scholarly journals How good are my data? Reference standards in superresolution microscopy

2020 ◽  
Vol 31 (19) ◽  
pp. 2093-2096
Author(s):  
Markus Mund ◽  
Jonas Ries
Keyword(s):  
Imaging Technique ◽  
Reference Standards ◽  
Reference Standard ◽  
Yield Data ◽  
Superresolution Microscopy ◽  
Experimental Parameters ◽  
Biological Discovery ◽  
Microscopy Data ◽  
Suitable Reference ◽  
Over Time

Superresolution microscopy is becoming increasingly widespread in biological labs. While it holds enormous potential for biological discovery, it is a complex imaging technique that requires thorough optimization of various experimental parameters to yield data of the highest quality. Unfortunately, it remains challenging even for seasoned users to judge from the acquired images alone whether their superresolution microscopy pipeline is performing at its optimum, or if the image quality could be improved. Here, we describe how superresolution microscopists can objectively characterize their imaging pipeline using suitable reference standards, which are stereotypic so that the same structure can be imaged everywhere, every time, on every microscope. Quantitative analysis of reference standard images helps characterizing the performance of one’s own microscopes over time, allows objective benchmarking of newly developed microscopy and labeling techniques, and finally increases comparability of superresolution microscopy data between labs.

scholarly journals ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic

2021 ◽  
Author(s):  
Nelson BC Serre ◽  
Matyas Fendrych
Keyword(s):  
Plant Root ◽  
Automated Image Analysis ◽  
Root Tip ◽  
Spatiotemporal Resolution ◽  
Bending Angle ◽  
Root Angle ◽  
Root Gravitropism ◽  
Microscopy Data ◽  
Automated Software ◽  
Over Time

Plants respond to the surrounding environment in countless ways. One of these responses is their ability to sense and orient their root growth toward the gravity vector. Root gravitropism is studied in many laboratories as a hallmark of auxin-related phenotypes. However, manual analysis of images and microscopy data is known to be subjected to human bias. This is particularly the case for manual measurements of root bending as the selection lines to calculate the angle are set subjectively. Therefore, it is essential to develop and use automated or semi-automated image analysis to produce reproducible and unbiased data. Moreover, the increasing usage of vertical-stage microscopy in plant root biology yields gravitropic experiments with an unprecedented spatiotemporal resolution. To this day, there is no available solution to measure root bending angle over time for vertical-stage microscopy. To address these problems, we developed ACORBA (Automatic Calculation Of Root Bending Angles), a fully automated software to measure root bending angle over time from vertical-stage microscope and flatbed scanner images. Moreover, the software can be used semi-automated for camera, mobile phone or stereomicroscope images. ACORBA represents a flexible approach based on both traditional image processing and deep machine learning segmentation to measure root angle progression over time. By its automated nature, the workflow is limiting human interactions and has high reproducibility. ACORBA will support the plant biologist community by reducing time and labor and by producing quality results from various kinds of inputs.

scholarly journals Automated tracking of S. pombe spindle elongation dynamics

2020 ◽  
Author(s):  
Ana Sofía M. Uzsoy ◽  
Parsa Zareiesfandabadi ◽  
Jamie Jennings ◽  
Alexander F. Kemper ◽  
Mary Williard Elting
Keyword(s):  
Principal Axis ◽  
Model Organism ◽  
Data Sets ◽  
Mitotic Progression ◽  
Automated Tracking ◽  
Spindle Elongation ◽  
Microscopy Data ◽  
Spindle Structure ◽  
Over Time ◽  
Imagej Plugin

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.

scholarly journals Nuclear pores as versatile reference standards for quantitative superresolution microscopy

2019 ◽  
Author(s):  
Jervis Vermal Thevathasan ◽  
Maurice Kahnwald ◽  
Konstanty Cieśliński ◽  
Philipp Hoess ◽  
Sudheer Kumar Peneti ◽  
...  
Keyword(s):  
Cell Lines ◽  
Fluorescent Protein ◽  
Reference Standards ◽  
Nuclear Pore ◽  
Biologically Relevant ◽  
Superresolution Microscopy ◽  
Absolute Measurements ◽  
Quantitative Fluorescence

AbstractQuantitative fluorescence and superresolution microscopy are often limited by insufficient data quality or artifacts. In this context, it is essential to have biologically relevant control samples to benchmark and optimize the quality of microscopes, labels and imaging conditions.Here we exploit the stereotypic arrangement of proteins in the nuclear pore complex as in situ reference structures to characterize the performance of a variety of microscopy modalities. We created four genome edited cell lines in which we endogenously labeled the nucleoporin Nup96 with mEGFP, SNAP-tag or HaloTag or the photoconvertible fluorescent protein mMaple. We demonstrate their use a) as 3D resolution standards for calibration and quality control, b) to quantify absolute labeling efficiencies and c) as precise reference standards for molecular counting.These cell lines will enable the broad community to assess the quality of their microscopes and labels, and to perform quantitative, absolute measurements.

scholarly journals Nuclear pores as versatile reference standards for quantitative superresolution microscopy

2019 ◽  
Vol 16 (10) ◽  
pp. 1045-1053 ◽  
Author(s):  
Jervis Vermal Thevathasan ◽  
Maurice Kahnwald ◽  
Konstanty Cieśliński ◽  
Philipp Hoess ◽  
Sudheer Kumar Peneti ◽  
...  
Keyword(s):  
Reference Standards ◽  
Nuclear Pores ◽  
Superresolution Microscopy

Generating the best superresolution microscopy data: Finding the right tool for the right job

