistant tools have been created in Python.

Compositional imaging in the Electron Microscope

1991 ◽  
Vol 49 ◽  
pp. 2-3
Author(s):  
C. E. Lyman
Keyword(s):  
Electron Microscopy ◽  
Electron Beam ◽  
Electron Microscope ◽  
Data Collection ◽  
Electron Probe ◽  
Compositional Data ◽  
Fine Scale ◽  
Bulk Specimen ◽  
Beam Position ◽  
X Ray

Imaging of elemental distributions on a fine scale is one of the triumphs of electron microscopy. Compositional imaging frees the operator from the necessity of making decisions about which features contain the elements of interest. Elements in unexpected locations, or in unexpected association with other elements, may be found easily without operator bias as to where to locate the electron probe for compositional data collection. This technique may be applied to bulk or thin specimens using a variety of composition-sensitive signals as shown in Figure 1.Cosslett and Duncumb obtained the first such compositional image in an electron microprobe modified to scan the electron beam and collect a characteristic x-ray signal as a function of beam position. Early images of this type were called x-ray “dot maps” and provided a qualitative indication of the location of elements on a flat polished bulk specimen to a spatial resolution of about 1 μm.

scholarly journals ImageJ and 3D Slicer: open source 2/3D morphometric software

2019 ◽  
Author(s):  
Fiona Pye ◽  
Nussaȉbah B Raja ◽  
Bryan Shirley ◽  
Ádám T Kocsis ◽  
Niklas Hohmann ◽  
...  
Keyword(s):  
Data Collection ◽  
Open Source ◽  
Programming Languages ◽  
Quality Data ◽  
Software Projects ◽  
High Quality Data ◽  
3D Slicer ◽  
Data Collection And Analysis ◽  
Digital Methods ◽  
Imagej Plugin

In a world where an increasing number of resources are hidden behind paywalls and monthly subscriptions, it is becoming crucial for the scientific community to invest energy into freely available, community-maintained systems. Open-source software projects offer a solution, with freely available code which users can utilise and modify, under an open source licence. In addition to software accessibility and methodological repeatability, this also enables and encourages the development of new tools. As palaeontology moves towards data driven methodologies, it is becoming more important to acquire and provide high quality data through reproducible systematic procedures. Within the field of morphometrics, it is vital to adopt digital methods that help mitigate human bias from data collection. In addition, mathematically founded approaches can reduce subjective decisions which plague classical data. This can be further developed through automation, which increases the efficiency of data collection and analysis. With these concepts in mind, we introduce two open-source shape analysis software, that arose from projects within the medical imaging field. These are ImageJ, an image processing program with batch processing features, and 3D Slicer which focuses on 3D informatics and visualisation. They are easily extensible using common programming languages, with 3D Slicer containing an internal python interactor, and ImageJ allowing the incorporation of several programming languages within its interface alongside its own simplified macro language. Additional features created by other users are readily available, on GitHub or through the software itself. In the examples presented, an ImageJ plugin “FossilJ” has been developed which provides semi-automated morphometric bivalve data collection. 3D Slicer is used with the extension SPHARM-PDM, applied to synchrotron scans of coniform conodonts for comparative morphometrics, for which small assistant tools have been created in Python.

Electron Probe Analysis of Muscle

1982 ◽  
Vol 40 ◽  
pp. 398-401
Author(s):  
A. V. Somlyo ◽  
H. Shuman ◽  
A. P. Somlyo
Keyword(s):  
Skeletal Muscle ◽  
Smooth Muscle ◽  
Sarcoplasmic Reticulum ◽  
Resting State ◽  
Binding Sites ◽  
Electron Probe ◽  
Frog Skeletal Muscle ◽  
Electron Probe Analysis ◽  
Probe Analysis

Electron probe analysis of frozen dried cryosections of frog skeletal muscle, rabbit vascular smooth muscle and of isolated, hyperpermeab1 e rabbit cardiac myocytes has been used to determine the composition of the cytoplasm and organelles in the resting state as well as during contraction. The concentration of elements within the organelles reflects the permeabilities of the organelle membranes to the cytoplasmic ions as well as binding sites. The measurements of [Ca] in the sarcoplasmic reticulum (SR) and mitochondria at rest and during contraction, have direct bearing on their role as release and/or storage sites for Ca in situ.

