scholarly journals Preparing Micrographs and Applying Scale Bars Using Adobe Photoshop Elements™

2008 ◽  
Vol 16 (6) ◽  
pp. 54-57
Author(s):  
Susan A. Lancelle
Keyword(s):  
Cell Biology ◽  
Software Package ◽  
Calibration Data ◽  
Camera System ◽  
Adobe Photoshop ◽  
With Memory

As part of our introductory Cell Biology course, our students acquire images through microscopes using consumer cameras with memory cards. They then transfer the images to a computer and prepare them using Adobe Photoshop Elements.™ An important part of this process is learning to apply a scale bar, which calibrates the specimen image. Photoshop Elements is a relatively cheap and widely available software package that easily accomplishes this task for anyone who is using a camera system or software that does not automatically apply a scale bar or calibration data to the image. The instructions and figures herein refer to Photoshop Elements version 4.0, but they apply to other versions of the software.

scholarly journals Using CCD’s in Introductory-Level College Astronomy Laboratories

1990 ◽  
Vol 105 ◽  
pp. 142-144
Author(s):  
Thomas J. Balonek
Keyword(s):  
Dark Current ◽  
Software Package ◽  
Multiple Access ◽  
Ccd Camera ◽  
Analysis Software ◽  
Camera System ◽  
Black And White ◽  
Standard Data ◽  
College Astronomy ◽  
Cooled Ccd

Our university recently purchased a liquid-nitrogen-cooled CCD camera system (from Photometrics Ltd., Tucson, Arizona) which has been installed on our campus’ 40-cm multiple access (Cassegrain/Newtonian) telescope. Images are reduced online at the observatory using Photometrics’ microcomputer-based analysis software package, which includes operations for standard data acquisition and initial stages of data reduction — including corrections for bias, dark current, and flat fielding. Images are displayed on a 256-level-gray-scale black and white monitor. Additional post-processing can be done either on the CCD system’s computer at the observatory or on IBM-AT/PC’s located both at the observatory and in the laboratory.

scholarly journals Application of the Adobe Photoshop Software Package in Leaf Blade Area Measurement of Woody Plants

2021 ◽  
pp. 185-191
Author(s):  
Ramis N. Babaev ◽  
Keyword(s):  
Software Package ◽  
Woody Plants ◽  
Leaf Blade ◽  
Morphometric Parameters ◽  
Area Measurement ◽  
Adhesive Tape ◽  
Scotch Tape ◽  
Adobe Photoshop ◽  
Blade Area ◽  
Method Accuracy

There are a number of applied methods for determining morphometric parameters, including the area of leaf blades of woody plants: millimeter graph paper method, method of direct measurements, punching method, and planimetric method. The analysis and practical application of the methods in the test mode revealed their shortcomings related to inaccuracy of measurements, experiment duration, and equipment inaccessibility. Many researchers have successfully acquired digitized images. However, capturing the parameters of the considered structure from the monitor screen is often impossible due to the low availability of morphometric programs and their high cost. The purpose of the work is to evaluate the effectiveness of existing methods for determining the area of leaf blades on the example of the birch genus (Betula L.) trees and to accumulate the algorithm for determining morphometric parameters of birch leaf blades in the Adobe Photoshop software package. We have developed a method for determining morphometric parameters of leaf blades of woody plants using the Adobe Photoshop software package. The research subject is the leaf blades of birch trees. This method requires: blank A4 sheets; a ruler with an angle of 90°; transparent adhesive tape (scotch tape); and a scanner. We draw a reference square of random (but fixed) dimensions in a random corner of each sheet, step by 10 mm from its borders, on a blank A4 sheet using a ruler with an angle of 90°. The square is placed strictly parallel to the sheet borders. Then, leaf blades of the desired wood species are attached to the sheet with scotch tape. Using the scanner, we convert the workpiece into electronic form and upload the image to Adobe Photoshop. In order to receive morphometric parameters, you can use the following program tools: “ruler”, “magic wand”, “magnetic lasso tool”. At the same time, it is possible to automatically select the borders of the studied object, which helps to avoid subjective errors. The resulting measurements are displayed in pixels and then converted to the required units. The obtained data is verified using the reference square. Verification showed that the method accuracy is more than 99.9 %. The proposed method allows to perform fast and accurate measurements of morphometric parameters of leaf blades, without requiring the purchase of expensive equipment, which makes it available to any researcher who faces with the task of measuring the surface of leaf blades of woody plants. For citation: Babaev R.N. Application of the Adobe Photoshop Software Package in Leaf Blade Area Measurement of Woody Plants. Lesnoy Zhurnal [Russian Forestry Journal], 2021, no. 5, pp. 185–191. DOI: 10.37482/0536-1036-2021-5-185-191

