ScatterJn: An ImageJ Plugin for Scatterplot-Matrix Analysis and Classification of Spatially Resolved Analytical Microscopy Data

The mitotic spindle is a microtubule-based machine that pulls the two identical sets of chromosomes to opposite ends of the cell during cell division. The fission yeast Schizosaccharomyces pombe is an important model organism for studying mitosis due to its simple, stereotyped spindle structure and well-established genetic toolset. S. pombe spindle length is a useful metric for mitotic progression, but manually tracking spindle ends in each frame to measure spindle length over time is laborious and can limit experimental throughput. We have developed an ImageJ plugin that can automatically track S. pombe spindle length over time and replace manual or semi-automated tracking of spindle elongation dynamics. Using an algorithm that detects the principal axis of the spindle and then finds its ends, we reliably track the length and angle of the spindle as the cell divides. The plugin integrates with existing ImageJ features, exports its data for further analysis outside of ImageJ, and does not require any programming by the user. Thus, the plugin provides an accessible tool for quantification of S. pombe spindle length that will allow automatic analysis of large microscopy data sets and facilitate screening for effects of cell biological perturbations on mitotic progression.

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Analysis and Classification of Liquid Samples Using Spatial Heterodyne Raman Spectroscopy

Applied Spectroscopy ◽

10.1177/0003702819863847 ◽

2019 ◽

Vol 73 (12) ◽

pp. 1409-1419

Author(s):

Ardian B. Gojani ◽

Dávid J. Palásti ◽

Andrea Paul ◽

Gábor Galbács ◽

Igor B. Gornushkin

Keyword(s):

Raman Spectra ◽

Michelson Interferometer ◽

Principal Component ◽

Resolving Power ◽

Calibration Plot ◽

Least Squares Regression ◽

Spatially Resolved ◽

Liquid Samples ◽

Diode Pumped

Spatial heterodyne spectroscopy (SHS) is used for quantitative analysis and classification of liquid samples. SHS is a version of a Michelson interferometer with no moving parts and with diffraction gratings in place of mirrors. The instrument converts frequency-resolved information into a spatially resolved one and records it in the form of interferograms. The back-extraction of spectral information is done by the fast Fourier transform. A SHS instrument is constructed with the resolving power 5000 and spectral range 522–593 nm. Two original technical solutions are used as compared to previous SHS instruments: the use of a high-frequency diode-pumped solid-state laser for excitation of Raman spectra and a microscope-based collection system. Raman spectra are excited at 532 nm at the repetition rate 80 kHz. Raman shifts between 330 cm−1 and 1600 cm−1 are measured. A new application of SHS is demonstrated: for the first time, it is used for quantitative Raman analysis to determine concentrations of cyclohexane in isopropanol and glycerol in water. Two calibration strategies are employed: univariate based on the construction of a calibration plot and multivariate based on partial least squares regression. The detection limits for both cyclohexane in isopropanol and glycerol in water are at a 0.5 mass% level. In addition to the Raman–SHS chemical analysis, classification of industrial oils (biodiesel, poly(1-decene), gasoline, heavy oil IFO380, polybutenes, and lubricant) is performed using the Raman–fluorescence spectra of the oils and principal component analysis. The oils are easily discriminated showing distinct non-overlapping patterns in the principal component space.

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AutoNeuriteJ: An ImageJ plugin for measurement and classification of neuritic extensions

PLoS ONE ◽

10.1371/journal.pone.0234529 ◽

2020 ◽

Vol 15 (7) ◽

pp. e0234529

Author(s):

Benoit Boulan ◽

Anne Beghin ◽

Charlotte Ravanello ◽

Jean-Christophe Deloulme ◽

Sylvie Gory-Fauré ◽

...

Keyword(s):

Imagej Plugin

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Classification of Individual Particles Based on Computer-Controlled Scanning Electron Microscopy Data

Aerosol Science and Technology ◽

10.1080/02786828808959201 ◽

1988 ◽

Vol 9 (2) ◽

pp. 133-151 ◽

Cited By ~ 31

Author(s):

D. Kim ◽

P. K. Hopke

Keyword(s):

Electron Microscopy ◽

Scanning Electron Microscopy ◽

Scanning Electron Microscopy Data ◽

Electron Microscopy Data ◽

Computer Controlled ◽

Microscopy Data ◽

Individual Particles ◽

Scanning Electron

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Atomistic Simulation and Density Functional Analysis of Ni(111)-ZrO2(100)(Cubic) and NiO(111)-Ni(111)-ZrO2(100)(Cubic) Interfaces

MRS Proceedings ◽

10.1557/proc-654-aa4.5.1 ◽

2000 ◽

Vol 654 ◽

Cited By ~ 3

Author(s):

Chang-Xin Guo ◽

Donald E. Ellis ◽

Vinayak P. Dravid ◽

Luke Brewer

Keyword(s):

First Principles ◽

Atomistic Simulation ◽

Density Functional ◽

Depth Profiling ◽

Interface Plane ◽

Functional Theory ◽

Spatially Resolved ◽

Microscopy Data ◽

Energy Profiling ◽

Good Agreement

AbstractThe atomic arrangement and electronic structure in the vicinity of Ni(111)- ZrO2(100)(Cubic) and NiO(111)-Ni(111)-ZrO2(100)(Cubic) interfaces have been studied by atomistic simulation and by first-principles Density Functional theory. “Depth Profiling” is carred out in both methodologies, to determine modifications of cohesive energy and electron distribution of atomic layers from the interface plane. The energy profiling results show the interface consists of only a few atomic layers. Simulation results and electron density analyses are in good agreement with High Resolution Spatially Resolved Electron Microscopy data.

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