Image quantification v1

protocols.io ◽  
2021 ◽  
Author(s):  
Chunmei not provided Chang
Keyword(s):  
2010 ◽  
Vol 99 (5) ◽  
pp. 688-701 ◽  
Author(s):  
J. M. Pereira ◽  
M. G. Stabin ◽  
F. R. A. Lima ◽  
M. I. C. C. Guimarães ◽  
J. W. Forrester

2012 ◽  
Vol 57 (SI-1 Track-B) ◽  
Author(s):  
A. Gryanik ◽  
T. Wittenberg ◽  
H. Walles ◽  
D. Steckhan ◽  
S. Thude ◽  
...  

2019 ◽  
Vol 26 (3) ◽  
pp. 412-423 ◽  
Author(s):  
Nicholas J. Tustison ◽  
Brian B. Avants ◽  
Zixuan Lin ◽  
Xue Feng ◽  
Nicholas Cullen ◽  
...  

2020 ◽  
Vol 21 (2) ◽  
pp. 435 ◽  
Author(s):  
Xiaoli Zhang ◽  
Luis R. Flores ◽  
Michael C. Keeling ◽  
Kristina Sliogeryte ◽  
Núria Gavara

Ezrin, a member of the ERM (ezrin/radixin/moesin) family of proteins, serves as a crosslinker between the plasma membrane and the actin cytoskeleton. By doing so, it provides structural links to strengthen the connection between the cell cortex and the plasma membrane, acting also as a signal transducer in multiple pathways during migration, proliferation, and endocytosis. In this study, we investigated the role of ezrin phosphorylation and its intracellular localization on cell motility, cytoskeleton organization, and cell stiffness, using fluorescence live-cell imaging, image quantification, and atomic force microscopy (AFM). Our results show that cells expressing constitutively active ezrin T567D (phosphomimetic) migrate faster and in a more directional manner, especially when ezrin accumulates at the cell rear. Similarly, image quantification results reveal that transfection with ezrin T567D alters the cell’s gross morphology and decreases cortical stiffness. In contrast, constitutively inactive ezrin T567A accumulates around the nucleus, and although it does not impair cell migration, it leads to a significant buildup of actin fibers, a decrease in nuclear volume, and an increase in cytoskeletal stiffness. Finally, cell transfection with the dominant negative ezrin FERM domain induces significant morphological and nuclear changes and affects actin, microtubules, and the intermediate filament vimentin, resulting in cytoskeletal fibers that are longer, thicker, and more aligned. Collectively, our results suggest that ezrin’s phosphorylation state and its intracellular localization plays a pivotal role in cell migration, modulating also biophysical properties, such as membrane–cortex linkage, cytoskeletal and nuclear organization, and the mechanical properties of cells.


2012 ◽  
Vol 18 (7) ◽  
pp. 507-516 ◽  
Author(s):  
Julie A. Rytlewski ◽  
Laura R. Geuss ◽  
Chinedu I. Anyaeji ◽  
Evan W. Lewis ◽  
Laura J. Suggs

Author(s):  
Marne C Hagemeijer ◽  
Annelotte M Vonk ◽  
Nikhil T Awatade ◽  
Iris A L Silva ◽  
Christian Tischer ◽  
...  

Abstract Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary information and a stepwise guide for software installation and data analysis for training purposes are available at Bioinformatics online.


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