scholarly journals ATLAS Tile Calorimeter Conditions Database architecture and operations in Run 2

2020 ◽  
Vol 245 ◽  
pp. 02006
Author(s):  
Yuri Smirnov ◽  
Dhiman Chakraborty ◽  
Alexander Solodkov ◽  
Siarhei Harkusha
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Control System ◽  
Software Package ◽  
Atlas Detector ◽  
Calibration Data ◽  
Design And Implementation ◽  
Custom Made ◽  
Cool Conditions ◽  
Detector Control System

An overview of the Conditions Database (DB) structure for the hadronic Tile Calorimeter (TileCal), one of the sub-systems of the ATLAS detector at LHC, is presented. ATLAS Conditions DB stores the data on the ORACLE backend, and the design and implementation have been developed using the COOL (Conditions Objects for LCG) software package as a common persistency solution for the storage and management of the conditions data. TileCal conditions and calibration data are stored in 4 separate Databases, each with its own schema: TileCal Online and Offline DBs for data, DB for Monte Carlo simulation and Detector Control System (DCS) DB. In order to ensure smooth operation of the TileCal during data taking, experts perform the necessary calibrations, add the changes of detector status and other conditions data, prepare new conditions for data reprocessing and Monte Carlo production campaigns, and upload the new up-to-date information into DB using custom-made software tools. The procedure of TileCal conditions’ preparation, validation, uploading to DBs is described, and some DB-related statistics collected in Run 2 is presented.

scholarly journals EXTRACTING SEMANTICALLY ANNOTATED 3D BUILDING MODELS WITH TEXTURES FROM OBLIQUE AERIAL IMAGERY

2015 ◽  
Vol XL-3/W2 ◽  
pp. 53-58 ◽  
Author(s):  
D. Frommholz ◽  
M. Linkiewicz ◽  
H. Meissner ◽  
D. Dahlke ◽  
A. Poznanska
Keyword(s):  
High Resolution ◽  
Software Package ◽  
Point Clouds ◽  
Aerial Imagery ◽  
Commercial Software ◽  
Camera System ◽  
3D Point Clouds ◽  
Building Models ◽  
Commercial Software Package

This paper proposes a method for the reconstruction of city buildings with automatically derived textures that can be directly used for façade element classification. Oblique and nadir aerial imagery recorded by a multi-head camera system is transformed into dense 3D point clouds and evaluated statistically in order to extract the hull of the structures. For the resulting wall, roof and ground surfaces high-resolution polygonal texture patches are calculated and compactly arranged in a texture atlas without resampling. The façade textures subsequently get analyzed by a commercial software package to detect possible windows whose contours are projected into the original oriented source images and sparsely ray-casted to obtain their 3D world coordinates. With the windows being reintegrated into the previously extracted hull the final building models are stored as semantically annotated CityGML ”LOD-2.5” objects.

scholarly journals Decoupling global biases and local interactions between cell biological variables

2016 ◽  
Author(s):  
Assaf Zaritsky ◽  
Uri Obolski ◽  
Zhuo Gan ◽  
Carlos R. Reis ◽  
Zuzana Kadlecova ◽  
...  
Keyword(s):  
Cell Biology ◽  
Software Package ◽  
Computational Method ◽  
Core Concept ◽  
Local Interactions ◽  
Cellular Behavior ◽  
Biological Variables ◽  
Mechanistic Insight ◽  
Global Bias ◽  
Insight Into

