AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy

We developed AutoscanJ, a suite of ImageJ scripts enabling to image targets of interest by automatically driving a motorized microscope at the corresponding locations. For live samples, our software can sequentially detect biological events from their onset and further image them at high resolution, an action that would be impractical by user operation. For fixed samples, the software can dramatically reduce the amount of data acquired and the acquisition duration in situations where statistically few targets of interest are observed per field of view. AutoScanJ is compatible with motorized fluorescence microscopes controlled by Leica LAS AF/X or Micro-Manager. The software is straightforward to set up and new custom image analysis workflows to detect targets of interest can be simply implemented and shared with minimal efforts as independent ImageJ macro functions. We illustrate five different application scenarios with the system ranging from samples fixed on micropatterned surfaces to live cells undergoing several rounds of division. The target detection functions for these applications are provided and can be used as a starting point and a source of inspiration for new applications. Overall, AutoScanJ helps to optimize microscope usage by autonomous operation, and it opens up new experimental avenues by enabling the real-time detection and selective imaging of transient events in live microscopy.

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Variable Curvature Displays: Optical Designs and Applications for VR/AR/MR Headsets

Applied Sciences ◽

10.3390/app10020712 ◽

2020 ◽

Vol 10 (2) ◽

pp. 712

Author(s):

Eduard Muslimov ◽

Thibault Behaghel ◽

Emmanuel Hugot ◽

Kelly Joaquina ◽

Ilya Guskov

Keyword(s):

Virtual Reality ◽

High Resolution ◽

Field Of View ◽

Projection System ◽

Object Position ◽

Focal Surface ◽

Variable Curvature ◽

Starting Point ◽

Low Distortion ◽

Aberration Theory

In the present paper, we discuss the design of a projection system with curved display and its enhancement by variably adjusting the curvature. We demonstrate that the focal surface curvature varies significantly with a change of the object position and that it can easily be computed with the Seidel aberration theory. Using this analytically derived curvature value as the starting point, we optimise a refocusable projection system with 90 ° field of view and F / # = 6.2 . It is demonstrated that such a system can provide stable image quality and illumination when refocusing from infinity to 1.5 m. The gain in spatial resolution is as high as 1.54 times with respect to a flat focal surface. Furthermore, we prove that a silicon die can be curved to the required shape with a safety factor of 4.3 in terms of the mechanical stress. Finally, it is shown that the developed system can be used in a virtual reality headset providing high resolution, low distortion and a flexible focusing mode.

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Very High Resolution Analysis of the Dynamics of a Coronal Plasmoid

International Astronomical Union Colloquium ◽

10.1017/s0252921100026117 ◽

1994 ◽

Vol 144 ◽

pp. 593-596

Author(s):

O. Bouchard ◽

S. Koutchmy ◽

L. November ◽

J.-C. Vial ◽

J. B. Zirker

Keyword(s):

High Resolution ◽

Solar Eclipse ◽

Total Solar Eclipse ◽

Field Of View ◽

Small Field ◽

High Resolution Analysis ◽

Ccd Observations ◽

Resolution Analysis ◽

Very High ◽

Small Field Of View

AbstractWe present the results of the analysis of a movie taken over a small field of view in the intermediate corona at a spatial resolution of 0.5“, a temporal resolution of 1 s and a spectral passband of 7 nm. These CCD observations were made at the prime focus of the 3.6 m aperture CFHT telescope during the 1991 total solar eclipse.

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Low-Loss Images in a Stem/Tem Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010009244x ◽

1976 ◽

Vol 34 ◽

pp. 496-497 ◽

Cited By ~ 1

Author(s):

David C. Joy ◽

Dennis M. Maher

Keyword(s):

High Resolution ◽

Surface Topography ◽

Beam Direction ◽

Low Loss ◽

Specimen Holder ◽

Glancing Angle ◽

High Resolution Images ◽

Set Up ◽

Conventional Manner ◽

Objective Type

High-resolution images of the surface topography of solid specimens can be obtained using the low-loss technique of Wells. If the specimen is placed inside a lens of the condenser/objective type, then it has been shown that the lens itself can be used to collect and filter the low-loss electrons. Since the probeforming lenses in TEM instruments fitted with scanning attachments are of this type, low-loss imaging should be possible.High-resolution, low-loss images have been obtained in a JEOL JEM 100B fitted with a scanning attachment and a thermal, fieldemission gun. No modifications were made to the instrument, but a wedge-shaped, specimen holder was made to fit the side-entry, goniometer stage. Thus the specimen is oriented initially at a glancing angle of about 30° to the beam direction. The instrument is set up in the conventional manner for STEM operation with all the lenses, including the projector, excited.

