scholarly journals TraCurate: efficiently curating cell tracks

2020 ◽  
Author(s):  
S. Wagner ◽  
K. Thierbach ◽  
T. Zerjatke ◽  
I. Glauche ◽  
I. Roeder ◽  
...  
Keyword(s):  
Open Source Software ◽  
Cell Tracking ◽  
User Interaction ◽  
Software Tool ◽  
Time Lapse ◽  
Tracking Data ◽  
Cellular Behavior ◽  
Data Source ◽  
Complete Cell

AbstractTraCurate is an open-source software tool to curate and manually annotate cell tracking data from time-lapse microscopy. Although many studies of cellular behavior require high-quality, long-term observations across generations of cells, automated cell tracking is often imperfect and typically yields fragmented results that still contain many errors. TraCurate provides the functionality for the curation and correction of cell tracking data with minimal user interaction and expenditure of time and supports the extraction of complete cell tracks and cellular genealogies from experimental data. Source code and binary packages for Linux, macOS and Windows are available at https://tracurate.gitlab.io/, as well as all other complementary tools described herein.

CellTracker (not only) for dummies

2015 ◽  
Vol 32 (6) ◽  
pp. 955-957 ◽  
Author(s):  
Filippo Piccinini ◽  
Alexa Kiss ◽  
Peter Horvath
Keyword(s):  
Graphical User Interface ◽  
Open Source Software ◽  
Phase Contrast ◽  
Cell Tracking ◽  
Source Code ◽  
Software Tool ◽  
Time Lapse ◽  
Supplementary Information ◽  
Differential Interference Contrast ◽  
User Friendly

Abstract Motivation: Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Availability and implementation: CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

scholarly journals Automated tracking of gene expression in individual cells and cell compartments

2006 ◽  
Vol 3 (11) ◽  
pp. 787-794 ◽  
Author(s):  
Hailin Shen ◽  
Glyn Nelson ◽  
David E Nelson ◽  
Stephnie Kennedy ◽  
David G Spiller ◽  
...  
Keyword(s):  
Cell Biology ◽  
Cell Tracking ◽  
Software Tool ◽  
Time Lapse ◽  
Automated Tracking ◽  
Nuclear Transcription Factor ◽  
Cell Compartments ◽  
Protein Molecules ◽  
Human Fatigue ◽  
Intracellular Signal

Many intracellular signal transduction processes involve the reversible translocation from the cytoplasm to the nucleus of transcription factors. The advent of fluorescently tagged protein derivatives has revolutionized cell biology, such that it is now possible to follow the location of such protein molecules in individual cells in real time. However, the quantitative analysis of the location of such proteins in microscopic images is very time consuming. We describe CellTracker, a software tool designed for the automated measurement of the cellular location and intensity of fluorescently tagged proteins. CellTracker runs in the MS Windows environment, is freely available (at http://www.dbkgroup.org/celltracker/ ), and combines automated cell tracking methods with powerful image-processing algorithms that are optimized for these applications. When tested in an application involving the nuclear transcription factor NF-κB, CellTracker is competitive in accuracy with the manual human analysis of such images but is more than 20 times faster, even on a small task where human fatigue is not an issue. This will lead to substantial benefits for time-lapse-based high-content screening.

scholarly journals Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX

2018 ◽  
Author(s):  
Ting Xu ◽  
Christos Langouras ◽  
Maral Adeli Koudehi ◽  
Bart E. Vos ◽  
Ning Wang ◽  
...  
Keyword(s):  
Open Source Software ◽  
Active Contours ◽  
Software Tool ◽  
Time Lapse ◽  
Live Cells ◽  
Loop Formation ◽  
Automated Tracking ◽  
Quantitative Studies ◽  
Global And Local ◽  
2D And 3D

AbstractStudies of how individual semi-flexible biopolymers and their network assemblies change over time reveal dynamical and mechanical properties important to the understanding of their function in tissues and living cells. Automatic tracking of biopolymer networks from fluorescence microscopy time-lapse sequences facilitates such quantitative studies. We present an open source software tool that combines a global and local correspondence algorithm to track biopolymer networks in 2D and 3D, using stretching open active contours. We demonstrate its application in fully automated tracking of elongating and intersecting actin filaments, detection of loop formation and constriction of tilted contractile rings in live cells, and tracking of network deformation under shear deformation.

scholarly journals Fertility and Pregnancy in End Stage Kidney Failure Patients and after Renal Transplantation: An Update