AbstractAnalysis of coupled variables is a core concept of cell biological inference, with co-localization of two molecules as a proxy for protein interaction being a ubiquitous example. However, external effectors may influence the observed co-localization independently from the local interaction of two proteins. Such global bias, although biologically meaningful, is often neglected when interpreting co-localization. Here, we describe DeBias, a computational method to quantify and decouple global bias from local interactions between variables by modeling the observed co-localization as the cumulative contribution of a global and a local component. We showcase four applications of DeBias in different areas of cell biology, and demonstrate that the global bias encapsulates fundamental mechanistic insight into cellular behavior. The DeBias software package is freely accessible online via a web-server at https://debias.biohpc.swmed.edu.Impact statement: DeBias, a generic method to decompose and quantify the confounding, global factors and direct interactions of pairwise interacting variables.

A Hybrid Approach for 3D Full-Field Measurement on a Closed Slinger Combustor by Hydraulic Simulations

2017 ◽  
Author(s):  
Lichao Jia ◽  
Lili Yang ◽  
Huijing Yuan ◽  
Yongxia Jia ◽  
Yiyang Wang ◽  
...  
Keyword(s):  
Particle Density ◽  
Sampling Rate ◽  
Hybrid Approach ◽  
Least Square ◽  
Calibration Data ◽  
Experimental Conditions ◽  
Match Probability ◽  
Camera System ◽  
Reconstruction Process ◽  
Full Field

This hybrid approach proposed in the present study is a mixture algorithm of the 3D PTV and Tomo-PIV based on a two-camera system, which is able to measure the flow field in a closed system with high refractive without in situ calibration. Knowing the calibration data in the air and refractive indices of different optical media, a simplified multimedia photogrammetry model is established based on the least square method. A new particle matching algorithm using the concept of match probability between the twin image frames has been developed to reconstruct the physical position of the particles. In order to overcome the disadvantage of low particle density, time-resolved PIV is utilized at a sampling rate being 2000 Hz to acquire the instantaneous particle images. Then, the spectrum superposition of the cross-correlation distribution is applied to increase the signal-to-noise ratio in the velocity prediction. The technique proposed here can be used to overcome the difficulty in conventional calibration method for closed measurement objects. Both the computer simulation and some experiments imaging a calibration target reference field are conducted to show the accuracies of the calibration and reconstruction process. The capability of the technique in real experimental conditions is assessed with the measurement of the flow structure in a closed slinger combustor by hydraulic simulations.

scholarly journals Decoupling global biases and local interactions between cell biological variables

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Assaf Zaritsky ◽  
Uri Obolski ◽  
Zhuo Gan ◽  
Carlos R Reis ◽  
Zuzana Kadlecova ◽  
...  
Keyword(s):  
Cell Biology ◽  
Software Package ◽  
Computational Method ◽  
Core Concept ◽  
Local Interactions ◽  
Cellular Behavior ◽  
Biological Variables ◽  
Mechanistic Insight ◽  
Global Bias ◽  
Insight Into

Analysis of coupled variables is a core concept of cell biological inference, with co-localization of two molecules as a proxy for protein interaction being a ubiquitous example. However, external effectors may influence the observed co-localization independently from the local interaction of two proteins. Such global bias, although biologically meaningful, is often neglected when interpreting co-localization. Here, we describe DeBias, a computational method to quantify and decouple global bias from local interactions between variables by modeling the observed co-localization as the cumulative contribution of a global and a local component. We showcase four applications of DeBias in different areas of cell biology, and demonstrate that the global bias encapsulates fundamental mechanistic insight into cellular behavior. The DeBias software package is freely accessible online via a web-server at https://debias.biohpc.swmed.edu.

