scholarly journals Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane

2020 ◽  
Vol 133 (24) ◽  
pp. jcs252254
Author(s):  
Domingos Castro ◽  
Vanessa Nunes ◽  
Joana T. Lima ◽  
Jorge G. Ferreira ◽  
Paulo Aguiar
Keyword(s):  
Nuclear Envelope ◽  
Cellular Membrane ◽  
Spatiotemporal Dynamics ◽  
Easy Access ◽  
Source Image ◽  
Imaging Data ◽  
Analysis Software ◽  
Model Free ◽  
Centrosome Separation ◽  
Oscillation Modes

ABSTRACTDuring the initial stages of mitosis, multiple mechanisms drive centrosome separation and positioning. How they are coordinated to promote centrosome migration to opposite sides of the nucleus remains unclear. Here, we present Trackosome, an open-source image analysis software for tracking centrosomes and reconstructing nuclear and cellular membranes, based on volumetric live-imaging data. The toolbox runs in MATLAB and provides a graphical user interface for easy access to the tracking and analysis algorithms. It provides detailed quantification of the spatiotemporal relationships between centrosomes, nuclear envelope and cellular membrane, and can also be used to measure the dynamic fluctuations of the nuclear envelope. These fluctuations are important because they are related to the mechanical forces exerted on the nucleus by its adjacent cytoskeletal structures. Unlike previous algorithms based on circular or elliptical approximations, Trackosome measures membrane movement in a model-free condition, making it viable for irregularly shaped nuclei. Using Trackosome, we demonstrate significant correlations between the movements of the centrosomes, and identify specific oscillation modes of the nuclear envelope. Overall, Trackosome is a powerful tool that can be used to help unravel new elements in the spatiotemporal dynamics of subcellular structures.

scholarly journals Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane

2020 ◽  
Author(s):  
Domingos Castro ◽  
Vanessa Nunes ◽  
Joana T. Lima ◽  
Jorge G. Ferreira ◽  
Paulo Aguiar
Keyword(s):  
Nuclear Envelope ◽  
Cellular Membrane ◽  
Spatiotemporal Dynamics ◽  
Imaging Analysis ◽  
Imaging Data ◽  
Analysis Software ◽  
Model Free ◽  
Centrosome Separation ◽  
Efficient Access ◽  
Spatiotemporal Relations

AbstractDuring the initial stages of mitosis, multiple mechanisms drive centrosome separation and positioning. How they are functionally coordinated to promote centrosome migration to opposite sides of the nucleus remains unclear. Imaging analysis software has been used to quantitatively study centrosome dynamics at this stage. However, available tracking tools are generic and not fine-tuned for the constrains and motion dynamics of centrosome pairs. Such generality limits the tracking performance and may require exhaustive optimization of parameters. Here, we present Trackosome, a freely available open-source computational tool to track the centrosomes and reconstruct the nuclear and cellular membranes, based on volumetric live-imaging data. The toolbox runs in MATLAB and provides a graphical user interface for easy and efficient access to the tracking and analysis algorithms. It outputs key metrics describing the spatiotemporal relations between centrosomes, nucleus and cellular membrane. Trackosome can also be used to measure the dynamic fluctuations of the nuclear envelope. A fine description of these fluctuations is important because they are correlated with the mechanical forces exerted on the nucleus by its adjacent cytoskeletal structures. Unlike previous algorithms based on circular/elliptical approximations of the nucleus, Trackosome measures membrane movement in a model-free condition, making it viable for irregularly shaped nuclei. Using Trackosome, we demonstrate significant correlations between the movements of the two centrosomes, and identify specific modes of oscillation of the nuclear envelope. Overall, Trackosome is a powerful tool to help unravel new elements in the spatiotemporal dynamics of subcellular structures.

scholarly journals Ultra-fast accurate reconstruction of spiking activity from calcium imaging data

2018 ◽  
Vol 119 (5) ◽  
pp. 1863-1878 ◽  
Author(s):  
Vahid Rahmati ◽  
Knut Kirmse ◽  
Knut Holthoff ◽  
Stefan J. Kiebel
Keyword(s):  
Calcium Imaging ◽  
Reconstruction Method ◽  
Imaging Data ◽  
Decay Kinetics ◽  
Experimental Conditions ◽  
Model Free ◽  
Reconstruction Methods ◽  
Wide Range ◽  
Fast Processing ◽  
Spiking Activity

