scholarly journals Detection of Mutations Affecting Heterogeneously Expressed Phenotypes by Colony Immunoblot and Dedicated Semi-Automated Image Analysis Pipeline

2017 ◽  
Vol 8 ◽  
Author(s):  
Erik Bakkeren ◽  
Tamas Dolowschiak ◽  
Médéric R. J. Diard
Keyword(s):  
Image Analysis ◽  
Automated Image Analysis ◽  
Analysis Pipeline ◽  
Detection Of Mutations

scholarly journals Machine learning-based classification of mitochondrial morphology in primary neurons and brain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Garrett M. Fogo ◽  
Anthony R. Anzell ◽  
Kathleen J. Maheras ◽  
Sarita Raghunayakula ◽  
Joseph M. Wider ◽  
...  
Keyword(s):  
Image Analysis ◽  
Cortical Neurons ◽  
Mitochondrial Dynamics ◽  
Automated Image Analysis ◽  
Mitochondrial Morphology ◽  
Analysis Pipeline ◽  
Genetic Ablation ◽  
Block Face

AbstractThe mitochondrial network continually undergoes events of fission and fusion. Under physiologic conditions, the network is in equilibrium and is characterized by the presence of both elongated and punctate mitochondria. However, this balanced, homeostatic mitochondrial profile can change morphologic distribution in response to various stressors. Therefore, it is imperative to develop a method that robustly measures mitochondrial morphology with high accuracy. Here, we developed a semi-automated image analysis pipeline for the quantitation of mitochondrial morphology for both in vitro and in vivo applications. The image analysis pipeline was generated and validated utilizing images of primary cortical neurons from transgenic mice, allowing genetic ablation of key components of mitochondrial dynamics. This analysis pipeline was further extended to evaluate mitochondrial morphology in vivo through immunolabeling of brain sections as well as serial block-face scanning electron microscopy. These data demonstrate a highly specific and sensitive method that accurately classifies distinct physiological and pathological mitochondrial morphologies. Furthermore, this workflow employs the use of readily available, free open-source software designed for high throughput image processing, segmentation, and analysis that is customizable to various biological models.

scholarly journals A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
M. Elena Garcia-Pardo ◽  
Jeremy C. Simpson ◽  
Niamh C. O’Sullivan
Keyword(s):  
Endoplasmic Reticulum ◽  
Image Analysis ◽  
Mammalian Cells ◽  
Large Scale ◽  
Morphological Changes ◽  
Methodological Approach ◽  
Automated Image Analysis ◽  
Adherent Cell ◽  
Analysis Pipeline ◽  
Cultured Human Cells

Abstract Background In mammalian cells the endoplasmic reticulum (ER) comprises a highly complex reticular morphology that is spread throughout the cytoplasm. This organelle is of particular interest to biologists, as its dysfunction is associated with numerous diseases, which often manifest themselves as changes to the structure and organisation of the reticular network. Due to its complex morphology, image analysis methods to quantitatively describe this organelle, and importantly any changes to it, are lacking. Results In this work we detail a methodological approach that utilises automated high-content screening microscopy to capture images of cells fluorescently-labelled for various ER markers, followed by their quantitative analysis. We propose that two key metrics, namely the area of dense ER and the area of polygonal regions in between the reticular elements, together provide a basis for measuring the quantities of rough and smooth ER, respectively. We demonstrate that a number of different pharmacological perturbations to the ER can be quantitatively measured and compared in our automated image analysis pipeline. Furthermore, we show that this method can be implemented in both commercial and open-access image analysis software with comparable results. Conclusions We propose that this method has the potential to be applied in the context of large-scale genetic and chemical perturbations to assess the organisation of the ER in adherent cell cultures.

scholarly journals 3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets

2020 ◽  
Author(s):  
E. C. Kugler ◽  
J. Frost ◽  
V. Silva ◽  
K. Plant ◽  
K. Chhabria ◽  
...  
Keyword(s):  
Image Analysis ◽  
Fluorescence Microscopy ◽  
Light Sheet ◽  
Relevant Information ◽  
Automated Image Analysis ◽  
Analysis Pipeline ◽  
Biologically Relevant ◽  
Branching Points ◽  
Light Sheet Fluorescence Microscopy

AbstractZebrafish transgenic lines and light sheet fluorescence microscopy allow in-depth insights into vascular development in vivo and 3D. However, robust quantification of the zebrafish cerebral vasculature in 3D remains a challenge, and would be essential to describe the vascular architecture. Here, we report an image analysis pipeline that allows 3D quantification of the total or regional zebrafish brain vasculature. This is achieved by landmark- or object-based inter-sample registration and extraction of quantitative parameters including vascular volume, surface area, density, branching points, length, radius, and complexity. Application of our analysis pipeline to a range of sixteen genetic or pharmacological manipulations shows that our quantification approach is robust, allows extraction of biologically relevant information, and provides novel insights into vascular biology. To allow dissemination, the code for quantification, a graphical user interface, and workflow documentation are provided. Together, we present the first 3D quantification approach to assess the whole 3D cerebrovascular architecture in zebrafish.

scholarly journals An Automated Image Analysis Pipeline Enables Genetic Studies of Shoot and Root Morphology in Carrot (Daucus carota L.)