2021 ◽  
Vol 2 (2) ◽  
pp. 92-108
Author(s):  
Maurizio Salvadori ◽  
Aris Tsalouchos
Keyword(s):  
Renal Transplantation ◽  
Time Lapse ◽  
Sexual Life ◽  
End Stage Kidney Disease ◽  
Correct Evaluation ◽  
Functional Aspects ◽  
Long Term Follow Up ◽  
End Stage

Sexual life and fertility are compromised in end stage kidney disease both in men and in women. Successful renal transplantation may rapidly recover fertility in the vast majority of patients. Pregnancy modifies anatomical and functional aspects in the kidney and represents a risk of sensitization that may cause acute rejection. Independently from the risks for the graft, pregnancy in kidney transplant may cause preeclampsia, gestational diabetes, preterm delivery, and low birth weight. The nephrologist has a fundamental role in correct counseling, in a correct evaluation of the mother conditions, and in establishing a correct time lapse between transplantation and conception. Additionally, careful attention must be given to the antirejection therapy, avoiding drugs that could be dangerous to the newborn. Due to the possibility of medical complications during pregnancy, a correct follow-up should be exerted. Even if pregnancy in transplant is considered a high risk one, several data and studies document that in the majority of patients, the long-term follow-up and outcomes for the graft may be similar to that of non-pregnant women.

scholarly journals Heatwaves in Kenya 1987–2016: Facts from CHIRTS High Resolution Satellite Remotely Sensed and Station Blended Temperature Dataset

Atmosphere ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 37
Author(s):  
Martial Amou ◽  
Amatus Gyilbag ◽  
Tsedale Demelash ◽  
Yinlong Xu
Keyword(s):  
High Resolution ◽  
Adaptation Strategies ◽  
Reference Period ◽  
The West ◽  
Tana River ◽  
Short Period ◽  
The World ◽  
Northern Side ◽  
Data Source

As global temperatures continue to rise unabated, episodes of heat-related catastrophes across the world have intensified. In Kenya, heatwave phenomena and their associated impacts are ignored and neglected due to several reasons, including unreliable and inconsistent weather datasets and heatwave detection metrics. Based on CHIRTS satellite infrared estimates and station blended temperature, this study investigated the spatiotemporal distribution of the heatwave events over Kenya during 1987–2016 using the Heatwave Magnitude Index daily (HWMId). The results showed that contrary to the absence of heatwave records in official national and international disaster database about Kenya, the country experienced heatwaves ranging from less severe (normal) to deadly (super-extreme) between 1987 and 2016. The most affected areas were located in the eastern parts of the country, especially in Garissa and Tana River, and in the west-northern side around the upper side of Turkana county. It was also found that the recent years’ heatwaves were more severe in magnitude, duration, and spatial extent. The highest magnitude of the heatwaves was recorded in 2015 (HWMId = 22.64) while the average over the reference period is around 6. CHIRTS and HWMId were able to reveal and capture most critical heatwave events over the study period. Therefore, they could be used respectively as data source and detection metrics, for heatwaves disaster emergency warning over short period as well as for long-term projection to provide insight for adaptation strategies.

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 Cell cycle inertia underlies a bifurcation in cell fates after DNA damage

2021 ◽  
Vol 7 (3) ◽  
pp. eabe3882
Author(s):  
Jenny F. Nathans ◽  
James A. Cornwell ◽  
Marwa M. Afifi ◽  
Debasish Paul ◽  
Steven D. Cappell
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Cell Tracking ◽  
Time Lapse ◽  
S Phase ◽  
Cdk Inhibitor ◽  
Cyclin Dependent Kinase ◽  
Cell Fates ◽  
Damage Response ◽  
Time Lapse Imaging

The G1-S checkpoint is thought to prevent cells with damaged DNA from entering S phase and replicating their DNA and efficiently arrests cells at the G1-S transition. Here, using time-lapse imaging and single-cell tracking, we instead find that DNA damage leads to highly variable and divergent fate outcomes. Contrary to the textbook model that cells arrest at the G1-S transition, cells triggering the DNA damage checkpoint in G1 phase route back to quiescence, and this cellular rerouting can be initiated at any point in G1 phase. Furthermore, we find that most of the cells receiving damage in G1 phase actually fail to arrest and proceed through the G1-S transition due to persistent cyclin-dependent kinase (CDK) activity in the interval between DNA damage and induction of the CDK inhibitor p21. These observations necessitate a revised model of DNA damage response in G1 phase and indicate that cells have a G1 checkpoint.

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