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A High Resolution Scanning Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100101529 ◽

1968 ◽

Vol 26 ◽

pp. 356-357

Author(s):

A. V. Crewe ◽

J. Wall ◽

L. M. Welter

Keyword(s):

High Resolution ◽

Field Emission ◽

Spherical Aberration ◽

Focal Length ◽

Spot Size ◽

Emission Source ◽

Field Of View ◽

Scanning Microscope ◽

Magnetic Lens ◽

High Quality

A scanning microscope using a field emission source has been described elsewhere. This microscope has now been improved by replacing the single magnetic lens with a high quality lens of the type described by Ruska. This lens has a focal length of 1 mm and a spherical aberration coefficient of 0.5 mm. The final spot size, and therefore the microscope resolution, is limited by the aberration of this lens to about 6 Å.The lens has been constructed very carefully, maintaining a tolerance of + 1 μ on all critical surfaces. The gun is prealigned on the lens to form a compact unit. The only mechanical adjustments are those which control the specimen and the tip positions. The microscope can be used in two modes. With the lens off and the gun focused on the specimen, the resolution is 250 Å over an undistorted field of view of 2 mm. With the lens on,the resolution is 20 Å or better over a field of view of 40 microns. The magnification can be accurately varied by attenuating the raster current.

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Algorithms for automated montage synthesis of images from laser-scanning confocal microscopes

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100139627 ◽

1995 ◽

Vol 53 ◽

pp. 650-651

Author(s):

D. E. Becker

Keyword(s):

Image Analysis ◽

High Resolution ◽

Laser Scanning ◽

Cell Counting ◽

Wide Area ◽

Data Set ◽

Computational Synthesis ◽

Automated Cell Counting ◽

Partial View ◽

The Individual

An efficient, robust, and widely-applicable technique is presented for computational synthesis of high-resolution, wide-area images of a specimen from a series of overlapping partial views. This technique can also be used to combine the results of various forms of image analysis, such as segmentation, automated cell counting, deblurring, and neuron tracing, to generate representations that are equivalent to processing the large wide-area image, rather than the individual partial views. This can be a first step towards quantitation of the higher-level tissue architecture. The computational approach overcomes mechanical limitations, such as hysterisis and backlash, of microscope stages. It also automates a procedure that is currently done manually. One application is the high-resolution visualization and/or quantitation of large batches of specimens that are much wider than the field of view of the microscope.The automated montage synthesis begins by computing a concise set of landmark points for each partial view. The type of landmarks used can vary greatly depending on the images of interest. In many cases, image analysis performed on each data set can provide useful landmarks. Even when no such “natural” landmarks are available, image processing can often provide useful landmarks.

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Going Beyond 3-D Imaging: Automated 3-D Montaged image Analysis of Cytological Specimens

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100163873 ◽

1996 ◽

Vol 54 ◽

pp. 282-283

Author(s):

Badrinath Roysam ◽

Hakan Ancin ◽

Douglas E. Becker ◽

Robert W. Mackin ◽

Matthew M. Chestnut ◽

...

Keyword(s):