2018 ◽  
Vol 9 ◽  
Author(s):  
Sarah D. Turner ◽  
Shelby L. Ellison ◽  
Douglas A. Senalik ◽  
Philipp W. Simon ◽  
Edgar P. Spalding ◽  
...  
Keyword(s):  
Image Analysis ◽  
Daucus Carota ◽  
Root Morphology ◽  
Automated Image Analysis ◽  
Analysis Pipeline ◽  
Genetic Studies ◽  
Daucus Carota L

Automated Image Analysis Of Nuclear And Cytoplasmic Changes In Exfoliated Cells From Tracheas Treated With Carcinogen

1977 ◽  
Vol 35 ◽  
pp. 220-221
Author(s):  
S.F. Stinson ◽  
J.C. Lilga ◽  
M.B. Sporn
Keyword(s):  
Image Analysis ◽  
Pattern Analysis ◽  
Relative Proportion ◽  
Automated Image Analysis ◽  
Image Analyzer ◽  
Cross Sectional ◽  
Exfoliated Cells ◽  
Neoplastic Lesions ◽  
Analysis System ◽  
Morphologic Criterion

Increased nuclear size, resulting in an increase in the relative proportion of nuclear to cytoplasmic sizes, is an important morphologic criterion for the evaluation of neoplastic and pre-neoplastic cells. This paper describes investigations into the suitability of automated image analysis for quantitating changes in nuclear and cytoplasmic cross-sectional areas in exfoliated cells from tracheas treated with carcinogen.Neoplastic and pre-neoplastic lesions were induced in the tracheas of Syrian hamsters with the carcinogen N-methyl-N-nitrosourea. Cytology samples were collected intra-tracheally with a specially designed catheter (1) and stained by a modified Papanicolaou technique. Three cytology specimens were selected from animals with normal tracheas, 3 from animals with dysplastic changes, and 3 from animals with epidermoid carcinoma. One hundred randomly selected cells on each slide were analyzed with a Bausch and Lomb Pattern Analysis System automated image analyzer.

Progress In The Practical Application Of Automated Image Analysis To Tem Negatives

1977 ◽  
Vol 35 ◽  
pp. 214-217
Author(s):  
F. A. Heckman ◽  
E. Redman ◽  
J.E. Connolly
Keyword(s):  
Image Analysis ◽  
Image Quality ◽  
Exposure Time ◽  
Image Contrast ◽  
Automated Image Analysis ◽  
Practical Application ◽  
Factors Affecting ◽  
High Image Quality ◽  
Qualitative Evidence ◽  
Comprehensive Study

In our initial publication on this subject1) we reported results demonstrating that contrast is the most important factor in producing the high image quality required for reliable image analysis. We also listed the factors which enhance contrast in order of the experimentally determined magnitude of their effect. The two most powerful factors affecting image contrast attainable with sheet film are beam intensity and KV. At that time we had only qualitative evidence for the ranking of enhancing factors. Later we carried out the densitometric measurements which led to the results outlined below.Meaningful evaluations of the cause-effect relationships among the considerable number of variables in preparing EM negatives depend on doing things in a systematic way, varying only one parameter at a time. Unless otherwise noted, we adhered to the following procedure evolved during our comprehensive study:Philips EM-300; 30μ objective aperature; magnification 7000- 12000X, exposure time 1 second, anti-contamination device operating.

Interfacing of a TEM/STEM System to a Computer

1981 ◽  
Vol 39 ◽  
pp. 250-251
Author(s):  
P. Hagemann
Keyword(s):  
Image Analysis ◽  
Transmission Rate ◽  
Analytical Electron Microscopy ◽  
Signal Beam ◽  
Automated Image Analysis ◽  
Beam Deflection ◽  
External Control ◽  
Computer Input ◽  
Instrument Control ◽  
Data Acquisition And Processing

The use of computers in the analytical electron microscopy today shows three different trends (1) automated image analysis with dedicated computer systems, (2) instrument control by microprocessors and (3) data acquisition and processing e.g. X-ray or EEL Spectroscopy.While image analysis in the T.E.M. usually needs a television chain to get a sequential transmission suitable as computer input, the STEM system already has this necessary facility. For the EM400T-STEM system therefore an interface was developed, that allows external control of the beam deflection in TEM as well as the control of the STEM probe and video signal/beam brightness on the STEM screen.The interface sends and receives analogue signals so that the transmission rate is determined by the convertors in the actual computer periphery.

scholarly journals Author Correction: Efficient microbial colony growth dynamics quantification with ColTapp, an automated image analysis application

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Julian Bär ◽  
Mathilde Boumasmoud ◽  
Roger D. Kouyos ◽  
Annelies S. Zinkernagel ◽  
Clément Vulin
Keyword(s):  
Image Analysis ◽  
Growth Dynamics ◽  
Colony Growth ◽  
Automated Image Analysis ◽  
Analysis Application

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Scoring of radiation-induced microuclei in cytokinesis-blocked human lymphocytes by automated image analysis

Cytometry ◽  
1994 ◽  
Vol 17 (2) ◽  
pp. 119-127 ◽  
Author(s):  
F. Verhaegen ◽  
A. Vral ◽  
J. Seuntjens ◽  
N. W. Schipper ◽  
L. de Ridder ◽  
...  
Keyword(s):  
Image Analysis ◽  
Human Lymphocytes ◽  
Automated Image Analysis ◽  
Radiation Induced
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