CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings

Methods ◽  
2015 ◽  
Vol 85 ◽  
pp. 3-11 ◽  
Author(s):  
Simon Blanchoud ◽  
Damien Nicolas ◽  
Benjamin Zoller ◽  
Onur Tidin ◽  
Félix Naef
Keyword(s):  
Single Cell ◽  
Time Lapse ◽  
Automated Segmentation ◽  
Segmentation And Tracking

Automated segmentation and tracking of mitochondria in live-cell time-lapse images

2021 ◽  
Vol 18 (9) ◽  
pp. 1091-1102 ◽  
Author(s):  
Austin E. Y. T. Lefebvre ◽  
Dennis Ma ◽  
Kai Kessenbrock ◽  
Devon A. Lawson ◽  
Michelle A. Digman
Keyword(s):  
Time Lapse ◽  
Live Cell ◽  
Automated Segmentation ◽  
Segmentation And Tracking

Automated segmentation and tracking of non-rigid objects in time-lapse microscopy videos of polymorphonuclear neutrophils

2015 ◽  
Vol 20 (1) ◽  
pp. 34-51 ◽  
Author(s):  
Susanne Brandes ◽  
Zeinab Mokhtari ◽  
Fabian Essig ◽  
Kerstin Hünniger ◽  
Oliver Kurzai ◽  
...  
Keyword(s):  
Time Lapse ◽  
Polymorphonuclear Neutrophils ◽  
Automated Segmentation ◽  
Time Lapse Microscopy ◽  
Rigid Objects ◽  
Segmentation And Tracking

scholarly journals Development of single-cell-level microfluidic technology for long-term growth visualization of living cultures of Mycobacterium smegmatis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Han Wang ◽  
Gloria M. Conover ◽  
Song-I Han ◽  
James C. Sacchettini ◽  
Arum Han
Keyword(s):  
Drug Treatment ◽  
Single Cell ◽  
Mycobacterium Smegmatis ◽  
Culture Media ◽  
Low Cost ◽  
Bacterial Pathogen ◽  
Growth Dynamics ◽  
Time Lapse ◽  
Cell Phenotype

AbstractAnalysis of growth and death kinetics at single-cell resolution is a key step in understanding the complexity of the nonreplicating growth phenotype of the bacterial pathogen Mycobacterium tuberculosis. Here, we developed a single-cell-resolution microfluidic mycobacterial culture device that allows time-lapse microscopy-based long-term phenotypic visualization of the live replication dynamics of mycobacteria. This technology was successfully applied to monitor the real-time growth dynamics of the fast-growing model strain Mycobacterium smegmatis (M. smegmatis) while subjected to drug treatment regimens during continuous culture for 48 h inside the microfluidic device. A clear morphological change leading to significant swelling at the poles of the bacterial membrane was observed during drug treatment. In addition, a small subpopulation of cells surviving treatment by frontline antibiotics was observed to recover and achieve robust replicative growth once regular culture media was provided, suggesting the possibility of identifying and isolating nonreplicative mycobacteria. This device is a simple, easy-to-use, and low-cost solution for studying the single-cell phenotype and growth dynamics of mycobacteria, especially during drug treatment.

scholarly journals Deciphering the Receptor Repertoire Encoding Specific Odorants by Time-Lapse Single-Cell Array Cytometry

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Masato Suzuki ◽  
Nobuo Yoshimoto ◽  
Ken Shimono ◽  
Shun’ichi Kuroda
Keyword(s):  
Single Cell ◽  
Time Lapse ◽  
Cell Array ◽  
Receptor Repertoire

scholarly journals Live-cell time-lapse imaging and single-cell tracking of in vitro cultured neural stem cells – Tools for analyzing dynamics of cell cycle, migration, and lineage selection

Methods ◽  
2018 ◽  
Vol 133 ◽  
pp. 81-90 ◽  
Author(s):  
Katja M. Piltti ◽  
Brian J. Cummings ◽  
Krystal Carta ◽  
Ayla Manughian-Peter ◽  
Colleen L. Worne ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Stem Cells ◽  
Neural Stem Cells ◽  
Single Cell ◽  
Cell Tracking ◽  
Time Lapse ◽  
Live Cell ◽  
Time Lapse Imaging

scholarly journals Cell-to-cell heterogeneity in Escherichia coli stress response originates from pulsatile expression and growth

2020 ◽  
Author(s):  
Nadia M. V. Sampaio ◽  
Caroline M. Blassick ◽  
Jean-Baptiste Lugagne ◽  
Mary J. Dunlop
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Stress Response ◽  
Single Cell ◽  
Phenotypic Variability ◽  
Growth Dynamics ◽  
Time Lapse ◽  
Cell Heterogeneity ◽  
Temporal Expression ◽  
Functional Consequences

AbstractCell-to-cell heterogeneity in gene expression and growth can have critical functional consequences, such as determining whether individual bacteria survive or die following stress. Although phenotypic variability is well documented, the dynamics that underlie it are often unknown. This information is critical because dramatically different outcomes can arise from gradual versus rapid changes in expression and growth. Using single-cell time-lapse microscopy, we measured the temporal expression of a suite of stress response reporters in Escherichia coli, while simultaneously monitoring growth rate. In conditions without stress, we found widespread examples of pulsatile expression. Single-cell growth rates were often anti-correlated with gene expression, with changes in growth preceding changes in expression. These pulsatile dynamics have functional consequences, which we demonstrate by measuring survival after challenging cells with the antibiotic ciprofloxacin. Our results suggest that pulsatile expression and growth dynamics are common in stress response networks and can have direct consequences for survival.

Toward Robust Fully 3D Filopodium Segmentation and Tracking in Time-Lapse Fluorescence Microscopy

2019 ◽  
Author(s):  
Martin Maska ◽  
Tereza Necasova ◽  
David Wiesner ◽  
Dmitry V. Sorokin ◽  
Igor Peterlik ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Time Lapse ◽  
Segmentation And Tracking
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