Image Analysis ◽

Structural Changes ◽

Sampling Methods ◽

Spatial Clustering ◽

Three Dimensional ◽

Field Of View ◽

Cell Counting ◽

Depth Of Field ◽

Tissue Cell ◽

Tissue Organization

This paper summarizes recent advances made by this group in the automated three-dimensional (3-D) image analysis of cytological specimens that are much thicker than the depth of field, and much wider than the field of view of the microscope. The imaging of thick samples is motivated by the need to sample large volumes of tissue rapidly, make more accurate measurements than possible with 2-D sampling, and also to perform analysis in a manner that preserves the relative locations and 3-D structures of the cells. The motivation to study specimens much wider than the field of view arises when measurements and insights at the tissue, rather than the cell level are needed.The term “analysis” indicates a activities ranging from cell counting, neuron tracing, cell morphometry, measurement of tracers, through characterization of large populations of cells with regard to higher-level tissue organization by detecting patterns such as 3-D spatial clustering, the presence of subpopulations, and their relationships to each other. Of even more interest are changes in these parameters as a function of development, and as a reaction to external stimuli. There is a widespread need to measure structural changes in tissue caused by toxins, physiologic states, biochemicals, aging, development, and electrochemical or physical stimuli. These agents could affect the number of cells per unit volume of tissue, cell volume and shape, and cause structural changes in individual cells, inter-connections, or subtle changes in higher-level tissue architecture. It is important to process large intact volumes of tissue to achieve adequate sampling and sensitivity to subtle changes. It is desirable to perform such studies rapidly, with utmost automation, and at minimal cost. Automated 3-D image analysis methods offer unique advantages and opportunities, without making simplifying assumptions of tissue uniformity, unlike random sampling methods such as stereology.12 Although stereological methods are known to be statistically unbiased, they may not be statistically efficient. Another disadvantage of sampling methods is the lack of full visual confirmation - an attractive feature of image analysis based methods.

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High-Resolution Large-Field-of-View Ultrasound Breast Imager

10.21236/ada612043 ◽

2014 ◽

Author(s):

Patrick LaRiviere

Keyword(s):

High Resolution ◽

Field Of View ◽

Large Field

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MODELING THE SOUTH ATLANTIC OCEAN FROM MEDIUM TO HIGH RESOLUTION

Brazilian Journal of Geophysics ◽

10.22564/rbgf.v31i2.27 ◽

2014 ◽

Vol 31 (2) ◽

Author(s):

Mariela Gabioux ◽

Vladimir Santos da Costa ◽

Joao Marcos Azevedo Correia de Souza ◽

Bruna Faria de Oliveira ◽

Afonso De Moraes Paiva

Keyword(s):

High Resolution ◽

Atlantic Ocean ◽

Large Scale ◽

South Atlantic ◽

Surface Relaxation ◽

The South ◽

Small Surface ◽

Basic Model ◽

Basic Set ◽

Set Up

Results of the basic model configuration of the REMO project, a Brazilian approach towards operational oceanography, are discussed. This configuration consists basically of a high-resolution eddy-resolving, 1/12 degree model for the Metarea V, nested in a medium-resolution eddy-permitting, 1/4 degree model of the Atlantic Ocean. These simulations performed with HYCOM model, aim for: a) creating a basic set-up for implementation of assimilation techniques leading to ocean prediction; b) the development of hydrodynamics bases for environmental studies; c) providing boundary conditions for regional domains with increased resolution. The 1/4 degree simulation was able to simulate realistic equatorial and south Atlantic large scale circulation, both the wind-driven and the thermohaline components. The high resolution simulation was able to generate mesoscale and represent well the variability pattern within the Metarea V domain. The BC mean transport values were well represented in the southwestern region (between Vitória-Trinidade sea mount and 29S), in contrast to higher latitudes (higher than 30S) where it was slightly underestimated. Important issues for the simulation of the South Atlantic with high resolution are discussed, like the ideal place for boundaries, improvements in the bathymetric representation and the control of bias SST, by the introducing of a small surface relaxation. In order to make a preliminary assessment of the model behavior when submitted to data assimilation, the Cooper & Haines (1996) method was used to extrapolate SSH anomalies fields to deeper layers every 7 days, with encouraging results.

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Neutron Imaging Using a Fine-Grained Nuclear Emulsion

Journal of Imaging ◽

10.3390/jimaging7010004 ◽

2021 ◽

Vol 7 (1) ◽

pp. 4

Author(s):

Katsuya Hirota ◽

Tomoko Ariga ◽

Masahiro Hino ◽

Go Ichikawa ◽

Shinsuke Kawasaki ◽

...

Keyword(s):

Image Analysis ◽

High Resolution ◽

Neutron Detector ◽

Nuclear Emulsion ◽

Neutron Imaging ◽

The Other ◽

Crystal Oscillator ◽

Fine Grained ◽

Cold Neutrons ◽

Track Analysis

A neutron detector using a fine-grained nuclear emulsion has a sub-micron spatial resolution and thus has potential to be applied as high-resolution neutron imaging. In this paper, we present two approaches to applying the emulsion detectors for neutron imaging. One is using a track analysis to derive the reaction points for high resolution. From an image obtained with a 9 μm pitch Gd grating with cold neutrons, periodic peak with a standard deviation of 1.3 μm was observed. The other is an approach without a track analysis for high-density irradiation. An internal structure of a crystal oscillator chip, with a scale of approximately 30 μm, was able to be observed after an image analysis.

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