Science ◽  
2015 ◽  
Vol 349 (6246) ◽  
pp. 441-441
Author(s):  
E. Betzig ◽  
R. Das ◽  
J. Taraska
Keyword(s):  
Superresolution Microscopy ◽  
Microscopy Data ◽  
The Right

Assessment of Protein Quality Methodology for Infant Formulas

1985 ◽  
Vol 68 (4) ◽  
pp. 680-683
Author(s):  
Geraldine Vaughan Mitchell ◽  
Mamie Young Jenkins
Keyword(s):  
Quality Evaluation ◽  
Protein Quality ◽  
Reference Standards ◽  
Infant Formulas ◽  
Casein Diet ◽  
Reference Standard ◽  
Powdered Milk ◽  
The Third ◽  
Net Protein

Abstract Rat bioassay was used to assess the protein quality of powdered infant formulas and to evaluate the feasibility of using modified casein diets (containing the same source and level of fat and carbohydrate contributed by the infant formulas) as reference standards. Modification of the casein diet to match the milk-based formulas caused a significant reduction in weekly protein efficiency ratios (PER) and net protein ratios (NPR) at the third and fourth weeks. Modification of the casein diet to simulate the soy-based formulas had no significant effect on NPR values; PER values were more varied. When PER and NPR values of the powdered milk-based formulas were expressed relative to the unmodified reference standard, the relative values were lower than when each matched reference was used. With few exceptions, the relative weekly PER values of the soy-based formulas were similar regardless of the standard used. The relative NPR values of the formulas had a pattern similar to the relative PER values. The data indicate that protein quality evaluation of infant formulas using rat bioassay warrants the use of matched casein reference diets for each type of formula.

scholarly journals Nuclear Pores as Versatile Reference Standards for Quantitative Superresolution Microscopy

2020 ◽  
Vol 118 (3) ◽  
pp. 150a
Author(s):  
Jervis V. Thevathasan ◽  
Maurice Kahnwald ◽  
Robin Diekmann ◽  
Jan Ellenberg ◽  
Jonas Ries
Keyword(s):  
Reference Standards ◽  
Nuclear Pores ◽  
Superresolution Microscopy

scholarly journals Chinese Preschool Children Growth Reference Standard and Related Curve: Based on GAMLSS Approach

2021 ◽  
Author(s):  
Sanhua Zhang ◽  
Chongmin Jiang ◽  
Chunjing Tu
Keyword(s):  
Preschool Children ◽  
Growth And Development ◽  
Reference Standards ◽  
Chest Circumference ◽  
Reference Standard ◽  
Sitting Height ◽  
Growth Reference ◽  
Percentile Curve ◽  
And Control ◽  
Height For Age

Background: The current national growth and development standard of preschool children in China was formulated in 2003, which has many deficiencies. It is necessary to construct more scientific percentile curve and growth reference standards in order to evaluate more effectively the growth, development and health status of Chinese children. Methods: Based on the physical and health data of 31 provinces in China measured in 2010 and 2014, the GAMLSS model was used to construct the growth reference standard and correlation curve. Results: We obtained growth reference standards for percentile curve and Z-score curve of height-for-age, sitting height-for-age, Weight-for-age, Chest circumference-for-age of Chinese preschool children. The C50 percentile of all indicators showed an obvious increasing trend with aged 3.0 to 6.5. Such as, the height of boys and girls increased by 21.1cm and 20.3cm respectively, the sitting height boys and girls increased by 10.3cm and 10.1cm respectively, the weight of boys and girls increased by 7.1 kg and 6.3 kg respectively, the Chest circumference of boys and girls increased by 6cm and 5.2 cm respectively. Conclusion: The children's growth and development charts provided in this study provide effective monitoring and personalized evaluation tools for the growth and development assessment of preschool children, as well as for the reduction of malnutrition, prevention and control of childhood obesity. It is recommended to be used in some areas such as child health, medical treatment and public health.

scholarly journals Publisher Correction: Nuclear pores as versatile reference standards for quantitative superresolution microscopy

2019 ◽  
Vol 16 (12) ◽  
pp. 1332-1332
Author(s):  
Jervis Vermal Thevathasan ◽  
Maurice Kahnwald ◽  
Konstanty Cieśliński ◽  
Philipp Hoess ◽  
Sudheer Kumar Peneti ◽  
...  
Keyword(s):  
Reference Standards ◽  
Nuclear Pores ◽  
Superresolution Microscopy

Revealing the Origin and Nature of Drug Resistance of Dynamic Tumour Systems

2010 ◽  
Vol 1 (4) ◽  
pp. 26-53 ◽  
Author(s):  
Ricardo Santiago-Mozos ◽  
Imtiaz A. Khan ◽  
Michael G. Madden
Keyword(s):  
Cytotoxic Effect ◽  
Statistical Significance ◽  
Cell Lineage ◽  
Clonal Expansion ◽  
Short Term ◽  
Interpretable Models ◽  
Microscopy Data ◽  
Mining Tools ◽  
Over Time

In this paper, the authors identify the strategies that resistant subpopulations of cancer cells undertake to overcome the effect of the anticancer drug Topotecan. For the analyses of cell lineage data encoded from timelapse microscopy, data mining tools are chosen that generate interpretable models of the data, addressing their statistical significance. By interpreting the short-term and long-term cytotoxic effect of Topotecan through these data models, the authors reveal the strategies that resistant subpopulations of cells undertake to maximize their clonal expansion potential. In this context, this paper identifies a pattern of cell death independent of cytotoxic effect. Finally, it is observed that cells exposed to Topotecan have higher movement over time, indicating a putative relationship between cytotoxic effect and cell motility.

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