The use of a Bent Grid to Improve the take-Off Angle for Electron Probe Analysis

1976 ◽  
Vol 34 ◽  
pp. 360-361
Author(s):  
Delbert E. Philpott ◽  
David Leaffer
Keyword(s):  
Quantitative Analysis ◽  
Tilt Angle ◽  
Count Rate ◽  
Electron Probe ◽  
Open Area ◽  
Electron Probe Analysis ◽  
Background Ratio ◽  
Probe Analysis

There are certain advantages for electron probe analysis if the sample can be tilted directly towards the detector. The count rate is higher, it optimizes the geometry since only one angle need be taken into account for quantitative analysis and the signal to background ratio is improved. The need for less tilt angle may be an advantage because the grid bars are not moved quite as close to each other, leaving a little more open area for observation. Our present detector (EDAX) and microscope (Philips 300) combination precludes moving the detector behind the microscope where it would point directly at the grid. Therefore, the angle of the specimen was changed in order to optimize the geometry between the specimen and the detector.

Electron Probe Analysis of Vertebrate Smooth Muscle: Distribution of Ca and Ci

1976 ◽  
Vol 34 ◽  
pp. 334-335 ◽  
Author(s):  
Avril V. Somlyo ◽  
H. Shuman ◽  
A.P. Somlyo
Keyword(s):  
Smooth Muscle ◽  
Electron Probe ◽  
Preliminary Report ◽  
Cell Damage ◽  
Electron Probe Analysis ◽  
Perinuclear Space ◽  
Probe Analysis ◽  
High K ◽  
Low K ◽  
Initial Results

This is a preliminary report of electron probe analysis of rabbit portal-anterior mesenteric vein (PAMV) smooth muscle cryosectioned without fixation or cryoprotection. The instrumentation and method of electron probe quantitation used (1) and our initial results with cardiac (2) and skeletal (3) muscle have been presented elsewhere.In preparations depolarized with high K (K2SO4) solution, significant calcium peaks were detected over the sarcoplasmic reticulum (Fig 1 and 2) and the continuous perinuclear space. In some of the fibers there were also significant (up to 200 mM/kg dry wt) calcium peaks over the mitochondria. However, in smooth muscle that was not depolarized, high mitochondrial Ca was found in fibers that also contained elevated Na and low K (Fig 3). Therefore, the possibility that these Ca-loaded mitochondria are indicative of cell damage remains to be ruled out.

A New Numerical Model for Electron-Probe Analysis at High Depth Resolution

1996 ◽  
Vol 54 ◽  
pp. 490-491
Author(s):  
P.-F. Staub ◽  
C. Bonnelle ◽  
F. Vergand ◽  
P. Jonnard
Keyword(s):  
Electron Probe ◽  
Surface Segregation ◽  
Depth Distribution ◽  
Computing Time ◽  
Depth Resolution ◽  
Physical Parameters ◽  
Electron Probe Analysis ◽  
Interface Phases ◽  
Excitation Conditions ◽  
High Depth

Characterizing dimensionally and chemically nanometric structures such as surface segregation or interface phases can be performed efficiently using electron probe (EP) techniques at very low excitation conditions, i.e. using small incident energies (0.5<E0<5 keV) and low incident overvoltages (1<U0<1.7). In such extreme conditions, classical analytical EP models are generally pushed to their validity limits in terms of accuracy and physical consistency, and Monte-Carlo simulations are not convenient solutions as routine tools, because of their cost in computing time. In this context, we have developed an intermediate procedure, called IntriX, in which the ionization depth distributions Φ(ρz) are numerically reconstructed by integration of basic macroscopic physical parameters describing the electron beam/matter interaction, all of them being available under pre-established analytical forms. IntriX’s procedure consists in dividing the ionization depth distribution into three separate contributions:

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