Calcium imaging provides an indirect observation of the underlying neural dynamics and enables the functional analysis of neuronal populations. However, the recorded fluorescence traces are temporally smeared, thus making the reconstruction of exact spiking activity challenging. Most of the established methods to tackle this issue are limited in dealing with issues such as the variability in the kinetics of fluorescence transients, fast processing of long-term data, high firing rates, and measurement noise. We propose a novel, heuristic reconstruction method to overcome these limitations. By using both synthetic and experimental data, we demonstrate the four main features of this method: 1) it accurately reconstructs both isolated spikes and within-burst spikes, and the spike count per fluorescence transient, from a given noisy fluorescence trace; 2) it performs the reconstruction of a trace extracted from 1,000,000 frames in less than 2 s; 3) it adapts to transients with different rise and decay kinetics or amplitudes, both within and across single neurons; and 4) it has only one key parameter, which we will show can be set in a nearly automatic way to an approximately optimal value. Furthermore, we demonstrate the ability of the method to effectively correct for fast and rather complex, slowly varying drifts as frequently observed in in vivo data. NEW & NOTEWORTHY Reconstruction of spiking activities from calcium imaging data remains challenging. Most of the established reconstruction methods not only have limitations in adapting to systematic variations in the data and fast processing of large amounts of data, but their results also depend on the user’s experience. To overcome these limitations, we present a novel, heuristic model-free-type method that enables an ultra-fast, accurate, near-automatic reconstruction from data recorded under a wide range of experimental conditions.

scholarly journals Timing of centrosome separation is important for accurate chromosome segregation

2012 ◽  
Vol 23 (3) ◽  
pp. 401-411 ◽  
Author(s):  
William T. Silkworth ◽  
Isaac K. Nardi ◽  
Raja Paul ◽  
Alex Mogilner ◽  
Daniela Cimini
Keyword(s):  
Nuclear Envelope ◽  
Chromosome Segregation ◽  
Intermediate Stage ◽  
Spindle Pole ◽  
Cellular Space ◽  
Nuclear Envelope Breakdown ◽  
Spindle Poles ◽  
Centrosome Separation ◽  
Large Numbers ◽  
Close Proximity

Spindle assembly, establishment of kinetochore attachment, and sister chromatid separation must occur during mitosis in a highly coordinated fashion to ensure accurate chromosome segregation. In most vertebrate cells, the nuclear envelope must break down to allow interaction between microtubules of the mitotic spindle and the kinetochores. It was previously shown that nuclear envelope breakdown (NEB) is not coordinated with centrosome separation and that centrosome separation can be either complete at the time of NEB or can be completed after NEB. In this study, we investigated whether the timing of centrosome separation affects subsequent mitotic events such as establishment of kinetochore attachment or chromosome segregation. We used a combination of experimental and computational approaches to investigate kinetochore attachment and chromosome segregation in cells with complete versus incomplete spindle pole separation at NEB. We found that cells with incomplete spindle pole separation exhibit higher rates of kinetochore misattachments and chromosome missegregation than cells that complete centrosome separation before NEB. Moreover, our mathematical model showed that two spindle poles in close proximity do not “search” the entire cellular space, leading to formation of large numbers of syntelic attachments, which can be an intermediate stage in the formation of merotelic kinetochores.

scholarly journals ChromaWizard: An open source image analysis software for multicolor fluorescence in situ hybridization analysis

2018 ◽  
Vol 93 (7) ◽  
pp. 749-754
Author(s):  
Norbert Auer ◽  
Astrid Hrdina ◽  
Chaitra Hiremath ◽  
Sabine Vcelar ◽  
Martina Baumann ◽  
...  
Keyword(s):  
Image Analysis ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Open Source ◽  
Hybridization Analysis ◽  
Source Image ◽  
Analysis Software ◽  
Image Analysis Software ◽  
Multicolor Fluorescence

scholarly journals Zbrowse: an interactive GWAS results browser

2015 ◽  
Author(s):  
Greg R Ziegler ◽  
Ryan H Hartsock ◽  
Ivan Baxter
Keyword(s):  
Candidate Gene ◽  
High Throughput ◽  
Experimental Results ◽  
Easy Access ◽  
Analysis Software ◽  
Multiple Traits ◽  
Desktop Computer ◽  
Web Browser ◽  
Specific Effects ◽  
High Throughput Phenotyping