scholarly journals CALIBRATING A LENS WITH A “LOCAL” DISTORTION MODEL

2020 ◽  
Vol XLIII-B2-2020 ◽  
pp. 765-769
Author(s):  
I. Detchev ◽  
D. Lichti
Keyword(s):  
Lens Distortion ◽  
Data Sets ◽  
Systematic Effect ◽  
Calibration Data ◽  
Lens System ◽  
Camera System ◽  
Local Distortion ◽  
Close Range ◽  
Estimated Error ◽  
Source Of Error

Abstract. This paper is about camera calibration where an abnormal systematic effect was discovered. The effect was first encountered in a multi-camera system used for close range 3D photogrammetric reconstruction. The objectives for this research were two-fold. The first objective is to identify the source of the systematic error, and the second objective is to model the error as rigorously as possible. The first objective was met after acquiring several calibration data sets where the camera bodies, the lenses, and the image formats were varied. It was concluded that the source of error is the lens system. The second objective was also met. The so called “local” lens distortion was modelled using second order polynomials as the plots of the residuals vs. the image coordinates resembled parabolic shapes. Overall, the final room mean square error for the residuals after applying radial and “local” lens distortion was reduced from 1/2 to 1/6 of a pixel or a 200% relative estimated error improvement.

scholarly journals Development of ultrafast camera-based imaging of single fluorescent molecules and live-cell PALM

2021 ◽  
Author(s):  
Takahiro K. Fujiwara ◽  
Shinji Takeuchi ◽  
Ziya Kalay ◽  
Yosuke Nagai ◽  
Taka A. Tsunoyama ◽  
...  
Keyword(s):  
Single Molecule ◽  
Cell Biology ◽  
Live Cell ◽  
Camera System ◽  
Bright Field Microscopy ◽  
Localization Precision ◽  
20 Nm ◽  
System 1 ◽  
Fluorescent Molecules ◽  
Biology Research

The spatial resolution of fluorescence microscopy has recently been greatly improved. However, its temporal resolution has not been improved much, despite its importance for examining living cells. Here, by developing an ultrafast camera system, we achieved the world′s highest time resolutions for single fluorescent-molecule imaging of 33 (100) µs (multiple single molecules simultaneously) with a single-molecule localization precision of 34 (20) nm for Cy3 (best dye found), and for PALM data acquisition of a view-field of 640x640 pixels at 1 kHz with a single-molecule localization precision of 29 nm for mEos3.2. Both are considered the ultimate rates with available probes. This camera system (1) successfully detected fast hop diffusion of membrane molecules in the plasma membrane, detectable previously only by using less preferable 40-nm gold probes and bright-field microscopy, and (2) enabled PALM imaging of the entire live cell, while revealing meso-scale dynamics and structures, caveolae and paxillin islands in the focal adhesion, proving its usefulness for cell biology research.

Ultrastructure of Some Planktonic Formainifera

1974 ◽  
Vol 32 ◽  
pp. 190-191
Author(s):  
William H. Zucker
Keyword(s):  
Cell Biology ◽  
Water Mass ◽  
Planktonic Foraminifera ◽  
Uranyl Acetate ◽  
Ethanol Dehydration ◽  
Globigerinoides Ruber ◽  
Light Microscope Level ◽  
Globigerina Bulloides ◽  
Glutaraldehyde Solution ◽  
Diamond Knife

Planktonic foraminifera are widely-distributed and abundant zooplankters. They are significant as water mass indicators and provide evidence of paleotemperatures and events which occurred during Pleistocene glaciation. In spite of their ecological and paleological significance, little is known of their cell biology. There are few cytological studies of these organisms at the light microscope level and some recent reports of their ultrastructure.Specimens of Globigerinoides ruber, Globigerina bulloides, Globigerinoides conglobatus and Globigerinita glutinata were collected in Bermuda waters and fixed in a cold cacodylate-buffered 6% glutaraldehyde solution for two hours. They were then rinsed, post-fixed in Palade's fluid, rinsed again and stained with uranyl acetate. This was followed by graded ethanol dehydration, during which they were identified and picked clean of debris. The specimens were finally embedded in Epon 812 by placing each organism in a separate BEEM capsule. After sectioning with a diamond knife, stained sections were viewed in a Philips 200 electron microscope.

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