The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is often tedious, involving many manual steps searching for genes in windows around a significant SNP. This problem rapidly becomes more complex when an analyst wishes to compare multiple GWAS studies for pleiotropic or environment specific effects. To this end, we have developed a fast and intuitive interactive browser for the viewing of GWAS results with a focus on an ability to compare results across multiple traits or experiments. The software can easily be run on a desktop computer with software that bioinformaticians are likely already familiar with. Additionally, the software can be hosted or embedded on a server for easy access by anyone with a modern web browser.

scholarly journals Nek9 Phosphorylation Defines a New Role for TPX2 in Eg5-Dependent Centrosome Separation before Nuclear Envelope Breakdown

2018 ◽  
Vol 28 (1) ◽  
pp. 121-129.e4 ◽  
Author(s):  
Susana Eibes ◽  
Núria Gallisà-Suñé ◽  
Miquel Rosas-Salvans ◽  
Paula Martínez-Delgado ◽  
Isabelle Vernos ◽  
...  
Keyword(s):  
Nuclear Envelope ◽  
Nuclear Envelope Breakdown ◽  
Centrosome Separation

scholarly journals CellProfiler 4: improvements in speed, utility and usability

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
David R. Stirling ◽  
Madison J. Swain-Bowden ◽  
Alice M. Lucas ◽  
Anne E. Carpenter ◽  
Beth A. Cimini ◽  
...  
Keyword(s):  
Large Scale ◽  
Biological Information ◽  
Source Image ◽  
Scale Analysis ◽  
Imaging Data ◽  
Computational Tools ◽  
Large Scale Analysis ◽  
Improved Performance ◽  
Free Open Source ◽  
Microscopy Images

Abstract Background Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automated and objective analysis of the resulting images is essential to effectively extract biological information from this data. CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Results Herein we describe CellProfiler 4, a new version of this software with expanded functionality. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimizations to reduce the time and cost associated with running common large-scale analysis pipelines. Conclusions CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to CellProfiler’s powerful computational tools in the coming years.

scholarly journals Pandas DataFrames for a FAST binned analysis at CMS

2019 ◽  
Vol 214 ◽  
pp. 06035
Author(s):  
Benjamin Edward Krikler ◽  
Olivier Davignon ◽  
Lukasz Kreczko ◽  
Jacob Linacre ◽  
Emmanuel Olatunji Olaiya ◽  
...  
Keyword(s):  
Machine Learning ◽  
Big Data ◽  
Easy Access ◽  
Learning Tools ◽  
Analysis Software ◽  
Data Frame ◽  
Industry Standard ◽  
Standard Tool ◽  
Scientific Libraries ◽  
Binned Data

Binned data frames are a generalisation of multi-dimensional histograms, represented in a tabular format with one category per row containing the labels, bin contents, uncertainties and so on. Pandas is an industry-standard tool, which provides a data frame implementation complete with routines for data frame manipultion, persistency, visualisation, and easy access to “big data” scientific libraries and machine learning tools. FAST (the Faster Analysis Software Taskforce) has developed a generic approach for typical binned HEP analyses, driving the summary of ROOT Trees to multiple binned DataFrames with a yaml-based analysis description. Using Continuous Integration to run subsets of the analysis, we can monitor and test changes to the analysis itself, and deploy documentation automatically. This report describes this approach using examples from a public CMS tutorial and details the benefit over traditional methods.

Development of CD3 cell quantitation algorithms for renal allograft biopsy rejection assessment utilizing open source image analysis software

2017 ◽  
Vol 472 (2) ◽  
pp. 259-269 ◽  
Author(s):  
Andres Moon ◽  
Geoffrey H. Smith ◽  
Jun Kong ◽  
Thomas E. Rogers ◽  
Carla L. Ellis ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Renal Allograft ◽  
Source Image ◽  
Analysis Software ◽  
Image Analysis Software ◽  
Allograft Biopsy
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